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Congratulations to Julia Adams who defended her PhD on Nov 15, 2024 on her project focused on landscape and population genomics of the lichen Acarospora socialis

Congratulations to Mark Adams who defended his PhD on Septemer 3, 2024 on his project focused on the amphibian pathogen Batrachochytrium dendrobatidis and pangenome and comparative genomics including discovery of a DNA virus that infects some populations of the fungus.

Congratulations to Talieh Ostovar who defended her PhD on June 28, 2024 on her project focused on plant comparative genomics in the genus Boechera as well as a project on the Citrus genome with our lab. Dr Ostovar was primarily advised by Liz Waters at SDSU but was co-advised in our lab through the UCR-EEOB Joint Doctoral Program with SDSU.

Congrats to Cassie who was awarded the 2022 CEPCEB Postdoc Award.

Congratulations to Dr. Tania Kurbessoian who completed her PhD work at the end of 2022. Tania was an integral part of the lab advancing new culturingi projects, a thoughtful and giving student mentor, and a key person in our data analysis of black yeast fungi. The lab greatly benefited from her efforts to keep the wet lab efficient for molecular biology, microbiology, and genomics techniques.

Congraulations in order for Cheng-Hung who passed his Qualifying exam in the Genetics, Genomics, and Bioinformatics program. We are excited him to continue his work on metagenomics methods and application to Citrus trees and soil microbiomes as part of the Citrus HLB Microbiome project.

A new project is launching for studying the Microbiome of Herptiles and the impacts of specific fungi. The work is supported by the NSF Understanding the Rules of Life: Microbiome Interactions and Mechanisms and will support a four year project to examine the dynamics of microbiomes from wild and captive animals, manipulation experiments, and genomic and metabolomic profiling of these communities and individual microbial members.

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Congrats to Derreck Carter-House, Ph.D.

Jesús Peña introduces his research on sexual reproduction in the zygomycete fungi in the lab through a new video as part of the UCR Microbiology Graduate Ambassador. Have a watch and learn more about the research Jesús is working on.

The end of summer meant goodbye to our excellent REU student Saisuki Putumbaka.

I am delighted to announce that Yan Wang a current postdoc in our group, will be a starting his next position as an Assistant Professor in the Department of Biology at the University of Toronto-Scarborough. Yan has spent the last two years in the lab working on Zygolife and Neocallomastigomycota fungi projects. We are super proud of all he has accomplished in his training and research. This includes multiple publications from his thesis work and several papers submitted from his current projects. The lab has greatly benefited from his phylogenetic and insect-fungi expertise. Luckily we still have ~6 more month together to continue projects and help him prepare for his next step in his career. <figcaption>Helping Yan celebrate his acceptance of offer at UTSC.</figcaption>

We enjoyed a wonderful spring flower season here in Southern California (Harford Springs Riverside County Regional Park) Several publications were accepted and published in last few months and want to highlight the hard work from lab members and collaborators. Jinfeng lead article published on the localized burst of Rice Transposable Elements Ping and Pong in only a subset of the domesticated lineages and clues to what changed to drive their increased activity. Variation of mPing, Ping, and Pong_ element copy number in rice subgroups https://www.nature.com/articles/s41467-019-08451-3/figures/2 A fun collaboration lead by Adam Bewick and Bob Schmitz we called #MycoMeth explored diversity of Cytosine DNA Methylation in Fungi looking at the 5-methylcytosine (5mC) marks and evolution of the fungal 5mC methyltransferases. Genomewide 5mC profiles https://www.nature.com/articles/s41559-019-0810-9/figures/2 Two Zygolife project papers. One on genome evolution and phylogenic position of Endogone - a truffle forming Mucoromycotina fungus.This was quite challenging but interesting project to tackle, lead by Ying Chang in the Spatafora Lab. Dr Chang took a metagenomics approach to capture these unculturable fungi followed by bioinformatic analyses to isolate the fungal and Mucoromycotina component of the dataset. <figcaption>Phylogenetic placement and divergence time estimation of Endogonales and the evolution of fungal plant‐cell‐wall‐degrading enzymes (PCWDEs) A second paper lead by William Davis from Tim James lab on the genomes and phylogeny of Zoopagomycotina fungi which include nematophagous and mycoparasites. Fig 5. Ancestral state reconstructions of trophic state on the best ML tree (A) and the ASTRAL consensus tree (B) using maximum likelihood. Pie graphs at nodes show the proportional likelihood of each character state. Jason participated in a Marine Fungi workshop on the unexplored diversity in the marine environments and co-authored this perspective on the opportunities and challenges in characterizing and studying these fungi. Morphological diversity of fungi collected from a biotic host. Fungal collection isolated from a marine sponge,Ircinia variabilis (formerly Psammocinia sp.). Former postdoc Ousmane Cissé developed FGMP, a tool for assessing completeness of fungal genomes which uses both conserved protein coding markers that can include multicopy gene families and conserved non-coding DNA regions. This was published this month as well, congrats Ousmane! Fig 2.Estimation of genome completeness in fungal genomes. A comparison of genome completeness by multiple software tools using initial and latest genome assembly versions of 45 fungi. Genome completeness expressed as a percentage of expected markers (y-axis) is plotted against assembly size in megabases (x-axis).

Sarah Johnson Lead Programmer

January 07, 2019 December 18, 2024

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Congrats Derreck! He was selected by the California Council on Science and Technology (CCST) to give a presentation and represent Dept of Microbiology and Plant Pathology and UCR at the California Science Translators Showcase. He will be giving a talk about his research at the California State Capitol to legislators/state senators, agency managers, and senior policy leaders. He was chosen out of a pool of California PhD students, post-docs, and career scientists from all different STEM fields and universities to talk about plant pathology/fungi.

Nat visited New Mexico State University several times this summer to complete work at the Jornada LTER site working with Nicole Pietrasiak (@drylandalgae) on the micro- and myco-biomes of biological crusts. Visits to Anza Borrego and Boyd Deep Canyon for Tania to scope out UCNRS research sites to explore desert rock varnish and rock or crust associated black fungi. Julia continued to develop her Joshua Tree research sites for lichen studies and has collected and sequenced new accessions for a reference library of lichens from Joshua Tree NP.Congrats to Jesús (IG: variety_hour) who passed his qualifying exam has continued to explore zygomycete diversity focusing on sexual reproduction.  Derreck has been working on bacteria-fungal interactions via volatiles and new work with N. crassa sensing of these. Yan has submitted a manuscript on his postdoc work on phylogenomics and dating the emergence of the the anaerobic gut fungi. Jinfeng has submitted and is revising work on characterizing the transposition and burst of the Ping, Pong, and mPing transposable elements across 3000 Rice accessions. Sawyer generated and analyzed whole genome sequence from strains of Rhizopus stolonifer in his population genomics project which he presented at the IMC11 conference.New publications including population genomic diversity of Candida lusitaniae, Entomophthorales proteases, space fungi!, and fungal & bacteria communities in Antarctic rocks came out in the last few months.Hopefully another update before the end of 2018 but check out pictures and tweets for shorter updates.

The lab is back from conferences this summer. The Cellular and Molecular Fungal Biology Gordon Research Conference in Holderness, NH and the 11th International Mycological Congress in Puerto Rico. Tania also gave her first talk  at the Black Yeast workshop held in Amsterdam as part of the ISHAM meeting.

There have been several manuscripts are now out from work that was done over the last few years. It has been great to be able to collaborate with many research teams as part of this work.Been slow to mention these but wanted to make sure and call out the hard work from everyone. A long term collaboration lead by Cene Gostinčar on population genomics in Hortaea, an ascomycete black yeast, complemented some reference genome work we published last year [1].  Former postdoc Ousmane Cissé published his work on Pneumocystis at the NIH in his current postdoc[2]. Figure 6 - Overview of the timing and evolution of Pneumocystis and their mammalian hosts Current postdoc Yan Wang published part of his thesis work and we worked on these data a bit as part of the zygolife project here [3].  Graduate students Nat Pombubpa collaborated with Plant Sciences and Jeff Diez lab graduate student Courtney Collins on her thesis work looking at the mycobiome differences of soils in an alpine gradient with and without invasive shrub introduction [4].  Andrii Gryganskyi’s work on Rhizopus phylogeny with some of the first multi-genome work on this genus that was one of the earliest collaborations on some ZyGoLife questions [5].  Work exploring whether Transposable elements have a role in stage-specific gene expression in Coccidioides with Theo Kirkland and Anna Muszewska [6].  A collaboration lead by Tom Richard’s lab and Guy Leonard sequence and assembled and annotated a genome of a ‘pseudofungus’ hyphochytriomycete called Hyphochytrium catenoides [7]. I think I forgot to also call out that last year postdoc Jinfeng Chen published work collaboratively with postdocs Lu Lu and Sofia Robb on the active Rice transposable element system mPing and Ping [8]. Good work all! Gostinčar C, Stajich JE, Zupančič J, Zalar P, Gunde-Cimerman N. Genomic evidence for intraspecific hybridization in a clonal and extremely halotolerant yeast.BMC Genomics. 2018 May 15;19(1):364. doi: 10.1186/s12864-018-4751-5. Wang Y, Stata M, Wang W, Stajich JE, White MM, Moncalvo JM. Comparative Genomics Reveals the Core Gene Toolbox for the Fungus-Insect Symbiosis. MBio. 2018 May 15;9(3). pii: e00636-18. doi: 10.1128/mBio.00636-18. Cissé OH, Ma L, Wei Huang D, Khil PP, Dekker JP, Kutty G, Bishop L, Liu Y, Deng X, Hauser PM, Pagni M, Hirsch V, Lempicki RA, Stajich JE, Cuomo CA, Kovacs JA. Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen Pneumocystis. MBio. 2018 May 8;9(3). pii: e00381-18. doi: 10.1128/mBio.00381-18. Gryganskyi AP, Golan J, Dolatabadi S, Mondo S, Robb S, Idnurm A, Muszewska A, Steczkiewicz K, Masonjones S, Liao HL, Gajdeczka MT, Anike F, Vuek A, Anishchenko IM, Voigt K, de Hoog GS, Smith ME, Heitman J, Vilgalys R, Stajich JE. Phylogenetic and Phylogenomic Definition of Rhizopus Species.  G3 (Bethesda). 2018 Apr 19. pii: g3.200235.2018. doi: 10.1534/g3.118.200235. Collins CG, Stajich JE, Weber SE, Pombubpa N, Diez JM. Shrub range expansion alters diversity and distribution of soil fungal communities across an alpine elevation gradient. Mol Ecol.2018 Apr 19. doi: 10.1111/mec.14694. Kirkland TN, Muszewska A, Stajich JE. Analysis of Transposable Elements in Coccidioides Species. J Fungi (Basel). 2018 Jan 19;4(1). pii: E13. doi: 10.3390/jof4010013. Leonard G, Labarre A, Milner DS, Monier A, Soanes D, Wideman JG, Maguire F, Stevens S, Sain D, Grau-Bové X, Sebé-Pedrós A, Stajich JE, Paszkiewicz K, Brown MW, Hall N, Wickstead B, Richards TA. Comparative genomic analysis of the ‘pseudofungus’ Hyphochytrium catenoides.  Open Biol. 2018 Jan;8(1). pii: 170184. doi: 10.1098/rsob.170184. Lu L, Chen J, Robb SMC, Okumoto Y, Stajich JE, Wessler SR. Tracking the genome-wide outcomes of a transposable element burst over decades of amplification. Proc Natl Acad Sci U S A. 2017 Dec 5;114(49):E10550-E10559. doi: 10.1073/pnas.1716459114.

Last week we hosted several visitors from our ZyGoLife collaborative team in sunny California. I wrote a few notes on Nicole Reynolds and Javier Tabima’s visit for the zygolife site on their extended research stay.

Nat and Jason headed out to the Mojave National Preserve to meet up with Erik Hom and his StudyUSA class from Univ of Mississippi. We started at the Sweeney Granite Mountains Desert Research Center which is one of 39 Natural Reserves in the University of California.  We were there to teach a bit about cryptogamic crusts, show the Kelso dunes off, and explore some more of the desert crust sampling sites that our collaborator Nicole Pietrasiak (@drylandalgae) and Paul De Ley have collected from. Nothing like seeing sites that previously I only knew from pictures or tubes of soil!A few pictures from our visit.Kelso DunesCrusts symbioses of algae and cyanobacteria with fungi, bacteria, and many uncounted single celled organisms.Lichen Crusts galore across from the Kelso dunesMoss Crusts are also rich symbioses with a predominant moss.Old volcanic flow in the Cima area also has cacti and crustsColorful lichens found on the granite faces. On closer looks, these are often 3 or more species competing for space on the same surface.

Our lab trip to Joshua Tree NP and photo session before the start of the quarter resulted in our 2017 album cover lab photo.

Welcome to first year graduate students Julia Adams (Plant  Biology) and Tania Kurbessoian (Microbiology). Tania joins us after completing a MS in Microbiology at Cal State-Northridge. She will starting out work on projects relating to genomics and physiology of extremophilic fungi,  black yeasts and efforts to culture and describe diversity of desert fungi. Julia completed a BS at Wellesley and has worked on a variety of projects related to lichen fungi. She will focus on lichen fungi from desert regions and will use genomic and potentially metabolomic tools to study evolution and unique properties of some lichenized fungi endemic to Joshua Tree National Park and the Mojave desert.

Congrats to Nuttapon (Nat) who passed his qualifying exam this week and is now a PhD Candidate. Along with Derreck he is the second Plant Pathology graduate student in the lab and is working towards his PhD on microbial diversity of cryptogamic or biological soil crusts found in the desert. His primary research area is Joshua Tree National Park and desert areas in the UC Reserve System. Nat and Jason have benefited greatly from collaboration with New Mexico State Univ Professor Nicole Pietrasiak who is an expert in crusts, desert algae, and did her PhD work in Joshua Tree which harbors tremendous diversity of biological soil crust types.[caption id=”attachment_1742” align=”alignnone” width=”1024”] Cross section of crust. Image by N. Pietrasiak[/caption] 

Congratulations to Derreck who passed his qualifying exam this week! Derreck’s projects focus on interactions between the zygomycete (Mucoromycota and Zoopagomycota) fungi and bacteria, primarily from the genus Serratia.

Great work by former student Steven Ahrendt (@sahrendt0), visiting student and current Duke graduate student Edgar Medina (@WhippingFungi) on the publication of a manuscript describing a Type II Opsin found in the zoosporic fungi. "Exploring the binding properties and structural stability of an opsin in the chytrid Spizellomyces punctatus using comparative and molecular modeling" in PeerJ! Thanks also to co-author and collaborator Angelina Chang in Chemistry Dept at UCR who helped mentor Steven on all the nuances of homology modeling and docking.

When Bacteria attack!

With Bob Schmitz at Univ of Georgia, We’re working on a project we call MycoMeth to examine evolution of methylation across Fungi. We would welcome contributions of ~2ug of DNA from diverse fungi that have a sequenced genome.  Please email Jason or Bob if you would like to contribute.

Just back from another fantastic Fungal Genetics Conference at Asilomar. An amazing number of helpful tweets under the #Fungal17 hashtag. Sarah Unruh (@sau916) and I are talking about how to best archive or building a storify this so it is easier to read. Always a fun meeting to see friends and nosh at the smorgasbord of fungal genetics, epigenetics, genomics, ecology, evolution, and chemistry that is going on. Jason got to give a Plenary talk and express the utility of sequencing fungal genomes in studying their evolution. Lab Alumnus Steven Ahrendt won a poster award on his work on Cryptomycota fungi and also gave a talk. > #fungal17 nuff said @hyphaltip @zygolife  pic.twitter.com/U78xgoXz7y — Jessie (@JessieUehling) March 17, 2017Also got some good news that our paper on structural analyses of a rhodopsin-like protein in the chytrid fungi has been accepted at PeerJ after some helpful revisions - (see the preprint).Onward!

Quick post to sum up some of the news from 2016 and head into 2017. - Six manuscripts were published and an additional two were accepted and three more were submitted or being revised in 2016 Three graduate students survived another year in the lab: Sawyer, Nat, Derreck Joined by one Microbiology graduate student Jesus Pena joined in Fall 2016. Nine undergraduates worked in the lab Deane, Josh, Jericho, Dillon, Na, Justin, Serena, Leandra, George and Travis has been part of bioinformatics projects One postdoc, Jinfeng has been the bioinformatics and genomics guru from genome assembly to transposon bioinformatics One new assembly of a Citrus genome At least 15 new genomes from our work with Zygolife and 1000 Fungal Genomes project were released or material processed. More than 100 cultures of some fungi are being examined in the lab. One NSF grant started on systematics of anaerobic chytrid fungi and one new grant awarded as part of the UC MRPI http://ucop.edu/research-initiatives/programs/mrpi/2017-Awards.html program on the “UC Valley Fever Research Initiative” lead by UCSF and including several other UC campus. Jason is on sabbatical in 2017 at Oregon State University.

Some us from the lab took a trip up to Berkeley, CA for the MSA 2016 meeting.

On August 4th, 2016, Nat, Derreck, Sawyer, and Jericho went to Joshua Tree National Park to collect more Biological Soil Crusts samples. They were lucky to find some Lichen crusts which we could not find in our last sampling trip. Here are some pictures of our sampling team.[caption id=”attachment_1525” align=”aligncenter” width=”604”] Stajich lab sampling team: Derreck, Nat, Sawyer, and Jericho[/caption][caption id=”attachment_1526” align=”aligncenter” width=”900”] Our first collection of Lichen crust from Joshua Tree National Park[/caption][caption id=”attachment_1527” align=”aligncenter” width=”604”] Derreck measured crust surface temperature, while Jericho was getting ready for sampling[/caption]

We celebrated a few events in April and May. - A new NSF grant was funded and started in April on rumen fungi ”Phylogenomics and evolutionary history of the anaerobic fungal group, Neocallimastigomycota”. This is a collaboration with Noha Youssef and Mostafa Elshahed at Oklahoma State University and will give the opportunity to work on systematics of these anaerobic gut fungi. Raúl Castanera who came to the lab for a short stay last year, authored a paper that was accepted this week on transposable elements in the Pleurotus (oyster mushroom) genome and comparisons in proliferation rates and impact on gene expression. Castanera R et al. PLoS Gen doi: 10.1371/journal.pgen.1006108 We just started to get our first microbial diversity (16S and ITS) results for rock and soil communities from California desert environments and Antarctica as part of project by visiting student Claudia Coleine and Nat Pombubpa. Claudia is a PhD student with Laura Selbmann of Tuscia University and visited for nine months, but we processed isolates the lab collected from Antartica expeditions. We are also sequencing genomes of a handful of cultured fungal species from Antarctic locations and the first assemblies look pretty good (200-400 contigs for these 25-40Mb genomes) for a MiSeq only assembly. Nat is collecting samples from Joshua Tree National Park and in collaboration with other desert crust researchers Paul De Ley and Nicole Pietrasiak examining fungal and bacterial distribution.

Jason was at the European Conference on Fungal Genetics in Paris this April and had a chance to deliver a lecture. It was a great meeting of science and there was a lot of social media coverage by participants.Jason and Ousmane also attended the 1st conference on multicellular development in fungi where Ousmane presented his work on the Neolecta genome and comparative biology of the Taphrinomycotina fungi.[caption id=”attachment_1490” align=”alignright” width=”604”] An ascus of Neurospora biologists…[/caption][caption id=”attachment_1489” align=”aligncenter” width=”590”] It was a bit imposing to be on stage with bright colored backdrop[/caption][caption id=”attachment_1488” align=”aligncenter” width=”590”] I showed some colorful trees[/caption][caption id=”attachment_1487” align=”aligncenter” width=”604”] Little Jason and big slides[/caption] [caption id=”attachment_1486” align=”aligncenter” width=”604”] Mural at a school with a mushroom little red riding hood and mushrooms in the forest[/caption]

We started some explorations on fungi in desert crusts this week with a project in Joshua Tree National Park. Nuttapom received a Robert Lee Graduate Student research grant to explore impacts of visitor disturbance on biodiversity of desert crusts in JTNP.  Nat with the help of Claudia, Derreck, and Prof Mike Allen did a first exploration of a few sites.  We are happy to see some rain falling this week so there should be some changes to the crusts in some subsequent visits this week and weekend and coinciding with a workshop on desert crusts in the park this weekend. Here’s a few pictures of the team out in the field last week.[caption id=”attachment_1475” align=”aligncenter” width=”863”] Mike and Derreck ahead in Hidden Valley[/caption][caption id=”attachment_1477” align=”aligncenter” width=”604”] Nat, getting his first taste of sampling in the desert.[/caption][caption id=”attachment_1473” align=”aligncenter” width=”604”] Dereck and Claudia helping to look for crusts. Claudia is researching sandstone associated fungi from a variety of habitats.[/caption][caption id=”attachment_1474” align=”aligncenter” width=”604”] Cyanobacteria dominated crust[/caption][caption id=”attachment_1476” align=”aligncenter” width=”778”] Moss & crusts[/caption]

We said bye to Marco Marconi, visiting student from the Wilkinson Lab in Madrid, in December. He worked on some data mining from the 1KFG project and brought some new R tools for looking for enrichment across the CAZY, Interpro, and Pfam differences in species. - We welcome Plant Pathology graduate student Derreck Carter-House to the lab in January - after spending time working on molecular biology projects in plants and plant-microbe interactions in another lab.  Jason went across to England to serve on Ensembl Genomes  SAB and give seminar at University of Exeter - he came back with more appreciation for sunny California winters.

The past few months have passed quickly but wanted to share a few updates.Jason presented at the EMBO Eukaryotes meeting in Spain, Mexican Mycology Congress, Univ of Arizona, attended the Kavli Frontiers meeting, co-organized the Southern California Eukaryotic Pathogens meeting held again at UCR and taught graduate course on Programming and Data analyses.The past few months we hosted Yinka Odebode from University of Lagos from August to November. He was supported by the West African Research Association. Yinka learned about ITS sequencing of fungi to identify his isolates in his work in Africa. He also explored properties of dust associated fungi in Nigeria before he returned home in November. We also welcomed Marco Marconi from Madrid for a few months and is working on comparative genomics of fungi using the 1KFG datasets.Starting in  September we welcomed new graduate student in Plant Pathology, Nuttapon Pombubpa (right). Here he is (right) enjoying lunch along with visiting student Claudia Coleine and graduate student Sawyer.We gathered to say goodbye to project scientist Peng Liu who returned to China in December. Here she is with postdoc Jinfeng and visiting student Zhinquan.<images/wp_upload/2015/12/lablunch2.jpg> Undergraduates Dillon and Jericho joined us for lunch as well. They have both worked closely with Peng this Summer and Fall.Most of the lab together for a farewell lunch for Peng including Deane on the far right.

A quick note to say congrats and good luck to postdocs and students who finished up the summer.Graduate student Steven Ahrendt who graduated from the GGB program and is now a postdoc at the JGI / UC Berkeley.Postdoc Ousmane Cissé finished his fellowship from the Swiss National Science Foundation and moved on to the NIH on a fellowship to work on Pneumocystis.Postdoc Rod Olarte moved to the University of Minnesota on a NSF postdoctoral fellowship.Undergraduates Dillon McDonald and Christina Uriarte also finished their summer projects in the HSI-STEM and MARCU programs. <images/wp_upload/2015/06/2015-06-03-14.17.11.jpg>

Congrats to Steven Ahrendt who successfully defended his PhD Dissertation this week. Graduation ceremony (and pictures) to follow next weekend before he moves on to his postdoc position at UC Berkeley/LBNL/JGI at the end of the month.<images/wp_upload/2015/06/2015-06-03-14.17.11.jpg>

We had a lab dumpling party at Yizhou’s house to celebrate his new job and my birthday, and a farewell to Edward Liaw. Fun evening for everyone to get together and eat homemade dumplings

Another great meeting of Fungal Genetics at Asilomar Conference center. Much exciting science, fungal genetics as a field is being driven by genomics and technology but there are nice cycles of experiments coming back to test and validate hypotheses generated from these data. A few pictures of the UCR group all together at dinner.

Members of the lab gathered for a Dim Sum outing in Rowland Heights on Monday’s MLK holiday.

The end of the quarter was a blur but I wanted to properly congratulate Yizhou Wang. Dr Wang successfully defended his PhD in December and submitted his dissertation “Discovery and Properties of Small RNAs from Meiotic Silencing by Unpaired DNA in Neurospora crassa”  in the Plant Biology graduate program. He is our newest graduate from the lab and we couldn’t be happier and proud for him. He was able to complete a concentration MS in Statistics at the same time and was able to master bioinformatics and data analysis of next generation sequencing and comparative genomics along with small RNA Northerns, Southern Blots, and Neurospora culturing and care. He has been a great asset to the lab and I am delighted that he has finished this part of his education and training and excited for his next steps.He is serious about his cooking, treating us to some great meals from BBQ to a Chinese seafood extravaganza.

Rod, Ousmane, Nichole, Jinfeng, Jason and family went on a short hike to Big Falls in Forest Falls. A few pictures of the fun.

A new NSF funded project on Zygomycete fungi was recently funded. The press release from UCR and NSF provide some more information on the scope of the project and the goals of the new Genealogy of Life initiative at the NSF.We’ll be sharing news, data and protocols, and progress on the project website ZyGoLife.org and @zygolife  and looking to recruit one graduate student and some undergraduates to work on the projects in our lab focused on genomics and phylogenomic studies of these diverse lineages.

I had the great opportunity to attend the International Mycological Congress 10 in Bangkok, Thailand during this summer. It was filled with talks from mycologists studying cell biology, genetics, evolution, symbioses, ecology, production of secondary metabolites, and many other aspects of mycology from across the world. It was a great chance to hear about new work in many different experimental systems.  I chaired a session on Population Genomics and GWAS in Fungi and got to hear some great perspectives and approaches on model and non-model systems. I presented my talk on data analysis tools in metagenomics. I got to catch up with many friends/collaborators/colleagues and meet some new folks.I’m jealous of the folks who got to take some of the post-conference excursions through Thailand or ventured even further to Laos and Cambodia. Hopefully next trip to this area I’ll have the chance to explore more.

Congrats to Divya and Jason as our paper with collaborators Hugo Melida and Vincent Bulone: 

Steven and Jason attended the Mycological Society of America’s 2014 conference in East Lansing, MI. This included  coming in a day early enough for some of us to go on the foray on Sunday after we attended the Microbiology of the Built Environment conference in Boulder, CO.MSA2104 was a great chance to catch up with friends and colleagues and hear some excellent talks on the current state of research in the fields of systematics & taxonomy; ecology & pathology; genetics & molecular biology. Genomics pervades a lot of the research where it was not quite part of the picture when I first started attending so it was great to see how many people taking advantage of the amazing resources produced by the JGI sequencing programs.  I also really enjoyed the Karling lecture from Bruce McDonald on domestication in fungi and plants and the “dark side” of this domestication (meaning mostly that there are unintended consequences).There was some tweeting going on at the meeting - I tried to capture some with a storify available here.Jason presented research on the evolution of the fungal cell wall examining early diverging lineages of fungi which is the work of former graduate student Divya Sain.Steven presented his poster on the inhibitory properties of a Chytridiomycota fungus we work on that affects growth of some filamentous fungi and won the award for best graduate student poster!Jason was also honored with the 2014 Alexopoulos Prize to honor a young Mycologist. The prize is in memory of C. J. Alexopoulos who among other things authored the great Introductory Mycology textbook. I have not yet decided how I will spend the prize money but I intend to support a project in the lab or to support travel for collecting more strains tied to chytrid work.A photo of Steven and Jason at the banquet. 

We published a paper on the manual curation of the literature for the Cryptococcus complex of species (C. neoformans _var neoformans_, C. neoformans var grubii, and  C. gattii) this includes associated gene names with systematic locus names, something that was not easy to lookup without reading the published literature. In all more than 600 loci had gene names associated with them and include updated Gene Ontology associations, gene product names and descriptions and a table of orthology relationships between the genes in the different species genomes.The early access to the paper is available was released at  Eukaryotic Cell in May and includes guidelines of how the community can go forward naming genes in these species. In addition we make available a table of these names available at FungiDB at this link. And future updates are being posted through GitHub so that community contributions can happen directly through edits to the file or through the comments section at FungiDB where comments can be added by any user indicating a gene name and these will be evaluated and curated by a Scientific Curator.This work was done my a lot of hard work from Diane Inglis and Marek Skrzypek who are scientific curators at (Stanford University)  under the direction of Gavin Sherlock and the gene names and descriptions are loaded and available in FungiDB through the work of Ed Liaw and Venky Moktali at UC Riverside. We were able to do this work through an NIH R03 grant and look forward to finishing the complete literature curation by the end of this year.

We congratulate Divya on defending her dissertation on “Discovery of fungal cell wall components using evolutionary and functional genomics”.  Her last revisions and formatting is taking place and she should be the first minted PhD from the Stajich lab before Christmas.  We are happy and proud of her accomplishment to complete this important milestone!   

We are happy to welcome Dr Ousmane Cisse to the lab to work on evolution of multicellularity in Fungi. He will primarily focus on comparative genomics and evolution of filamentous fungal growth in the fungal kingdom, examining the genome of Neolecta and taking advantage of data from the 1000 fungal genomes project and other data sets. He joins us after completing his PhD at the University of Lausanne in Switzerland. He focused on comparative genomics of several Taphrinamycotina fungi and will continue this theme working on Neolecta. He was awarded a prestigious early postdoc mobility fellowship from the Swiss National Science Foundation Fellowship.

We’re excited that several manuscripts were published in the last month.One presents the first genome from the Cryptomycota, Rozella allomycis, in a manuscript published in Current Biology along with a nice companion piece from Mark van der Giezen about the work. Steven and Divya participating in this project in collaboration with Tim James at Michigan and Nico Corradi in Montreal. Some of the scripts used for this project are available as well here on github and other associated genome data are available here. We are working to get this into the next FungiDB release as well.A manuscript from Andrii Gryganskyi who was a lab visitor last summer was published on the Entomopthorales fungus Entomophthora muscae._A review on the application of genomics to mycology was published in Mycologia celebrating the new era of mycology and the first genome sequences published in this journal.Work from Anastasia Gioti, who was a lab visitor for several months this year and has visited several times in the past years, wrapped up genome comparisons of _Neurospora species which have transitioning from outcrossing (heterothallic) to self-fertile (homothallic) lifestyles. Our manuscript was made available in Evolution this summer and will be published in the Fall.A paper on the population genomics of amphibian killing chytrid fungus B. dendrobatidis that culminated several years of work and large collection of researchers was published in PNAS at the beginning of the summer.

Today was the presentations from UCR RISE summer program and undergraduate student Na Jeong showed her work on studying the inhibitory properties of the H. polyrhiza species of chytrid on several Ascomycete fungi. She was mentored by Steven Ahrendt in the lab who first made this observation. Here is Na presenting her work and with Jason and Steven.

We headed over to Lake Perris for a lab BBQ and fun afternoon in the sun.  Here’s a few pictures of the group all together.

Congrats to the lab for a great Fungal Genetics meeting. Everyone was participating in the meeting, presenting their work, and hearing about the new things coming out in other research laboratories. Was exhausting pace with 8AM to 10 PM (or later) every day but I think the fun and science excitement overshadowed the tiredness.  Congratulations to Steven who won a poster prize and to Jason for his election to the Fungal Genetics Policy Committee.  FungiDB was demoed in a workshop and poster sessions and we seemed to get a lot of interest and feedback along with the excellent presentation by Omar Harb from the EuPathDB team to lead the workshop.We will post some pictures and upload our poster PDFs in the coming weeks I expect, still catching up on sleep and reengaging in our research after that.Thanks to all who came by to talk with us at our posters and it was great fun to make new friends and reconnected with long-time ones.

We had a little celebration to recognize Steven passing his qualifying exam this week.

Wordle/Tagxedo graphs from Pubmed2Wordle on all papers published from the lab And here is the abstract wordle for the 2012 papers  

We welcome back Anastasia Gioti to the lab visiting from Sweden by way of Greece. She has been to the lab for a a couple of two-month visits over the past three years working on genomics of Neurospora mating systems. Now she has returned this month as a visiting scholar to stay through the winter to continue our collaboration on evolution of mating systems, focusing on the genomic consequences of transitions in homothallic and heterothallic fungi. She gets to have a nice SoCal instead of a Swedish winter.

Talks from the Sloan Foundation sponsored session at Lake Arrowhead meeting on Microbiology of the Built Environment are now posted on Microbe.net (which was jokingly pronounced as micro-beignet by some) including my talk on fungi in the Built environment.  Go take a look if you want to see an overview of some of the ways researchers are studying microbes in the built environment.  The Microbe.net team also recorded an interview with me about our work on the MicroBE data coordinating center and work to make identifying fungi from metagenomic sequencing easier.

Andrii has returned to Durham after a short stint in the lab to pick up some new skills and teach us more about culturing and major questions in Entomophthorales fungi.  He did a nice writeup on his establishment of a copepod colony which we will use for our future attempt to get Coelomomyces colonies in the lab.He has posted his farewell talk that spans a few of the projects he has been working on his website too -take a look here.

Check out a video of Jason answering questions about our project to build a database supporting identification of Fungi in the Microbiome of the Built Environment supported by the Sloan Foundation.

Welcome to Edward Liaw who will start working on FungiDB for the genome.  Edward joins us after finishing a MS in Bioinformatics at UC Santa Cruz.Also a welcome to Greg Gu who is joining us after working as a specialist in Plant Pathology. Greg is transitioning to bioinformatics to work on fungal identification from environmental sequencing using bioinformatics approaches and will support our work to build a database for ITS sequences as part of the Sloan project’s Microbiome of the Built Environment.

Congratulations to Divya who was awarded the Guru Gobind Singh Fellowship for 2012-13! This fellowship is awarded to one graduate student in the UC system who is a student of an Indian or Pakistani university and committed to returning to her country of origin after receiving her doctoral degree at a UC campus. This is a great honor and we’re all proud of Divya for applying for and receiving the award.  An article in UCR Today describes her work and the award.

A warm Southern California welcome to Andrii Gryganskyi who is here visiting the lab for several months to work on genomics of Entomophthorales fungi and some other insect-associated fungi from the basal linages.  We’re excited to learn from his expertise in phylogenetics and culturing of these strains in the lab. We are helping to assemble and annotate several genomes in progress he has worked on as postdoc at Duke University to better understand relationships and genomic changes that have occurred some of the basal fungal lineages.

Congratulations to PhD candidate Divya Sain, who just learned she will be awarded a Guru Gobind Singh Fellowship for 2012-2013.  In 1988 the University of California established an endowment to support graduate fellowships (named for Guru Gobind Singh, the Sikh religious leader) to be awarded to graduates of universities in a specific area of India and Pakistan for the purpose of pursuing graduate study at the University of California.Way to go Divya!

[Update 8/2012 - this position has been filled]Position DescriptionAn NSF funded postdoctoral position is available in the laboratories of Dr Susan Wessler and Dr Jason Stajich to study the impact of a very recent burst in copy number of a transposable element in rice. This work will involve analysis of high throughput genomic sequencing using Illumina/Solexa technology to examine the genomes of hundreds of recombinant inbred lines of rice. This position requires excellent bioinformatics and programming skills to analyze and synthesize genome assemblies, identify polymorphisms, and perform quantitative trait mapping. Background information on the biology underlying the project can be found in: K. Naito et al, Nature 2009 461: 131; K. Naito et al, PNAS 2006 103: 17620; N. Jiang et al, Nature 2003 421: 163.The successful candidate will be expected to contribute and lead data analysis for the project. Applications will be accepted until the position is filled and review will begin on July 15, 2012.  Salary and benefits are commensurate with NSF guidelines and the University of California Postdoctoral Union agreement. Special consideration will be given to candidates with exceptional bioinformatics and genome evolution experience.QualificationsMinimum qualifications include a Ph.D. in Biological Sciences, Computer Science, Statistics, or a related field. Demonstrated experience in bioinformatics and high proficiency in programming is necessary along with an understanding of the mechanisms and methods of studying population biology. Experience with next generation sequence data is highly desirable. Ability to communicate clearly, work independently, and interact collaboratively is essential.The researcher will also work closely with co-PIs and collaborators at the Donald Danforth Center, Cornell University, and USDA ARS Dale Bumpers National Rice Research Center.To ApplyContact Jason Stajich (jason.stajich@ucr.edu) or Susan Wessler (susan.wessler@ucr.edu) with a current CV and names of three references.More information can be found online about the Stajich lab http://lab.stajich.org, Wessler lab http://wesslerlab.ucr.edu, and the research project http://dynamiterice.org and UC Riverside http://www.ucr.edu.Information about UCRIn the Heart of Inland Southern California, UC Riverside is located on nearly 1,200 acres near Box Springs Mountain in Southern California, the park-like campus provides convenient access to the vibrant and growing Inland region. The campus is a living laboratory for the exploration of issues critical to growing communities — air, water, energy, transportation, politics, the arts, history and culture. UCR gives every student the resources to explore, engage, imagine and excel.UCR is ranked 43rd among top public universities (US News and World Report 2010).At UC Riverside we celebrate diversity and are proud of our #5 ranking among the nation’s for most diverse universities (US News and World Report 2010). Become part of a place that fosters success for all its constituents, students, faculty, and staff, and where work/life balance and campus culture are integral to our way of life.UCR is an affirmative action and equal opportunity employer with a commitment to workforce diversity.  AA/EOE 

A wonderful symposium reunion of alumni and current Duke and the RTP area Mycology and pathogenesis labs is being held April 5 & 6 at Duke University. The talks have so far been an interesting collection of model pathogen systems, drug development, and host-pathogen interactions. Tomorrow myself,  Tim James, and others will hit the evolutionary biology of fungi a bit focusing on chytrid pathogens.  Feeling a lot of pride in the training program here at Duke and some nostalgia for days past when many of us were together in the same institution. The gathering is also a celebration of great mentoring and so it is great to see so many of those who taught and mentored us here - in particular Joe Heitman was also awarded a mentoring honor by Duke for his leadership and mentoring.

Several postdocs have joined the group in the last few months, though I’ve been remiss to make an announcement.Dr Sofia Robb, who completed her PhD at the University of Utah, joined the lab in August 2011 and has been working on the NSF funded Rice transposable element project in collaboration with Susan Wessler’s lab. She has already developed a new tool for identification of TEs from high throughput sequencing which we are employing on several varieties of rice and expanding it to be a more general purpose tool. Sofia is also co-developing teaching modules for the Dynamic Genomes course.Dr Brad Cavinder, who completed his PhD at Michigan State University, joined the lab in January 2012 and is working on transposable elements in mosquitoes as part of the WM Keck funded project to identify and utilize active TEs as molecular tools in mosquitoes.A third new member of the lab, Peng Liu who completed her PhD at the Chinese Academy of Sciences, will start in February to work on molecular characterization of some pathogenesis factors in the amphibian pathogen Batrachochytrium dendrobatidis.

Congrats to graduate student Yizhou Wang who passed his qualifying exam today. We’re proud to have him through this hurdle and to continue working on his research into genome defense and silencing of transposable elements in Neurospora crassa.[caption id=”attachment_701” align=”aligncenter” width=”300” caption=”Jason and Yizhou at Asilomar 2011”][/caption]

Our community sequencing project at the JGI was awarded which will allow a consortium of researchers to sequence 1000 fungal genomes through the DOE’s Joint Genome Institute. The intention is to sample two species from every major lineage of Fungi.Some press releases on the project below and we will coordinate it through several websites including a forum for discussion about potential species beyond the target list.- International Team to Sequence Genomes of Fungi International team to sequence genomes of fungi Forest Service Part of Team Sequencing 1,000 Fungal Genomes

We’ve started doing Perl training on Wednesdays for any IIGB and UCR students and postdocs (or curious faculty). This is starting at beginning with command line usage and will hopefully build to advanced bioinformatics. Sofia and Steven are leading these currently and hope it will be a good jumpstart to improving programming skills of our lab and others. Join the mailing list if you want to get updates on the meeting times and locations and will also try and post useful slide sets and problems here as well.

We wished postdoc John Abramyan a farewell and happy trails last week.  He was the first postdoc to join the lab and completed a projects relating to Bd, chytrid cell wall genes, and some a gene regulation bioinformatics project. He also was main force in getting the experimental portion of our lab started when the group was established.  John is moving on to work on vertebrate evolutionary questions at the University of British Columbia in Vancouver, BC, CANADA. We’ll miss having him in the lab and wish him much luck in his next adventure. [caption id=”attachment_612” align=”aligncenter” width=”779” caption=”John (Left) enjoyed a farewell dinner with the lab”][/caption]

This week the summer student programs ended and Carlos Rojas, Ramy Wissa and Lorena Rivera all gave presentations and posters on their work.  We really enjoyed having them around for the summer and look forward to their possible continuation in the Fall.Carlos worked with postdoc John Abramyan on the CBM18 gene family in _Bd_to confirm gene expression of the members of the family by RT-PCR before we choose a subset to work on further.[caption id=”attachment_638” align=”aligncenter” width=”614” caption=”Carlos Rojas explaining his poster on CBM18”][/caption]Lorena and Ramy worked with graduate student Divya Sain on a screen of _Neurospora_strains with candidate cell wall genes knocked out.  They completed a screen of 115 mutants x 3 replicates = a lot of petri dishes for their first time in the laboratory. Below is a picture of Ramy and Lorena with their peers from the MARCU program.[caption id=”attachment_643” align=”aligncenter” width=”1024” caption=”The 2011 MARCU* students gather before their presentations”][/caption]

Welcome to two new programmers to the team working on FungiDB.Daniel Borcherding and Ragu Ramamurthy join us to work full time on the FungiDB project to support genomic data integration, website improvements, and supporting the system move from beta into production mode.  We look forward to new improvements in the system and establishing a release cycle for the website and DB.

Sofia Robb joined the lab this week to begin work as a postdoc scholar on genomics and bioinformatics aspects of studying transposable elements in Rice. She will also participate in developing teaching modules for the Dynamic Genomes course in collaboration with the Wessler lab.  Sofia recently completed her PhD from the University of Utah working on planaria in the Sanchez lab.

Edgar Medina has been visiting the lab for the last few months from the Universidad de los Andes, Bogotá, Colombia to work on Batrachochytrium genome evolution.  This past Friday he completed his Master’s degree, defending his thesis via Skype.  Was quite fun to see him adeptly switched between Spanish and English in the Q&A period while showing his slides that were remotely projected onto the screen back in Bogotá. It was a real pleasure to have him here for the few months and look forward to a chance to keep interacting on many of our projects.  Way to go Edgar!

[This position filled as of Aug 2011]A programmer position is available in the lab to work on FungiDB. The duties include performing data loading into relational database system, development and improvement of scripts for data importing & downloading, and website development. This project is part of a collaborative project with members of the EuPathDB team.More information and online application to the position is available at the UCR job listing.

A warm welcome to graduate student Steven Ahrendt to lab. Steven is working on questions relating structural evolution of light sensing proteins in fungi, metagenomics, and bioinformatics. He will be co-advised by Assistant Professor Chia-en Angelina Chang.

I can safely say everyone had a good time at Fungal Genetics at the Asilomar Conference Grounds earlier this month. So much fun it too us a week to catch up on sleep and dig out from work left undone. Here are a few pictures from poster presentations. We didn’t get everyone’s picture captured in the chaotic swirl of the poster session unfortunately. I’m really proud of how well everyone did and the apparent interest in our projects.I also launched our fungidb.org database website at the meeting and got chance to tell more people about our ambitions and hopes for it. It was also a real treat to see longtime friends and mentors and have the chance to swap stories.

Snow on the mountains while the temps are in the 70s here. A wet winter means there are lush hillsides…for now, until the dry season starts in another month.

 We will be working on discovery of active transposable element discovery in three mosquitos thanks to a grant that began this year from the W. M. Keck Foundation.  We will be using Illumina based resequencing of populations of mosquitos, RNA-Seq to study expression of genes and TEs to determine differences between active and silenced elements, bioinformatics to identify and characterize transposable elements in the genomes of 3 mosquitos, and experimentally test for activity of the transposases that are thought to match the target TEs.  The grant is highlighted in a campus press release and will be a collaboration between our lab and the labs of Dr Susan Wessler, and Dr Peter Atkinson. Should be a fun exploration and will help inform other TE work in the laboratory as well.

Postdoctoral Research in Bioinformatics and Transposon Biology in RiceUniversity of California, Riverside[Position filled as of 6/2011]Position DescriptionAn NSF funded postdoctoral position is available in the laboratories of Dr Susan Wessler and Dr Jason Stajich to study the evolutionary dynamics of transposable elements in the rice genome and their contribution to phenotypic variation. This postdoctoral scientist will be involved in research using bioinformatics, next generation sequencing of multiple rice strains, and RNA-Seq based transcriptional profiling. This position requires excellent bioinformatics and programming skills to analyze and synthesize genome assemblies from next generation sequencing data produced by Illumina/Solexa technology. Background information on the biology underlying the project can be found in: K. Naito et al, Nature 2009 461: 131; K. Naito et al, PNAS 2006 103: 17620; N. Jiang et al, Nature 2003 421: 163.The successful candidate will be expected to contribute and lead data analysis for the project. There will be opportunities for molecular biology, if desired, as part of validation of analyses. In addition, data and software from this project will be used to develop teaching materials as part of the HHMI funded Dynamic Genomes course at UC Riverside providing an opportunity to participate in teaching in an innovative topic-focused course for undergraduates. Applications will be accepted until the position is filled and review will begin on February 15, 2011.  Salary and benefits are commensurate with NIH guidelines and the University of California Postdoctoral Union agreement. Special consideration will be given to candidates with exceptional bioinformatics and genome evolution experience.QualificationsMinimum qualifications include a Ph.D. in Biological Sciences, Computer Science, Statistics, or a related field. Demonstrated experience in bioinformatics and high proficiency in programming is necessary along with an understanding of the mechanisms underlying genome evolution. Experience with next generation sequence data is highly desirable. Ability to communicate clearly, work independently, and interact collaboratively is essential.The researcher will also work closely with co-PIs and collaborators at the Boyce-Thompson Institute and Cornell University.To ApplyContact Jason Stajich (jason.stajich@ucr.edu) or Susan Wessler (susan.wessler@ucr.edu) with a current CV and names of three references.More information can be found online about the Stajich lab http://lab.stajich.org Wessler lab http://wesslerlab.ucr.edu and UC Riverside http://www.ucr.edu.Information about UCRIn the Heart of Inland Southern California, UC Riverside is located on nearly 1,200 acres near Box Springs Mountain in Southern California, the park-like campus provides convenient access to the vibrant and growing Inland region. The campus is a living laboratory for the exploration of issues critical to growing communities — air, water, energy, transportation, politics, the arts, history and culture. UCR gives every student the resources to explore, engage, imagine and excel.UCR is ranked 43rd among top public universities (US News and World Report 2010).At UC Riverside we celebrate diversity and are proud of our #5 ranking among the nation’s for most diverse universities (US News and World Report 2010). Become part of a place that fosters success for all its constituents, students, faculty, and staff, and where work/life balance and campus culture are integral to our way of life.UCR is an affirmative action and equal opportunity employer with a commitment to workforce diversity.  **AA/EOE ** 

[Update May 5, 2011 – This position is on hold to focus on hiring a programmer to work on data development and loading]There is an open position in the lab to support development of FungiDB, a database for fungal genome data integration.## Postdoctoral fellow supporting fungal genome database development Position DescriptionA postdoc position is available in the laboratory of Dr. Jason Stajich to support the development of FungiDB, a database for fungal genomic and functional data.   Strong candidates will be proficient in the Perl programming language; modern biology in general and bioinformatics in particular; show a demonstrated ability to quickly pick up new biology and computer science concepts; be comfortable using relational databases; and possess core Unix skills to do these tasks efficiently.  Experience using Perl for genome sequence data processing a plus.You’ll also have a relentless attention to detail, the ability to work independently on challenging problems with no direct easy solution.  You will use these skills to help organize, analyze, and display a vast amount of disparate biological data and interact with the fungal community. There will be opportunities for self-directed research utilizing this collection of genomics and comparative database and tools.Application evaluation will begin Feb 1, 2011 until the position is filled. Salary and benefits will be commensurate with experience and University of California Postdoctoral Union agreement.QualificationsMinimum qualifications include a Ph.D. in Biological Sciences, Computer Science, Statistics, or a related field. Demonstrated experience in bioinformatics and high proficiency in Perl programming is required.  Demonstrated experience in web or bioinformatics software development is a plus. The ability to work with a small, distributed team is essential including exceptional written and verbal communication skills.To ApplyContact Jason Stajich jason.stajich@ucr.edu with a CV and the names of three references letter writers.Information available on UC Riverside and the Stajich lab.Information about UCRIn the Heart of Inland Southern California, UC Riverside is located on nearly 1,200 acres near Box Springs Mountain in Southern California, the park-like campus provides convenient access to the vibrant and growing Inland region. The campus is a living laboratory for the exploration of issues critical to growing communities — air, water, energy, transportation, politics, the arts, history and culture. UCR gives every student the resources to explore, engage, imagine and excel.At UC Riverside we celebrate diversity and are proud of our #5 ranking among the nation’s for most diverse universities (US News and World Report 2010). Become part of a place that fosters success for all its constituents, students, faculty, and staff, and where work/life balance and campus culture are integral to our way of life.UCR is ranked 43rd among top public universities (US News and World Report 2010).UCR is an affirmative action and equal opportunity employer with a commitment to workforce diversity.AA/EOE

Here’s our 2010 publications Wordle made with pubmed2wordle.

UCR undergraduate Jessica De Anda has been working in the lab this summer and Fall will be starting in the MARC U* STAR program at UCR.  This program provides mentoring to students interested in pursuing a graduate degree in science and supports laboratory research during the school year and the summers. We’re excited she was selected to be part of this program and look forward to her continued work in the lab on aspects of transposon dynamics and evolution in fungi.

Some pictures from a recent lab lunch to help celebrate Divya passing her qualifying exam.

A few papers from our work are now appearing. This includes several collaborative papers that have been in progress for several years, so I’m happy to see them published.- See the latest issue of PLoS Genetics for our work on analysis of the transcriptome during meiosis in _C. cinerea _in collaboration with several labs at UNC-CH, Indiana University, and SEMO. A chapter on bioinformatics protocols for using the Gbrowse_synteny tools The final version of our paper from a collaboration with Kristina Smith and Mike Freitag, Deb Bell-Pedersen, and Michael Brunner labs on ChIP-Seq and profiling of the White Collar Complex in Neurospora to identify the network of genes regulated by light.

Congrats to grad student Divya Sain, who passed her prelim qualifying exam in September and is now a PhD candidate as she begins her 3rd year at UCR in the GGB program.

We had a productive period over the last year and finally saw set of papers representing this work come out in the last month. This represents great collaborations with several different groups.  In addition to the Coprinus genome, we were involved in the publication of two other genome sequences thus summer. One a basidiomycete mushroom and one for an oomycete and pathogen of plants, both with a host of collaborating labs. Two papers on Neurospora also appeared as part of collaborations with Hanna Johannesson’s group and Michael Freitag, Michael Brunner, and Deb Bell-Pedersen.  A fifth paper on Coprinopsis meiotic genes is in press but will post about it when it appears.- Transcription factors in light and circadian clock signaling networks revealed by genome-wide mapping of direct targets for Neurospora WHITE COLLAR COMPLEX. Smith KM, Sancar G, Dekhang R, Sullivan CM, Li S, Tag AG, Sancar C, Bredeweg EL, Priest HD, McCormick RF, Thomas TL, Carrington JC, Stajich JE, Bell-Pedersen D, Brunner M, Freitag M. Eukaryot Cell. 2010 Jul 30. Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Lévesque CA, Brouwer H, Cano L, Hamilton JP, Holt C, Huitema E, Raffaele S, Robideau GP, Thines M, Win J, Zerillo MM, Beakes GW, Boore JL, Busam D, Dumas B, Ferriera S, Fuerstenberg SI, Gachon CM, Gaulin E, Govers F, Grenville-Briggs L, Horner N, Hostetler J, Jiang RH, Johnson J, Krajaejun T, Lin H, Meijer HJ, Moore B, Morris P, Phuntmart V, Puiu D, Shetty J, Stajich JE, Tripathy S, Wawra S, van West P, Whitty BR, Coutinho PM, Henrissat B, Martin F, Thomas PD, Tyler BM, De Vries RP, Kamoun S, Yandell M, Tisserat N, Buell CR. Genome Biol. 2010;11(7):R73. Epub 2010 Jul 13. Genome sequence of the model mushroom Schizophyllum commune. Ohm RA, de Jong JF, Lugones LG, Aerts A, Kothe E, Stajich JE, de Vries RP, Record E, Levasseur A, Baker SE, Bartholomew KA, Coutinho PM, Erdmann S, Fowler TJ, Gathman AC, Lombard V, Henrissat B, Knabe N, Kües U, Lilly WW, Lindquist E, Lucas S, Magnuson JK, Piumi F, Raudaskoski M, Salamov A, Schmutz J, Schwarze FW, Vankuyk PA, Horton JS, Grigoriev IV, Wösten HA. Nat Biotechnol. 2010 Jul 11. Conflict between reproductive gene trees and species phylogeny among heterothallic and pseudohomothallic members of the filamentous ascomycete genus Neurospora. Strandberg R, Nygren K, Menkis A, James TY, Wik L, Stajich JE, Johannesson H. Fungal Genet Biol. 2010 Jul 1.

Our work on the mushroom genome of Coprinopsis cinerea is featured on the cover of this week’s PNAS.  Check out the blog post and the article.

We bid farewell last weekend to our lab visitor, Nastassa Gioti, who is headed back to Sweden after 6 fun weeks in Riverside.  We learned from her, and she got to dig into her genome datasets for Neurospora in the context of the comparative and genome annotation tools we have, so it was fun all around!This also marked the second get together (but the first where we remembered to bring a camera). Since we gathered at a local mexican restaurant with whimsical and amazing sculptures and art from recycled material, it was fitting we document it with pictures.

Spring is flying along. We’ve been presenting some of our work at conferences and getting ready for a full summer of meetings and Divya preparing for her qualifying exam.A few papers have come out or are now accepted. One I’ll highlight here is the publication of the Sordaria macrospora genome.  This was a fun collaboration with groups in Germany, France, Oregon State, and Edinburgh where we sequenced Sordaria with 454 and Illumina sequence and assembled the genome using de novo assembler and comparative scaffolding to the available Neurospora genomes.  Sordaria is an important model system for sexual development and provides a great evolutionary not-too-distant outgroup to the Neurospora clade for evolutionary genomic analyses we are trying to finish off.Also have had a chance to interact with colleagues at the JGI User meeting, the Neurospora conference, and a special treat of speaking at the PBoFF symposium at Texas A&M.Everyone is getting their projects underway in the lab and we’ve had two visitors come to work on Neurospora and Chytrid genome project analyses so a busy but exciting time for us.Several more weeks left in the quarter where I’m teaching introductory biology and  then the Gordon Conference, MSA, and IMC9 will be conferences to finish preparing for.  The lab will also be represented at Evolution meetings in Portland as John attending.

Congrats to graduate student Divya Sain a co-author on a paper published in Nature on mobile chromosomes in Fusarium, stemming from her work her work during a rotation in the Borkovich laboratory.The work highlights the important aspect of how pathogenicity factors can be exchanged via mobile chromosomes and can be an important pathway for adaptive evolution and acquisition of new function through whole chromosome exchange between strains.

I am back from a short trip to Ireland where I gave a seminar at National University of Ireland, Maynooth and spend some time with folks interested in evolution or fungi like David Fitzpatrick, James McInerney, Davide Pisani. I also learned about a new spinoff company from one of the faculty producing media that will help Bee immune systems. In my chats with some of the faculty I found out that I had lots in common with Sean Doyle on Aspergillus and some basidiomycete genomics questions and also much in common with Gary Jones working on prions in yeast.  After my trip to Maynooth, I spent a few days in Dublin afterwards to see the town which included a visit with some Dublin yeast researchers Ken Wolfe and Geraldine Butler who took me out to see Newgrange.I learned that there is an abundance of yeast research in Ireland.  In addition to the researchers there is a whole shop devoted to Yeast.And my visit to the Guinness Brewery at St. James Gate taught me that that Yeast is a national treasure in Ireland.Complete with an important safe for insuring there are backup strains. I have to assume there is a -80 freezer somewhere in the Guinness complex holding old strains as well.Did you know one of the master brewers at Guinness was also the inventor of the Student’s T-test? Here’s the proofSo it was great to visit and look forward to going back at least in 2012 when SMBE will be held in Dublin.

PLoS Pathogens has a short review format called Pearls.  We were invited to write a short summary on Batrachochytrium which was published in the January issue.Rosenblum, E., Voyles, J., Poorten, T., & Stajich, J. (2010). The Deadly Chytrid Fungus: A Story of an Emerging Pathogen PLoS Pathogens, 6 (1) DOI: 10.1371/journal.ppat.1000550

A quick January update.  Jason was appointed to a two year term as Councilor for Genetics/Molecular Biology for the Mycological Society of America, began a term on the editorial board of Eukaryotic Cell, and was also profiled in the GSA reporter. Finishing grants and working towards completing manuscripts from postdoc-land while we are computing results on from genome and RNA-Seq datasets. Working to getting our laboratory production up and running to generate more of our data.Currently the lab is four strong with 3 graduate students. They are Divya Sain and Yi (Zoe) Zhou who have joined for the long haul of doing a PhD in the GGB program, and Yizhou Wang, a rotation student from Plant Biology.  Divya is working on a project that uses bioinformatics and phylogenetics to reconstruct history of the genes involved in the fungal cell wall across the fungi.  Zoe is using bioinformatics and phylogenetics to focus on duplicated gene evolution and is exploring other aspects of duplication in fungal genomes.  Yizhou will be getting going in the laboratory learning how to grow Neurospora and preparing some RNA extractions for some transcriptomics and RT-PCR validation.In February John Abramyan will join us as a postdoctoral scholar to work on some molecular biology and genomics work on at least two fungi along with applying  bioinformatic analyses of these data.I also setup the Gbrowse2 for Sordaria and Coprinopsis, worked on some new template themes for the blogs, and we setup a bioinformatics group website at UCR (which is still coming together). Hoping the rest of Jan and Feb will be clearing a few more to do things off the list and getting a chance to do a bit more research blogging on the Hyphal Tip.

Although I’m not going to be at PAG this year, I’ll be in San Diego for  the BioPerl and part of the GMOD meeting on Wed and Thursday.

Well the 1st quarter is over and had a few observations about life of an assistant professor.1. Remember to check that you don’t need to turn in grades! I thought I could safely ignore emails about sending in grades, since I wasn’t teaching this quarter, but meant I forgot to turn in grades for grad students working in the lab. Whoops! Lesson learned. Spending money isn’t that hard, but researching how to spend it on equipment is time consuming.  The optimization of trying to find the best deal, planning for current and future experiments, and establishing new technologies took more time than I expected.  Planning how to best spend money longer term is also taking some time, I don’t know if there is any good formula to rely on because it depends on what future grant support is awarded. But I think that I am getting better at making the equipment decisions - but I am my own sysadmin for macs in the lab and also the new separate (from the shared bioinformatics cluster) linux machines I have for our web and specialized compute needs and find that very time consuming. Travel is good, but takes up time that can be spent writing, instructing, and my own research. While I can do much of my research from my laptop and an internet connect, I am distracted when away from lab and doing a disservice to the meeting I am attending if I am always working while on the road.  Better to divide my time better and focus on the meeting at hand. Course this means I should always have the talks finished before I get to the meeting and that has been difficult to guarantee. People are important. I can’t do all the research myself. Getting students and postdocs into the lab who can be trained on techniques and the background of the research questions is the most important thing to get the lab moving forward.  I am excited about the teaching and learning process but it is a process that needs a vision and schedule that I establish.  I’m still fine tuning that schedule and the approaches while keeping us aimed toward a vision of the kind of research we will do in the next 3-5 years. Time flies - take stock of how you spent it! Stopping and reflecting on what was accomplished is good to remind me and remind trainees that we have done things even if it feels like there is a mountain of work ahead.  As the gets better at this I’ll probably be able to give better feedback about dead-ends and keeping people on track earlier in the game.  We are still getting our timing together to have regular lab meetings and journal clubs that I expect to be the heart of the learning that happens in the lab at this point. I’m teaching programming, bioinformatics, phylogenetics & molecular evolution, and mycology at the outset and so am working to make these subjects more approachable with the right kind of background reading materials.  Probably will have to turn this into a review or primer someday as I feel like this synthesis of different fields is not something I can point anyone to just one or two resources for. I’m still getting aquatinted with who to ask for help and where to go for advice, but I’ve been lucky to have generous junior and senior colleagues who have provided encouragement and advice.  Here’s to hoping next quarter I learn a little more about how to do things, focus on the grant writing, and make some tangible progress on the research projects that need some new data before this summer. A lot of papers are queued up from collaborative work that were submitted this month and I hope that means more focus on the two main project foci of the lab.  New folks will be joining us next quarter and I’m excited about the progress we have made and will be able to make as everyone comes up to speed.Happy New Year!

  Chris Fields and I spoke about BioPerl past and present and tried to convince computer science types that biology is in fact interesting on TWiT.tv FLOSS. Check out the podcast for Episode 96.

A talk today in the CS department on open problems in bioinformatics and hope to entice some computer scientists to work on more of the problems here.

Back from an excellent meeting in St Feliu du Guixols for the EMBO Comparative Genomics of Eukaryotic Microorganisms. Not a strictly fungi focused meeting, but lots of genome comparisons of yeasts and molds were presented.  It will be held again in 2 years so mark your calendars as it is a great scientific exchange and a beautiful location.

Our primer on the Fungi is available (currently free) on the Current Biology website.  A version with extra refs inserted is available in pre-print format here. In this primer we provide a broad overview of the major evolutionary defined groups within Fungal kingdom. Our intention is make the kingdom a little less mysterious for non-mycologists and introduce some open areas of research that require integrating evolutionary, morphological, and molecular research. This was joint work with Mary Berbee, Meredith Blackwell, David Hibbett, Tim James, Joey Spatafora, & John Taylor.Also thanks to several people for access to images: Jeffrey Rollins, Sabine Huhndorf, David McLaughlin & lab,George L Barron, Greg Jedd and Michelle Momany.  

Making some signs for the doors to offices.  Here’s a Wordle plot from abstracts of last 7 years of papers. Tip the hat to M. Dunham for the idea to make it part of the lab signs.      

Well, the doors have been opened and things are moving into the new Genomics building. Since we are so new, no things to really move into the lab as they will come from vendors directly. I got into my new office with furniture installed and everything. We have ordered some of the big equipment for the lab and started getting supplies. Will be some adjustment as we all learn the new space for the labs on the same floor as we start sharing space, supplies, and also ideas and collaborations.  An exciting time and with any luck some fun and productive ways of doing science will emerge.

To the newly finished Genomics building on campus.  Our (well only me still ) move date in mid-September or when the office furniture is installed.

My presentation from BSA/MSA 2009 on early fungal evolution inferred from the chytrid genome is available here.  The conference was great for the time I could be there and the interaction with mycologists and botanists at the meeting seemed to be really helpful (I caught a few botany talks) and catching up with new and old friends is a great bonus at these meetings.

I will be at the Botany & Mycology conference (mainly to see the MSA members) and present a talk on Tuesday morning of the meeting. Hope to run into some old friends and meet new people at the meeting which will see Botanists and Mycologists mixing (oh my).  I get to stop by Univ of Utah a few days early and give a quick talk and visit with some friends at the Eccles institute at the U and maybe will get to see a few more Salt Lake City sites.

Went from CA to OR to ID, MT, and WY for work (Bioinformatics symposium at Oregon State) and a little vacation.

Saw this beauty while on our hike in Pt Reyes before the Miller Institute Annual Symposium

RT @NikonSmallWorld: 1 week to enter the competition! Submit yr best photomicrographs at http://www.nikonsmallworld.com #microscope #science # Save the Frogs day is April 29th http://savethefrogs.com/day/ #

Word on the street is we will be moving into the new Genomics building at the end of the summer.

RT @hyphaltip: Lichen named for Pres Obama by UCR herbarium curator Kerry Knudsen http://is.gd/sMwk #

git archiving code from my thesis http://github.com/hyphaltip/thesis/tree/master #

Adding some OrthoMCL processing scripts to github to convert FASTA processed genome-pair search results for proper input http://is.gd/qOoM #

Live blogging JGI User meeting where the talks range from application of sequencing to problems in biofuels, comparative genomics and evolution, and the discussion of new sequencing technologies.Here are some links from Day 1. We’ll probably have the rest of the days’ coverage in the Friend Feed Room.- Friend Feed Room Jonathan Eisen’s page with some aggregated links for coverage A few of the posts I wrote are on another site, Mike Mendez, Cameron Currie on Ant farming of fungi Joe Ecker on Arabidopsis quick wrap-up from day 1.

Setting up lab pages #

I will be at Asilomar for the Fungal Genetics 2009 meeting presenting some work on the transcriptional landscape in Neurospora and collaborative work on Coccidioides, Neurospora tetrasperma, and Coprinopsis cinerea.

The lab will open in July 2009 at UC Riverside and be housed in the new genomics building on campus.

Congratulations to Julia Adams who defended her PhD on Nov 15, 2024 on her project focused on landscape and population genomics of the lichen Acarospora socialis

Congratulations to Mark Adams who defended his PhD on Septemer 3, 2024 on his project focused on the amphibian pathogen Batrachochytrium dendrobatidis and pangenome and comparative genomics including discovery of a DNA virus that infects some populations of the fungus.

Congratulations to Talieh Ostovar who defended her PhD on June 28, 2024 on her project focused on plant comparative genomics in the genus Boechera as well as a project on the Citrus genome with our lab. Dr Ostovar was primarily advised by Liz Waters at SDSU but was co-advised in our lab through the UCR-EEOB Joint Doctoral Program with SDSU.

Congrats to Cassie who was awarded the 2022 CEPCEB Postdoc Award.

Congratulations to Dr. Tania Kurbessoian who completed her PhD work at the end of 2022. Tania was an integral part of the lab advancing new culturingi projects, a thoughtful and giving student mentor, and a key person in our data analysis of black yeast fungi. The lab greatly benefited from her efforts to keep the wet lab efficient for molecular biology, microbiology, and genomics techniques.

Congraulations in order for Cheng-Hung who passed his Qualifying exam in the Genetics, Genomics, and Bioinformatics program. We are excited him to continue his work on metagenomics methods and application to Citrus trees and soil microbiomes as part of the Citrus HLB Microbiome project.

A new project is launching for studying the Microbiome of Herptiles and the impacts of specific fungi. The work is supported by the NSF Understanding the Rules of Life: Microbiome Interactions and Mechanisms and will support a four year project to examine the dynamics of microbiomes from wild and captive animals, manipulation experiments, and genomic and metabolomic profiling of these communities and individual microbial members.

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Congrats to Derreck Carter-House, Ph.D.

Jesús Peña introduces his research on sexual reproduction in the zygomycete fungi in the lab through a new video as part of the UCR Microbiology Graduate Ambassador. Have a watch and learn more about the research Jesús is working on.

The end of summer meant goodbye to our excellent REU student Saisuki Putumbaka.

I am delighted to announce that Yan Wang a current postdoc in our group, will be a starting his next position as an Assistant Professor in the Department of Biology at the University of Toronto-Scarborough. Yan has spent the last two years in the lab working on Zygolife and Neocallomastigomycota fungi projects. We are super proud of all he has accomplished in his training and research. This includes multiple publications from his thesis work and several papers submitted from his current projects. The lab has greatly benefited from his phylogenetic and insect-fungi expertise. Luckily we still have ~6 more month together to continue projects and help him prepare for his next step in his career. <figcaption>Helping Yan celebrate his acceptance of offer at UTSC.</figcaption>

We enjoyed a wonderful spring flower season here in Southern California (Harford Springs Riverside County Regional Park) Several publications were accepted and published in last few months and want to highlight the hard work from lab members and collaborators. Jinfeng lead article published on the localized burst of Rice Transposable Elements Ping and Pong in only a subset of the domesticated lineages and clues to what changed to drive their increased activity. Variation of mPing, Ping, and Pong_ element copy number in rice subgroups https://www.nature.com/articles/s41467-019-08451-3/figures/2 A fun collaboration lead by Adam Bewick and Bob Schmitz we called #MycoMeth explored diversity of Cytosine DNA Methylation in Fungi looking at the 5-methylcytosine (5mC) marks and evolution of the fungal 5mC methyltransferases. Genomewide 5mC profiles https://www.nature.com/articles/s41559-019-0810-9/figures/2 Two Zygolife project papers. One on genome evolution and phylogenic position of Endogone - a truffle forming Mucoromycotina fungus.This was quite challenging but interesting project to tackle, lead by Ying Chang in the Spatafora Lab. Dr Chang took a metagenomics approach to capture these unculturable fungi followed by bioinformatic analyses to isolate the fungal and Mucoromycotina component of the dataset. <figcaption>Phylogenetic placement and divergence time estimation of Endogonales and the evolution of fungal plant‐cell‐wall‐degrading enzymes (PCWDEs) A second paper lead by William Davis from Tim James lab on the genomes and phylogeny of Zoopagomycotina fungi which include nematophagous and mycoparasites. Fig 5. Ancestral state reconstructions of trophic state on the best ML tree (A) and the ASTRAL consensus tree (B) using maximum likelihood. Pie graphs at nodes show the proportional likelihood of each character state. Jason participated in a Marine Fungi workshop on the unexplored diversity in the marine environments and co-authored this perspective on the opportunities and challenges in characterizing and studying these fungi. Morphological diversity of fungi collected from a biotic host. Fungal collection isolated from a marine sponge,Ircinia variabilis (formerly Psammocinia sp.). Former postdoc Ousmane Cissé developed FGMP, a tool for assessing completeness of fungal genomes which uses both conserved protein coding markers that can include multicopy gene families and conserved non-coding DNA regions. This was published this month as well, congrats Ousmane! Fig 2.Estimation of genome completeness in fungal genomes. A comparison of genome completeness by multiple software tools using initial and latest genome assembly versions of 45 fungi. Genome completeness expressed as a percentage of expected markers (y-axis) is plotted against assembly size in megabases (x-axis).

Sarah Johnson Lead Programmer

January 07, 2019 December 18, 2024

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Congrats Derreck! He was selected by the California Council on Science and Technology (CCST) to give a presentation and represent Dept of Microbiology and Plant Pathology and UCR at the California Science Translators Showcase. He will be giving a talk about his research at the California State Capitol to legislators/state senators, agency managers, and senior policy leaders. He was chosen out of a pool of California PhD students, post-docs, and career scientists from all different STEM fields and universities to talk about plant pathology/fungi.

Nat visited New Mexico State University several times this summer to complete work at the Jornada LTER site working with Nicole Pietrasiak (@drylandalgae) on the micro- and myco-biomes of biological crusts. Visits to Anza Borrego and Boyd Deep Canyon for Tania to scope out UCNRS research sites to explore desert rock varnish and rock or crust associated black fungi. Julia continued to develop her Joshua Tree research sites for lichen studies and has collected and sequenced new accessions for a reference library of lichens from Joshua Tree NP.Congrats to Jesús (IG: variety_hour) who passed his qualifying exam has continued to explore zygomycete diversity focusing on sexual reproduction.  Derreck has been working on bacteria-fungal interactions via volatiles and new work with N. crassa sensing of these. Yan has submitted a manuscript on his postdoc work on phylogenomics and dating the emergence of the the anaerobic gut fungi. Jinfeng has submitted and is revising work on characterizing the transposition and burst of the Ping, Pong, and mPing transposable elements across 3000 Rice accessions. Sawyer generated and analyzed whole genome sequence from strains of Rhizopus stolonifer in his population genomics project which he presented at the IMC11 conference.New publications including population genomic diversity of Candida lusitaniae, Entomophthorales proteases, space fungi!, and fungal & bacteria communities in Antarctic rocks came out in the last few months.Hopefully another update before the end of 2018 but check out pictures and tweets for shorter updates.

The lab is back from conferences this summer. The Cellular and Molecular Fungal Biology Gordon Research Conference in Holderness, NH and the 11th International Mycological Congress in Puerto Rico. Tania also gave her first talk  at the Black Yeast workshop held in Amsterdam as part of the ISHAM meeting.

There have been several manuscripts are now out from work that was done over the last few years. It has been great to be able to collaborate with many research teams as part of this work.Been slow to mention these but wanted to make sure and call out the hard work from everyone. A long term collaboration lead by Cene Gostinčar on population genomics in Hortaea, an ascomycete black yeast, complemented some reference genome work we published last year [1].  Former postdoc Ousmane Cissé published his work on Pneumocystis at the NIH in his current postdoc[2]. Figure 6 - Overview of the timing and evolution of Pneumocystis and their mammalian hosts Current postdoc Yan Wang published part of his thesis work and we worked on these data a bit as part of the zygolife project here [3].  Graduate students Nat Pombubpa collaborated with Plant Sciences and Jeff Diez lab graduate student Courtney Collins on her thesis work looking at the mycobiome differences of soils in an alpine gradient with and without invasive shrub introduction [4].  Andrii Gryganskyi’s work on Rhizopus phylogeny with some of the first multi-genome work on this genus that was one of the earliest collaborations on some ZyGoLife questions [5].  Work exploring whether Transposable elements have a role in stage-specific gene expression in Coccidioides with Theo Kirkland and Anna Muszewska [6].  A collaboration lead by Tom Richard’s lab and Guy Leonard sequence and assembled and annotated a genome of a ‘pseudofungus’ hyphochytriomycete called Hyphochytrium catenoides [7]. I think I forgot to also call out that last year postdoc Jinfeng Chen published work collaboratively with postdocs Lu Lu and Sofia Robb on the active Rice transposable element system mPing and Ping [8]. Good work all! Gostinčar C, Stajich JE, Zupančič J, Zalar P, Gunde-Cimerman N. Genomic evidence for intraspecific hybridization in a clonal and extremely halotolerant yeast.BMC Genomics. 2018 May 15;19(1):364. doi: 10.1186/s12864-018-4751-5. Wang Y, Stata M, Wang W, Stajich JE, White MM, Moncalvo JM. Comparative Genomics Reveals the Core Gene Toolbox for the Fungus-Insect Symbiosis. MBio. 2018 May 15;9(3). pii: e00636-18. doi: 10.1128/mBio.00636-18. Cissé OH, Ma L, Wei Huang D, Khil PP, Dekker JP, Kutty G, Bishop L, Liu Y, Deng X, Hauser PM, Pagni M, Hirsch V, Lempicki RA, Stajich JE, Cuomo CA, Kovacs JA. Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen Pneumocystis. MBio. 2018 May 8;9(3). pii: e00381-18. doi: 10.1128/mBio.00381-18. Gryganskyi AP, Golan J, Dolatabadi S, Mondo S, Robb S, Idnurm A, Muszewska A, Steczkiewicz K, Masonjones S, Liao HL, Gajdeczka MT, Anike F, Vuek A, Anishchenko IM, Voigt K, de Hoog GS, Smith ME, Heitman J, Vilgalys R, Stajich JE. Phylogenetic and Phylogenomic Definition of Rhizopus Species.  G3 (Bethesda). 2018 Apr 19. pii: g3.200235.2018. doi: 10.1534/g3.118.200235. Collins CG, Stajich JE, Weber SE, Pombubpa N, Diez JM. Shrub range expansion alters diversity and distribution of soil fungal communities across an alpine elevation gradient. Mol Ecol.2018 Apr 19. doi: 10.1111/mec.14694. Kirkland TN, Muszewska A, Stajich JE. Analysis of Transposable Elements in Coccidioides Species. J Fungi (Basel). 2018 Jan 19;4(1). pii: E13. doi: 10.3390/jof4010013. Leonard G, Labarre A, Milner DS, Monier A, Soanes D, Wideman JG, Maguire F, Stevens S, Sain D, Grau-Bové X, Sebé-Pedrós A, Stajich JE, Paszkiewicz K, Brown MW, Hall N, Wickstead B, Richards TA. Comparative genomic analysis of the ‘pseudofungus’ Hyphochytrium catenoides.  Open Biol. 2018 Jan;8(1). pii: 170184. doi: 10.1098/rsob.170184. Lu L, Chen J, Robb SMC, Okumoto Y, Stajich JE, Wessler SR. Tracking the genome-wide outcomes of a transposable element burst over decades of amplification. Proc Natl Acad Sci U S A. 2017 Dec 5;114(49):E10550-E10559. doi: 10.1073/pnas.1716459114.

Last week we hosted several visitors from our ZyGoLife collaborative team in sunny California. I wrote a few notes on Nicole Reynolds and Javier Tabima’s visit for the zygolife site on their extended research stay.

Nat and Jason headed out to the Mojave National Preserve to meet up with Erik Hom and his StudyUSA class from Univ of Mississippi. We started at the Sweeney Granite Mountains Desert Research Center which is one of 39 Natural Reserves in the University of California.  We were there to teach a bit about cryptogamic crusts, show the Kelso dunes off, and explore some more of the desert crust sampling sites that our collaborator Nicole Pietrasiak (@drylandalgae) and Paul De Ley have collected from. Nothing like seeing sites that previously I only knew from pictures or tubes of soil!A few pictures from our visit.Kelso DunesCrusts symbioses of algae and cyanobacteria with fungi, bacteria, and many uncounted single celled organisms.Lichen Crusts galore across from the Kelso dunesMoss Crusts are also rich symbioses with a predominant moss.Old volcanic flow in the Cima area also has cacti and crustsColorful lichens found on the granite faces. On closer looks, these are often 3 or more species competing for space on the same surface.

Our lab trip to Joshua Tree NP and photo session before the start of the quarter resulted in our 2017 album cover lab photo.

Welcome to first year graduate students Julia Adams (Plant  Biology) and Tania Kurbessoian (Microbiology). Tania joins us after completing a MS in Microbiology at Cal State-Northridge. She will starting out work on projects relating to genomics and physiology of extremophilic fungi,  black yeasts and efforts to culture and describe diversity of desert fungi. Julia completed a BS at Wellesley and has worked on a variety of projects related to lichen fungi. She will focus on lichen fungi from desert regions and will use genomic and potentially metabolomic tools to study evolution and unique properties of some lichenized fungi endemic to Joshua Tree National Park and the Mojave desert.

Congrats to Nuttapon (Nat) who passed his qualifying exam this week and is now a PhD Candidate. Along with Derreck he is the second Plant Pathology graduate student in the lab and is working towards his PhD on microbial diversity of cryptogamic or biological soil crusts found in the desert. His primary research area is Joshua Tree National Park and desert areas in the UC Reserve System. Nat and Jason have benefited greatly from collaboration with New Mexico State Univ Professor Nicole Pietrasiak who is an expert in crusts, desert algae, and did her PhD work in Joshua Tree which harbors tremendous diversity of biological soil crust types.[caption id=”attachment_1742” align=”alignnone” width=”1024”] Cross section of crust. Image by N. Pietrasiak[/caption] 

Congratulations to Derreck who passed his qualifying exam this week! Derreck’s projects focus on interactions between the zygomycete (Mucoromycota and Zoopagomycota) fungi and bacteria, primarily from the genus Serratia.

Great work by former student Steven Ahrendt (@sahrendt0), visiting student and current Duke graduate student Edgar Medina (@WhippingFungi) on the publication of a manuscript describing a Type II Opsin found in the zoosporic fungi. "Exploring the binding properties and structural stability of an opsin in the chytrid Spizellomyces punctatus using comparative and molecular modeling" in PeerJ! Thanks also to co-author and collaborator Angelina Chang in Chemistry Dept at UCR who helped mentor Steven on all the nuances of homology modeling and docking.

When Bacteria attack!

With Bob Schmitz at Univ of Georgia, We’re working on a project we call MycoMeth to examine evolution of methylation across Fungi. We would welcome contributions of ~2ug of DNA from diverse fungi that have a sequenced genome.  Please email Jason or Bob if you would like to contribute.

Just back from another fantastic Fungal Genetics Conference at Asilomar. An amazing number of helpful tweets under the #Fungal17 hashtag. Sarah Unruh (@sau916) and I are talking about how to best archive or building a storify this so it is easier to read. Always a fun meeting to see friends and nosh at the smorgasbord of fungal genetics, epigenetics, genomics, ecology, evolution, and chemistry that is going on. Jason got to give a Plenary talk and express the utility of sequencing fungal genomes in studying their evolution. Lab Alumnus Steven Ahrendt won a poster award on his work on Cryptomycota fungi and also gave a talk. > #fungal17 nuff said @hyphaltip @zygolife  pic.twitter.com/U78xgoXz7y — Jessie (@JessieUehling) March 17, 2017Also got some good news that our paper on structural analyses of a rhodopsin-like protein in the chytrid fungi has been accepted at PeerJ after some helpful revisions - (see the preprint).Onward!

Quick post to sum up some of the news from 2016 and head into 2017. - Six manuscripts were published and an additional two were accepted and three more were submitted or being revised in 2016 Three graduate students survived another year in the lab: Sawyer, Nat, Derreck Joined by one Microbiology graduate student Jesus Pena joined in Fall 2016. Nine undergraduates worked in the lab Deane, Josh, Jericho, Dillon, Na, Justin, Serena, Leandra, George and Travis has been part of bioinformatics projects One postdoc, Jinfeng has been the bioinformatics and genomics guru from genome assembly to transposon bioinformatics One new assembly of a Citrus genome At least 15 new genomes from our work with Zygolife and 1000 Fungal Genomes project were released or material processed. More than 100 cultures of some fungi are being examined in the lab. One NSF grant started on systematics of anaerobic chytrid fungi and one new grant awarded as part of the UC MRPI http://ucop.edu/research-initiatives/programs/mrpi/2017-Awards.html program on the “UC Valley Fever Research Initiative” lead by UCSF and including several other UC campus. Jason is on sabbatical in 2017 at Oregon State University.

Some us from the lab took a trip up to Berkeley, CA for the MSA 2016 meeting.

On August 4th, 2016, Nat, Derreck, Sawyer, and Jericho went to Joshua Tree National Park to collect more Biological Soil Crusts samples. They were lucky to find some Lichen crusts which we could not find in our last sampling trip. Here are some pictures of our sampling team.[caption id=”attachment_1525” align=”aligncenter” width=”604”] Stajich lab sampling team: Derreck, Nat, Sawyer, and Jericho[/caption][caption id=”attachment_1526” align=”aligncenter” width=”900”] Our first collection of Lichen crust from Joshua Tree National Park[/caption][caption id=”attachment_1527” align=”aligncenter” width=”604”] Derreck measured crust surface temperature, while Jericho was getting ready for sampling[/caption]

We celebrated a few events in April and May. - A new NSF grant was funded and started in April on rumen fungi ”Phylogenomics and evolutionary history of the anaerobic fungal group, Neocallimastigomycota”. This is a collaboration with Noha Youssef and Mostafa Elshahed at Oklahoma State University and will give the opportunity to work on systematics of these anaerobic gut fungi. Raúl Castanera who came to the lab for a short stay last year, authored a paper that was accepted this week on transposable elements in the Pleurotus (oyster mushroom) genome and comparisons in proliferation rates and impact on gene expression. Castanera R et al. PLoS Gen doi: 10.1371/journal.pgen.1006108 We just started to get our first microbial diversity (16S and ITS) results for rock and soil communities from California desert environments and Antarctica as part of project by visiting student Claudia Coleine and Nat Pombubpa. Claudia is a PhD student with Laura Selbmann of Tuscia University and visited for nine months, but we processed isolates the lab collected from Antartica expeditions. We are also sequencing genomes of a handful of cultured fungal species from Antarctic locations and the first assemblies look pretty good (200-400 contigs for these 25-40Mb genomes) for a MiSeq only assembly. Nat is collecting samples from Joshua Tree National Park and in collaboration with other desert crust researchers Paul De Ley and Nicole Pietrasiak examining fungal and bacterial distribution.

Jason was at the European Conference on Fungal Genetics in Paris this April and had a chance to deliver a lecture. It was a great meeting of science and there was a lot of social media coverage by participants.Jason and Ousmane also attended the 1st conference on multicellular development in fungi where Ousmane presented his work on the Neolecta genome and comparative biology of the Taphrinomycotina fungi.[caption id=”attachment_1490” align=”alignright” width=”604”] An ascus of Neurospora biologists…[/caption][caption id=”attachment_1489” align=”aligncenter” width=”590”] It was a bit imposing to be on stage with bright colored backdrop[/caption][caption id=”attachment_1488” align=”aligncenter” width=”590”] I showed some colorful trees[/caption][caption id=”attachment_1487” align=”aligncenter” width=”604”] Little Jason and big slides[/caption] [caption id=”attachment_1486” align=”aligncenter” width=”604”] Mural at a school with a mushroom little red riding hood and mushrooms in the forest[/caption]

We started some explorations on fungi in desert crusts this week with a project in Joshua Tree National Park. Nuttapom received a Robert Lee Graduate Student research grant to explore impacts of visitor disturbance on biodiversity of desert crusts in JTNP.  Nat with the help of Claudia, Derreck, and Prof Mike Allen did a first exploration of a few sites.  We are happy to see some rain falling this week so there should be some changes to the crusts in some subsequent visits this week and weekend and coinciding with a workshop on desert crusts in the park this weekend. Here’s a few pictures of the team out in the field last week.[caption id=”attachment_1475” align=”aligncenter” width=”863”] Mike and Derreck ahead in Hidden Valley[/caption][caption id=”attachment_1477” align=”aligncenter” width=”604”] Nat, getting his first taste of sampling in the desert.[/caption][caption id=”attachment_1473” align=”aligncenter” width=”604”] Dereck and Claudia helping to look for crusts. Claudia is researching sandstone associated fungi from a variety of habitats.[/caption][caption id=”attachment_1474” align=”aligncenter” width=”604”] Cyanobacteria dominated crust[/caption][caption id=”attachment_1476” align=”aligncenter” width=”778”] Moss & crusts[/caption]

We said bye to Marco Marconi, visiting student from the Wilkinson Lab in Madrid, in December. He worked on some data mining from the 1KFG project and brought some new R tools for looking for enrichment across the CAZY, Interpro, and Pfam differences in species. - We welcome Plant Pathology graduate student Derreck Carter-House to the lab in January - after spending time working on molecular biology projects in plants and plant-microbe interactions in another lab.  Jason went across to England to serve on Ensembl Genomes  SAB and give seminar at University of Exeter - he came back with more appreciation for sunny California winters.

The past few months have passed quickly but wanted to share a few updates.Jason presented at the EMBO Eukaryotes meeting in Spain, Mexican Mycology Congress, Univ of Arizona, attended the Kavli Frontiers meeting, co-organized the Southern California Eukaryotic Pathogens meeting held again at UCR and taught graduate course on Programming and Data analyses.The past few months we hosted Yinka Odebode from University of Lagos from August to November. He was supported by the West African Research Association. Yinka learned about ITS sequencing of fungi to identify his isolates in his work in Africa. He also explored properties of dust associated fungi in Nigeria before he returned home in November. We also welcomed Marco Marconi from Madrid for a few months and is working on comparative genomics of fungi using the 1KFG datasets.Starting in  September we welcomed new graduate student in Plant Pathology, Nuttapon Pombubpa (right). Here he is (right) enjoying lunch along with visiting student Claudia Coleine and graduate student Sawyer.We gathered to say goodbye to project scientist Peng Liu who returned to China in December. Here she is with postdoc Jinfeng and visiting student Zhinquan.<images/wp_upload/2015/12/lablunch2.jpg> Undergraduates Dillon and Jericho joined us for lunch as well. They have both worked closely with Peng this Summer and Fall.Most of the lab together for a farewell lunch for Peng including Deane on the far right.

A quick note to say congrats and good luck to postdocs and students who finished up the summer.Graduate student Steven Ahrendt who graduated from the GGB program and is now a postdoc at the JGI / UC Berkeley.Postdoc Ousmane Cissé finished his fellowship from the Swiss National Science Foundation and moved on to the NIH on a fellowship to work on Pneumocystis.Postdoc Rod Olarte moved to the University of Minnesota on a NSF postdoctoral fellowship.Undergraduates Dillon McDonald and Christina Uriarte also finished their summer projects in the HSI-STEM and MARCU programs. <images/wp_upload/2015/06/2015-06-03-14.17.11.jpg>

Congrats to Steven Ahrendt who successfully defended his PhD Dissertation this week. Graduation ceremony (and pictures) to follow next weekend before he moves on to his postdoc position at UC Berkeley/LBNL/JGI at the end of the month.<images/wp_upload/2015/06/2015-06-03-14.17.11.jpg>

We had a lab dumpling party at Yizhou’s house to celebrate his new job and my birthday, and a farewell to Edward Liaw. Fun evening for everyone to get together and eat homemade dumplings

Another great meeting of Fungal Genetics at Asilomar Conference center. Much exciting science, fungal genetics as a field is being driven by genomics and technology but there are nice cycles of experiments coming back to test and validate hypotheses generated from these data. A few pictures of the UCR group all together at dinner.

Members of the lab gathered for a Dim Sum outing in Rowland Heights on Monday’s MLK holiday.

The end of the quarter was a blur but I wanted to properly congratulate Yizhou Wang. Dr Wang successfully defended his PhD in December and submitted his dissertation “Discovery and Properties of Small RNAs from Meiotic Silencing by Unpaired DNA in Neurospora crassa”  in the Plant Biology graduate program. He is our newest graduate from the lab and we couldn’t be happier and proud for him. He was able to complete a concentration MS in Statistics at the same time and was able to master bioinformatics and data analysis of next generation sequencing and comparative genomics along with small RNA Northerns, Southern Blots, and Neurospora culturing and care. He has been a great asset to the lab and I am delighted that he has finished this part of his education and training and excited for his next steps.He is serious about his cooking, treating us to some great meals from BBQ to a Chinese seafood extravaganza.

Rod, Ousmane, Nichole, Jinfeng, Jason and family went on a short hike to Big Falls in Forest Falls. A few pictures of the fun.

A new NSF funded project on Zygomycete fungi was recently funded. The press release from UCR and NSF provide some more information on the scope of the project and the goals of the new Genealogy of Life initiative at the NSF.We’ll be sharing news, data and protocols, and progress on the project website ZyGoLife.org and @zygolife  and looking to recruit one graduate student and some undergraduates to work on the projects in our lab focused on genomics and phylogenomic studies of these diverse lineages.

I had the great opportunity to attend the International Mycological Congress 10 in Bangkok, Thailand during this summer. It was filled with talks from mycologists studying cell biology, genetics, evolution, symbioses, ecology, production of secondary metabolites, and many other aspects of mycology from across the world. It was a great chance to hear about new work in many different experimental systems.  I chaired a session on Population Genomics and GWAS in Fungi and got to hear some great perspectives and approaches on model and non-model systems. I presented my talk on data analysis tools in metagenomics. I got to catch up with many friends/collaborators/colleagues and meet some new folks.I’m jealous of the folks who got to take some of the post-conference excursions through Thailand or ventured even further to Laos and Cambodia. Hopefully next trip to this area I’ll have the chance to explore more.

Congrats to Divya and Jason as our paper with collaborators Hugo Melida and Vincent Bulone: 

Steven and Jason attended the Mycological Society of America’s 2014 conference in East Lansing, MI. This included  coming in a day early enough for some of us to go on the foray on Sunday after we attended the Microbiology of the Built Environment conference in Boulder, CO.MSA2104 was a great chance to catch up with friends and colleagues and hear some excellent talks on the current state of research in the fields of systematics & taxonomy; ecology & pathology; genetics & molecular biology. Genomics pervades a lot of the research where it was not quite part of the picture when I first started attending so it was great to see how many people taking advantage of the amazing resources produced by the JGI sequencing programs.  I also really enjoyed the Karling lecture from Bruce McDonald on domestication in fungi and plants and the “dark side” of this domestication (meaning mostly that there are unintended consequences).There was some tweeting going on at the meeting - I tried to capture some with a storify available here.Jason presented research on the evolution of the fungal cell wall examining early diverging lineages of fungi which is the work of former graduate student Divya Sain.Steven presented his poster on the inhibitory properties of a Chytridiomycota fungus we work on that affects growth of some filamentous fungi and won the award for best graduate student poster!Jason was also honored with the 2014 Alexopoulos Prize to honor a young Mycologist. The prize is in memory of C. J. Alexopoulos who among other things authored the great Introductory Mycology textbook. I have not yet decided how I will spend the prize money but I intend to support a project in the lab or to support travel for collecting more strains tied to chytrid work.A photo of Steven and Jason at the banquet. 

We published a paper on the manual curation of the literature for the Cryptococcus complex of species (C. neoformans _var neoformans_, C. neoformans var grubii, and  C. gattii) this includes associated gene names with systematic locus names, something that was not easy to lookup without reading the published literature. In all more than 600 loci had gene names associated with them and include updated Gene Ontology associations, gene product names and descriptions and a table of orthology relationships between the genes in the different species genomes.The early access to the paper is available was released at  Eukaryotic Cell in May and includes guidelines of how the community can go forward naming genes in these species. In addition we make available a table of these names available at FungiDB at this link. And future updates are being posted through GitHub so that community contributions can happen directly through edits to the file or through the comments section at FungiDB where comments can be added by any user indicating a gene name and these will be evaluated and curated by a Scientific Curator.This work was done my a lot of hard work from Diane Inglis and Marek Skrzypek who are scientific curators at (Stanford University)  under the direction of Gavin Sherlock and the gene names and descriptions are loaded and available in FungiDB through the work of Ed Liaw and Venky Moktali at UC Riverside. We were able to do this work through an NIH R03 grant and look forward to finishing the complete literature curation by the end of this year.

We congratulate Divya on defending her dissertation on “Discovery of fungal cell wall components using evolutionary and functional genomics”.  Her last revisions and formatting is taking place and she should be the first minted PhD from the Stajich lab before Christmas.  We are happy and proud of her accomplishment to complete this important milestone!   

We are happy to welcome Dr Ousmane Cisse to the lab to work on evolution of multicellularity in Fungi. He will primarily focus on comparative genomics and evolution of filamentous fungal growth in the fungal kingdom, examining the genome of Neolecta and taking advantage of data from the 1000 fungal genomes project and other data sets. He joins us after completing his PhD at the University of Lausanne in Switzerland. He focused on comparative genomics of several Taphrinamycotina fungi and will continue this theme working on Neolecta. He was awarded a prestigious early postdoc mobility fellowship from the Swiss National Science Foundation Fellowship.

We’re excited that several manuscripts were published in the last month.One presents the first genome from the Cryptomycota, Rozella allomycis, in a manuscript published in Current Biology along with a nice companion piece from Mark van der Giezen about the work. Steven and Divya participating in this project in collaboration with Tim James at Michigan and Nico Corradi in Montreal. Some of the scripts used for this project are available as well here on github and other associated genome data are available here. We are working to get this into the next FungiDB release as well.A manuscript from Andrii Gryganskyi who was a lab visitor last summer was published on the Entomopthorales fungus Entomophthora muscae._A review on the application of genomics to mycology was published in Mycologia celebrating the new era of mycology and the first genome sequences published in this journal.Work from Anastasia Gioti, who was a lab visitor for several months this year and has visited several times in the past years, wrapped up genome comparisons of _Neurospora species which have transitioning from outcrossing (heterothallic) to self-fertile (homothallic) lifestyles. Our manuscript was made available in Evolution this summer and will be published in the Fall.A paper on the population genomics of amphibian killing chytrid fungus B. dendrobatidis that culminated several years of work and large collection of researchers was published in PNAS at the beginning of the summer.

Today was the presentations from UCR RISE summer program and undergraduate student Na Jeong showed her work on studying the inhibitory properties of the H. polyrhiza species of chytrid on several Ascomycete fungi. She was mentored by Steven Ahrendt in the lab who first made this observation. Here is Na presenting her work and with Jason and Steven.

We headed over to Lake Perris for a lab BBQ and fun afternoon in the sun.  Here’s a few pictures of the group all together.

Congrats to the lab for a great Fungal Genetics meeting. Everyone was participating in the meeting, presenting their work, and hearing about the new things coming out in other research laboratories. Was exhausting pace with 8AM to 10 PM (or later) every day but I think the fun and science excitement overshadowed the tiredness.  Congratulations to Steven who won a poster prize and to Jason for his election to the Fungal Genetics Policy Committee.  FungiDB was demoed in a workshop and poster sessions and we seemed to get a lot of interest and feedback along with the excellent presentation by Omar Harb from the EuPathDB team to lead the workshop.We will post some pictures and upload our poster PDFs in the coming weeks I expect, still catching up on sleep and reengaging in our research after that.Thanks to all who came by to talk with us at our posters and it was great fun to make new friends and reconnected with long-time ones.

We had a little celebration to recognize Steven passing his qualifying exam this week.

Wordle/Tagxedo graphs from Pubmed2Wordle on all papers published from the lab And here is the abstract wordle for the 2012 papers  

We welcome back Anastasia Gioti to the lab visiting from Sweden by way of Greece. She has been to the lab for a a couple of two-month visits over the past three years working on genomics of Neurospora mating systems. Now she has returned this month as a visiting scholar to stay through the winter to continue our collaboration on evolution of mating systems, focusing on the genomic consequences of transitions in homothallic and heterothallic fungi. She gets to have a nice SoCal instead of a Swedish winter.

Talks from the Sloan Foundation sponsored session at Lake Arrowhead meeting on Microbiology of the Built Environment are now posted on Microbe.net (which was jokingly pronounced as micro-beignet by some) including my talk on fungi in the Built environment.  Go take a look if you want to see an overview of some of the ways researchers are studying microbes in the built environment.  The Microbe.net team also recorded an interview with me about our work on the MicroBE data coordinating center and work to make identifying fungi from metagenomic sequencing easier.

Andrii has returned to Durham after a short stint in the lab to pick up some new skills and teach us more about culturing and major questions in Entomophthorales fungi.  He did a nice writeup on his establishment of a copepod colony which we will use for our future attempt to get Coelomomyces colonies in the lab.He has posted his farewell talk that spans a few of the projects he has been working on his website too -take a look here.

Check out a video of Jason answering questions about our project to build a database supporting identification of Fungi in the Microbiome of the Built Environment supported by the Sloan Foundation.

Welcome to Edward Liaw who will start working on FungiDB for the genome.  Edward joins us after finishing a MS in Bioinformatics at UC Santa Cruz.Also a welcome to Greg Gu who is joining us after working as a specialist in Plant Pathology. Greg is transitioning to bioinformatics to work on fungal identification from environmental sequencing using bioinformatics approaches and will support our work to build a database for ITS sequences as part of the Sloan project’s Microbiome of the Built Environment.

Congratulations to Divya who was awarded the Guru Gobind Singh Fellowship for 2012-13! This fellowship is awarded to one graduate student in the UC system who is a student of an Indian or Pakistani university and committed to returning to her country of origin after receiving her doctoral degree at a UC campus. This is a great honor and we’re all proud of Divya for applying for and receiving the award.  An article in UCR Today describes her work and the award.

A warm Southern California welcome to Andrii Gryganskyi who is here visiting the lab for several months to work on genomics of Entomophthorales fungi and some other insect-associated fungi from the basal linages.  We’re excited to learn from his expertise in phylogenetics and culturing of these strains in the lab. We are helping to assemble and annotate several genomes in progress he has worked on as postdoc at Duke University to better understand relationships and genomic changes that have occurred some of the basal fungal lineages.

Congratulations to PhD candidate Divya Sain, who just learned she will be awarded a Guru Gobind Singh Fellowship for 2012-2013.  In 1988 the University of California established an endowment to support graduate fellowships (named for Guru Gobind Singh, the Sikh religious leader) to be awarded to graduates of universities in a specific area of India and Pakistan for the purpose of pursuing graduate study at the University of California.Way to go Divya!

[Update 8/2012 - this position has been filled]Position DescriptionAn NSF funded postdoctoral position is available in the laboratories of Dr Susan Wessler and Dr Jason Stajich to study the impact of a very recent burst in copy number of a transposable element in rice. This work will involve analysis of high throughput genomic sequencing using Illumina/Solexa technology to examine the genomes of hundreds of recombinant inbred lines of rice. This position requires excellent bioinformatics and programming skills to analyze and synthesize genome assemblies, identify polymorphisms, and perform quantitative trait mapping. Background information on the biology underlying the project can be found in: K. Naito et al, Nature 2009 461: 131; K. Naito et al, PNAS 2006 103: 17620; N. Jiang et al, Nature 2003 421: 163.The successful candidate will be expected to contribute and lead data analysis for the project. Applications will be accepted until the position is filled and review will begin on July 15, 2012.  Salary and benefits are commensurate with NSF guidelines and the University of California Postdoctoral Union agreement. Special consideration will be given to candidates with exceptional bioinformatics and genome evolution experience.QualificationsMinimum qualifications include a Ph.D. in Biological Sciences, Computer Science, Statistics, or a related field. Demonstrated experience in bioinformatics and high proficiency in programming is necessary along with an understanding of the mechanisms and methods of studying population biology. Experience with next generation sequence data is highly desirable. Ability to communicate clearly, work independently, and interact collaboratively is essential.The researcher will also work closely with co-PIs and collaborators at the Donald Danforth Center, Cornell University, and USDA ARS Dale Bumpers National Rice Research Center.To ApplyContact Jason Stajich (jason.stajich@ucr.edu) or Susan Wessler (susan.wessler@ucr.edu) with a current CV and names of three references.More information can be found online about the Stajich lab http://lab.stajich.org, Wessler lab http://wesslerlab.ucr.edu, and the research project http://dynamiterice.org and UC Riverside http://www.ucr.edu.Information about UCRIn the Heart of Inland Southern California, UC Riverside is located on nearly 1,200 acres near Box Springs Mountain in Southern California, the park-like campus provides convenient access to the vibrant and growing Inland region. The campus is a living laboratory for the exploration of issues critical to growing communities — air, water, energy, transportation, politics, the arts, history and culture. UCR gives every student the resources to explore, engage, imagine and excel.UCR is ranked 43rd among top public universities (US News and World Report 2010).At UC Riverside we celebrate diversity and are proud of our #5 ranking among the nation’s for most diverse universities (US News and World Report 2010). Become part of a place that fosters success for all its constituents, students, faculty, and staff, and where work/life balance and campus culture are integral to our way of life.UCR is an affirmative action and equal opportunity employer with a commitment to workforce diversity.  AA/EOE 

A wonderful symposium reunion of alumni and current Duke and the RTP area Mycology and pathogenesis labs is being held April 5 & 6 at Duke University. The talks have so far been an interesting collection of model pathogen systems, drug development, and host-pathogen interactions. Tomorrow myself,  Tim James, and others will hit the evolutionary biology of fungi a bit focusing on chytrid pathogens.  Feeling a lot of pride in the training program here at Duke and some nostalgia for days past when many of us were together in the same institution. The gathering is also a celebration of great mentoring and so it is great to see so many of those who taught and mentored us here - in particular Joe Heitman was also awarded a mentoring honor by Duke for his leadership and mentoring.

Several postdocs have joined the group in the last few months, though I’ve been remiss to make an announcement.Dr Sofia Robb, who completed her PhD at the University of Utah, joined the lab in August 2011 and has been working on the NSF funded Rice transposable element project in collaboration with Susan Wessler’s lab. She has already developed a new tool for identification of TEs from high throughput sequencing which we are employing on several varieties of rice and expanding it to be a more general purpose tool. Sofia is also co-developing teaching modules for the Dynamic Genomes course.Dr Brad Cavinder, who completed his PhD at Michigan State University, joined the lab in January 2012 and is working on transposable elements in mosquitoes as part of the WM Keck funded project to identify and utilize active TEs as molecular tools in mosquitoes.A third new member of the lab, Peng Liu who completed her PhD at the Chinese Academy of Sciences, will start in February to work on molecular characterization of some pathogenesis factors in the amphibian pathogen Batrachochytrium dendrobatidis.

Congrats to graduate student Yizhou Wang who passed his qualifying exam today. We’re proud to have him through this hurdle and to continue working on his research into genome defense and silencing of transposable elements in Neurospora crassa.[caption id=”attachment_701” align=”aligncenter” width=”300” caption=”Jason and Yizhou at Asilomar 2011”][/caption]

Our community sequencing project at the JGI was awarded which will allow a consortium of researchers to sequence 1000 fungal genomes through the DOE’s Joint Genome Institute. The intention is to sample two species from every major lineage of Fungi.Some press releases on the project below and we will coordinate it through several websites including a forum for discussion about potential species beyond the target list.- International Team to Sequence Genomes of Fungi International team to sequence genomes of fungi Forest Service Part of Team Sequencing 1,000 Fungal Genomes

We’ve started doing Perl training on Wednesdays for any IIGB and UCR students and postdocs (or curious faculty). This is starting at beginning with command line usage and will hopefully build to advanced bioinformatics. Sofia and Steven are leading these currently and hope it will be a good jumpstart to improving programming skills of our lab and others. Join the mailing list if you want to get updates on the meeting times and locations and will also try and post useful slide sets and problems here as well.

We wished postdoc John Abramyan a farewell and happy trails last week.  He was the first postdoc to join the lab and completed a projects relating to Bd, chytrid cell wall genes, and some a gene regulation bioinformatics project. He also was main force in getting the experimental portion of our lab started when the group was established.  John is moving on to work on vertebrate evolutionary questions at the University of British Columbia in Vancouver, BC, CANADA. We’ll miss having him in the lab and wish him much luck in his next adventure. [caption id=”attachment_612” align=”aligncenter” width=”779” caption=”John (Left) enjoyed a farewell dinner with the lab”][/caption]

This week the summer student programs ended and Carlos Rojas, Ramy Wissa and Lorena Rivera all gave presentations and posters on their work.  We really enjoyed having them around for the summer and look forward to their possible continuation in the Fall.Carlos worked with postdoc John Abramyan on the CBM18 gene family in _Bd_to confirm gene expression of the members of the family by RT-PCR before we choose a subset to work on further.[caption id=”attachment_638” align=”aligncenter” width=”614” caption=”Carlos Rojas explaining his poster on CBM18”][/caption]Lorena and Ramy worked with graduate student Divya Sain on a screen of _Neurospora_strains with candidate cell wall genes knocked out.  They completed a screen of 115 mutants x 3 replicates = a lot of petri dishes for their first time in the laboratory. Below is a picture of Ramy and Lorena with their peers from the MARCU program.[caption id=”attachment_643” align=”aligncenter” width=”1024” caption=”The 2011 MARCU* students gather before their presentations”][/caption]

Welcome to two new programmers to the team working on FungiDB.Daniel Borcherding and Ragu Ramamurthy join us to work full time on the FungiDB project to support genomic data integration, website improvements, and supporting the system move from beta into production mode.  We look forward to new improvements in the system and establishing a release cycle for the website and DB.

Sofia Robb joined the lab this week to begin work as a postdoc scholar on genomics and bioinformatics aspects of studying transposable elements in Rice. She will also participate in developing teaching modules for the Dynamic Genomes course in collaboration with the Wessler lab.  Sofia recently completed her PhD from the University of Utah working on planaria in the Sanchez lab.

Edgar Medina has been visiting the lab for the last few months from the Universidad de los Andes, Bogotá, Colombia to work on Batrachochytrium genome evolution.  This past Friday he completed his Master’s degree, defending his thesis via Skype.  Was quite fun to see him adeptly switched between Spanish and English in the Q&A period while showing his slides that were remotely projected onto the screen back in Bogotá. It was a real pleasure to have him here for the few months and look forward to a chance to keep interacting on many of our projects.  Way to go Edgar!

[This position filled as of Aug 2011]A programmer position is available in the lab to work on FungiDB. The duties include performing data loading into relational database system, development and improvement of scripts for data importing & downloading, and website development. This project is part of a collaborative project with members of the EuPathDB team.More information and online application to the position is available at the UCR job listing.

A warm welcome to graduate student Steven Ahrendt to lab. Steven is working on questions relating structural evolution of light sensing proteins in fungi, metagenomics, and bioinformatics. He will be co-advised by Assistant Professor Chia-en Angelina Chang.

I can safely say everyone had a good time at Fungal Genetics at the Asilomar Conference Grounds earlier this month. So much fun it too us a week to catch up on sleep and dig out from work left undone. Here are a few pictures from poster presentations. We didn’t get everyone’s picture captured in the chaotic swirl of the poster session unfortunately. I’m really proud of how well everyone did and the apparent interest in our projects.I also launched our fungidb.org database website at the meeting and got chance to tell more people about our ambitions and hopes for it. It was also a real treat to see longtime friends and mentors and have the chance to swap stories.

Snow on the mountains while the temps are in the 70s here. A wet winter means there are lush hillsides…for now, until the dry season starts in another month.

 We will be working on discovery of active transposable element discovery in three mosquitos thanks to a grant that began this year from the W. M. Keck Foundation.  We will be using Illumina based resequencing of populations of mosquitos, RNA-Seq to study expression of genes and TEs to determine differences between active and silenced elements, bioinformatics to identify and characterize transposable elements in the genomes of 3 mosquitos, and experimentally test for activity of the transposases that are thought to match the target TEs.  The grant is highlighted in a campus press release and will be a collaboration between our lab and the labs of Dr Susan Wessler, and Dr Peter Atkinson. Should be a fun exploration and will help inform other TE work in the laboratory as well.

Postdoctoral Research in Bioinformatics and Transposon Biology in RiceUniversity of California, Riverside[Position filled as of 6/2011]Position DescriptionAn NSF funded postdoctoral position is available in the laboratories of Dr Susan Wessler and Dr Jason Stajich to study the evolutionary dynamics of transposable elements in the rice genome and their contribution to phenotypic variation. This postdoctoral scientist will be involved in research using bioinformatics, next generation sequencing of multiple rice strains, and RNA-Seq based transcriptional profiling. This position requires excellent bioinformatics and programming skills to analyze and synthesize genome assemblies from next generation sequencing data produced by Illumina/Solexa technology. Background information on the biology underlying the project can be found in: K. Naito et al, Nature 2009 461: 131; K. Naito et al, PNAS 2006 103: 17620; N. Jiang et al, Nature 2003 421: 163.The successful candidate will be expected to contribute and lead data analysis for the project. There will be opportunities for molecular biology, if desired, as part of validation of analyses. In addition, data and software from this project will be used to develop teaching materials as part of the HHMI funded Dynamic Genomes course at UC Riverside providing an opportunity to participate in teaching in an innovative topic-focused course for undergraduates. Applications will be accepted until the position is filled and review will begin on February 15, 2011.  Salary and benefits are commensurate with NIH guidelines and the University of California Postdoctoral Union agreement. Special consideration will be given to candidates with exceptional bioinformatics and genome evolution experience.QualificationsMinimum qualifications include a Ph.D. in Biological Sciences, Computer Science, Statistics, or a related field. Demonstrated experience in bioinformatics and high proficiency in programming is necessary along with an understanding of the mechanisms underlying genome evolution. Experience with next generation sequence data is highly desirable. Ability to communicate clearly, work independently, and interact collaboratively is essential.The researcher will also work closely with co-PIs and collaborators at the Boyce-Thompson Institute and Cornell University.To ApplyContact Jason Stajich (jason.stajich@ucr.edu) or Susan Wessler (susan.wessler@ucr.edu) with a current CV and names of three references.More information can be found online about the Stajich lab http://lab.stajich.org Wessler lab http://wesslerlab.ucr.edu and UC Riverside http://www.ucr.edu.Information about UCRIn the Heart of Inland Southern California, UC Riverside is located on nearly 1,200 acres near Box Springs Mountain in Southern California, the park-like campus provides convenient access to the vibrant and growing Inland region. The campus is a living laboratory for the exploration of issues critical to growing communities — air, water, energy, transportation, politics, the arts, history and culture. UCR gives every student the resources to explore, engage, imagine and excel.UCR is ranked 43rd among top public universities (US News and World Report 2010).At UC Riverside we celebrate diversity and are proud of our #5 ranking among the nation’s for most diverse universities (US News and World Report 2010). Become part of a place that fosters success for all its constituents, students, faculty, and staff, and where work/life balance and campus culture are integral to our way of life.UCR is an affirmative action and equal opportunity employer with a commitment to workforce diversity.  **AA/EOE ** 

[Update May 5, 2011 – This position is on hold to focus on hiring a programmer to work on data development and loading]There is an open position in the lab to support development of FungiDB, a database for fungal genome data integration.## Postdoctoral fellow supporting fungal genome database development Position DescriptionA postdoc position is available in the laboratory of Dr. Jason Stajich to support the development of FungiDB, a database for fungal genomic and functional data.   Strong candidates will be proficient in the Perl programming language; modern biology in general and bioinformatics in particular; show a demonstrated ability to quickly pick up new biology and computer science concepts; be comfortable using relational databases; and possess core Unix skills to do these tasks efficiently.  Experience using Perl for genome sequence data processing a plus.You’ll also have a relentless attention to detail, the ability to work independently on challenging problems with no direct easy solution.  You will use these skills to help organize, analyze, and display a vast amount of disparate biological data and interact with the fungal community. There will be opportunities for self-directed research utilizing this collection of genomics and comparative database and tools.Application evaluation will begin Feb 1, 2011 until the position is filled. Salary and benefits will be commensurate with experience and University of California Postdoctoral Union agreement.QualificationsMinimum qualifications include a Ph.D. in Biological Sciences, Computer Science, Statistics, or a related field. Demonstrated experience in bioinformatics and high proficiency in Perl programming is required.  Demonstrated experience in web or bioinformatics software development is a plus. The ability to work with a small, distributed team is essential including exceptional written and verbal communication skills.To ApplyContact Jason Stajich jason.stajich@ucr.edu with a CV and the names of three references letter writers.Information available on UC Riverside and the Stajich lab.Information about UCRIn the Heart of Inland Southern California, UC Riverside is located on nearly 1,200 acres near Box Springs Mountain in Southern California, the park-like campus provides convenient access to the vibrant and growing Inland region. The campus is a living laboratory for the exploration of issues critical to growing communities — air, water, energy, transportation, politics, the arts, history and culture. UCR gives every student the resources to explore, engage, imagine and excel.At UC Riverside we celebrate diversity and are proud of our #5 ranking among the nation’s for most diverse universities (US News and World Report 2010). Become part of a place that fosters success for all its constituents, students, faculty, and staff, and where work/life balance and campus culture are integral to our way of life.UCR is ranked 43rd among top public universities (US News and World Report 2010).UCR is an affirmative action and equal opportunity employer with a commitment to workforce diversity.AA/EOE

Here’s our 2010 publications Wordle made with pubmed2wordle.

UCR undergraduate Jessica De Anda has been working in the lab this summer and Fall will be starting in the MARC U* STAR program at UCR.  This program provides mentoring to students interested in pursuing a graduate degree in science and supports laboratory research during the school year and the summers. We’re excited she was selected to be part of this program and look forward to her continued work in the lab on aspects of transposon dynamics and evolution in fungi.

Some pictures from a recent lab lunch to help celebrate Divya passing her qualifying exam.

A few papers from our work are now appearing. This includes several collaborative papers that have been in progress for several years, so I’m happy to see them published.- See the latest issue of PLoS Genetics for our work on analysis of the transcriptome during meiosis in _C. cinerea _in collaboration with several labs at UNC-CH, Indiana University, and SEMO. A chapter on bioinformatics protocols for using the Gbrowse_synteny tools The final version of our paper from a collaboration with Kristina Smith and Mike Freitag, Deb Bell-Pedersen, and Michael Brunner labs on ChIP-Seq and profiling of the White Collar Complex in Neurospora to identify the network of genes regulated by light.

Congrats to grad student Divya Sain, who passed her prelim qualifying exam in September and is now a PhD candidate as she begins her 3rd year at UCR in the GGB program.

We had a productive period over the last year and finally saw set of papers representing this work come out in the last month. This represents great collaborations with several different groups.  In addition to the Coprinus genome, we were involved in the publication of two other genome sequences thus summer. One a basidiomycete mushroom and one for an oomycete and pathogen of plants, both with a host of collaborating labs. Two papers on Neurospora also appeared as part of collaborations with Hanna Johannesson’s group and Michael Freitag, Michael Brunner, and Deb Bell-Pedersen.  A fifth paper on Coprinopsis meiotic genes is in press but will post about it when it appears.- Transcription factors in light and circadian clock signaling networks revealed by genome-wide mapping of direct targets for Neurospora WHITE COLLAR COMPLEX. Smith KM, Sancar G, Dekhang R, Sullivan CM, Li S, Tag AG, Sancar C, Bredeweg EL, Priest HD, McCormick RF, Thomas TL, Carrington JC, Stajich JE, Bell-Pedersen D, Brunner M, Freitag M. Eukaryot Cell. 2010 Jul 30. Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Lévesque CA, Brouwer H, Cano L, Hamilton JP, Holt C, Huitema E, Raffaele S, Robideau GP, Thines M, Win J, Zerillo MM, Beakes GW, Boore JL, Busam D, Dumas B, Ferriera S, Fuerstenberg SI, Gachon CM, Gaulin E, Govers F, Grenville-Briggs L, Horner N, Hostetler J, Jiang RH, Johnson J, Krajaejun T, Lin H, Meijer HJ, Moore B, Morris P, Phuntmart V, Puiu D, Shetty J, Stajich JE, Tripathy S, Wawra S, van West P, Whitty BR, Coutinho PM, Henrissat B, Martin F, Thomas PD, Tyler BM, De Vries RP, Kamoun S, Yandell M, Tisserat N, Buell CR. Genome Biol. 2010;11(7):R73. Epub 2010 Jul 13. Genome sequence of the model mushroom Schizophyllum commune. Ohm RA, de Jong JF, Lugones LG, Aerts A, Kothe E, Stajich JE, de Vries RP, Record E, Levasseur A, Baker SE, Bartholomew KA, Coutinho PM, Erdmann S, Fowler TJ, Gathman AC, Lombard V, Henrissat B, Knabe N, Kües U, Lilly WW, Lindquist E, Lucas S, Magnuson JK, Piumi F, Raudaskoski M, Salamov A, Schmutz J, Schwarze FW, Vankuyk PA, Horton JS, Grigoriev IV, Wösten HA. Nat Biotechnol. 2010 Jul 11. Conflict between reproductive gene trees and species phylogeny among heterothallic and pseudohomothallic members of the filamentous ascomycete genus Neurospora. Strandberg R, Nygren K, Menkis A, James TY, Wik L, Stajich JE, Johannesson H. Fungal Genet Biol. 2010 Jul 1.

Our work on the mushroom genome of Coprinopsis cinerea is featured on the cover of this week’s PNAS.  Check out the blog post and the article.

We bid farewell last weekend to our lab visitor, Nastassa Gioti, who is headed back to Sweden after 6 fun weeks in Riverside.  We learned from her, and she got to dig into her genome datasets for Neurospora in the context of the comparative and genome annotation tools we have, so it was fun all around!This also marked the second get together (but the first where we remembered to bring a camera). Since we gathered at a local mexican restaurant with whimsical and amazing sculptures and art from recycled material, it was fitting we document it with pictures.

Spring is flying along. We’ve been presenting some of our work at conferences and getting ready for a full summer of meetings and Divya preparing for her qualifying exam.A few papers have come out or are now accepted. One I’ll highlight here is the publication of the Sordaria macrospora genome.  This was a fun collaboration with groups in Germany, France, Oregon State, and Edinburgh where we sequenced Sordaria with 454 and Illumina sequence and assembled the genome using de novo assembler and comparative scaffolding to the available Neurospora genomes.  Sordaria is an important model system for sexual development and provides a great evolutionary not-too-distant outgroup to the Neurospora clade for evolutionary genomic analyses we are trying to finish off.Also have had a chance to interact with colleagues at the JGI User meeting, the Neurospora conference, and a special treat of speaking at the PBoFF symposium at Texas A&M.Everyone is getting their projects underway in the lab and we’ve had two visitors come to work on Neurospora and Chytrid genome project analyses so a busy but exciting time for us.Several more weeks left in the quarter where I’m teaching introductory biology and  then the Gordon Conference, MSA, and IMC9 will be conferences to finish preparing for.  The lab will also be represented at Evolution meetings in Portland as John attending.

Congrats to graduate student Divya Sain a co-author on a paper published in Nature on mobile chromosomes in Fusarium, stemming from her work her work during a rotation in the Borkovich laboratory.The work highlights the important aspect of how pathogenicity factors can be exchanged via mobile chromosomes and can be an important pathway for adaptive evolution and acquisition of new function through whole chromosome exchange between strains.

I am back from a short trip to Ireland where I gave a seminar at National University of Ireland, Maynooth and spend some time with folks interested in evolution or fungi like David Fitzpatrick, James McInerney, Davide Pisani. I also learned about a new spinoff company from one of the faculty producing media that will help Bee immune systems. In my chats with some of the faculty I found out that I had lots in common with Sean Doyle on Aspergillus and some basidiomycete genomics questions and also much in common with Gary Jones working on prions in yeast.  After my trip to Maynooth, I spent a few days in Dublin afterwards to see the town which included a visit with some Dublin yeast researchers Ken Wolfe and Geraldine Butler who took me out to see Newgrange.I learned that there is an abundance of yeast research in Ireland.  In addition to the researchers there is a whole shop devoted to Yeast.And my visit to the Guinness Brewery at St. James Gate taught me that that Yeast is a national treasure in Ireland.Complete with an important safe for insuring there are backup strains. I have to assume there is a -80 freezer somewhere in the Guinness complex holding old strains as well.Did you know one of the master brewers at Guinness was also the inventor of the Student’s T-test? Here’s the proofSo it was great to visit and look forward to going back at least in 2012 when SMBE will be held in Dublin.

PLoS Pathogens has a short review format called Pearls.  We were invited to write a short summary on Batrachochytrium which was published in the January issue.Rosenblum, E., Voyles, J., Poorten, T., & Stajich, J. (2010). The Deadly Chytrid Fungus: A Story of an Emerging Pathogen PLoS Pathogens, 6 (1) DOI: 10.1371/journal.ppat.1000550

A quick January update.  Jason was appointed to a two year term as Councilor for Genetics/Molecular Biology for the Mycological Society of America, began a term on the editorial board of Eukaryotic Cell, and was also profiled in the GSA reporter. Finishing grants and working towards completing manuscripts from postdoc-land while we are computing results on from genome and RNA-Seq datasets. Working to getting our laboratory production up and running to generate more of our data.Currently the lab is four strong with 3 graduate students. They are Divya Sain and Yi (Zoe) Zhou who have joined for the long haul of doing a PhD in the GGB program, and Yizhou Wang, a rotation student from Plant Biology.  Divya is working on a project that uses bioinformatics and phylogenetics to reconstruct history of the genes involved in the fungal cell wall across the fungi.  Zoe is using bioinformatics and phylogenetics to focus on duplicated gene evolution and is exploring other aspects of duplication in fungal genomes.  Yizhou will be getting going in the laboratory learning how to grow Neurospora and preparing some RNA extractions for some transcriptomics and RT-PCR validation.In February John Abramyan will join us as a postdoctoral scholar to work on some molecular biology and genomics work on at least two fungi along with applying  bioinformatic analyses of these data.I also setup the Gbrowse2 for Sordaria and Coprinopsis, worked on some new template themes for the blogs, and we setup a bioinformatics group website at UCR (which is still coming together). Hoping the rest of Jan and Feb will be clearing a few more to do things off the list and getting a chance to do a bit more research blogging on the Hyphal Tip.

Although I’m not going to be at PAG this year, I’ll be in San Diego for  the BioPerl and part of the GMOD meeting on Wed and Thursday.

Well the 1st quarter is over and had a few observations about life of an assistant professor.1. Remember to check that you don’t need to turn in grades! I thought I could safely ignore emails about sending in grades, since I wasn’t teaching this quarter, but meant I forgot to turn in grades for grad students working in the lab. Whoops! Lesson learned. Spending money isn’t that hard, but researching how to spend it on equipment is time consuming.  The optimization of trying to find the best deal, planning for current and future experiments, and establishing new technologies took more time than I expected.  Planning how to best spend money longer term is also taking some time, I don’t know if there is any good formula to rely on because it depends on what future grant support is awarded. But I think that I am getting better at making the equipment decisions - but I am my own sysadmin for macs in the lab and also the new separate (from the shared bioinformatics cluster) linux machines I have for our web and specialized compute needs and find that very time consuming. Travel is good, but takes up time that can be spent writing, instructing, and my own research. While I can do much of my research from my laptop and an internet connect, I am distracted when away from lab and doing a disservice to the meeting I am attending if I am always working while on the road.  Better to divide my time better and focus on the meeting at hand. Course this means I should always have the talks finished before I get to the meeting and that has been difficult to guarantee. People are important. I can’t do all the research myself. Getting students and postdocs into the lab who can be trained on techniques and the background of the research questions is the most important thing to get the lab moving forward.  I am excited about the teaching and learning process but it is a process that needs a vision and schedule that I establish.  I’m still fine tuning that schedule and the approaches while keeping us aimed toward a vision of the kind of research we will do in the next 3-5 years. Time flies - take stock of how you spent it! Stopping and reflecting on what was accomplished is good to remind me and remind trainees that we have done things even if it feels like there is a mountain of work ahead.  As the gets better at this I’ll probably be able to give better feedback about dead-ends and keeping people on track earlier in the game.  We are still getting our timing together to have regular lab meetings and journal clubs that I expect to be the heart of the learning that happens in the lab at this point. I’m teaching programming, bioinformatics, phylogenetics & molecular evolution, and mycology at the outset and so am working to make these subjects more approachable with the right kind of background reading materials.  Probably will have to turn this into a review or primer someday as I feel like this synthesis of different fields is not something I can point anyone to just one or two resources for. I’m still getting aquatinted with who to ask for help and where to go for advice, but I’ve been lucky to have generous junior and senior colleagues who have provided encouragement and advice.  Here’s to hoping next quarter I learn a little more about how to do things, focus on the grant writing, and make some tangible progress on the research projects that need some new data before this summer. A lot of papers are queued up from collaborative work that were submitted this month and I hope that means more focus on the two main project foci of the lab.  New folks will be joining us next quarter and I’m excited about the progress we have made and will be able to make as everyone comes up to speed.Happy New Year!

  Chris Fields and I spoke about BioPerl past and present and tried to convince computer science types that biology is in fact interesting on TWiT.tv FLOSS. Check out the podcast for Episode 96.

A talk today in the CS department on open problems in bioinformatics and hope to entice some computer scientists to work on more of the problems here.

Back from an excellent meeting in St Feliu du Guixols for the EMBO Comparative Genomics of Eukaryotic Microorganisms. Not a strictly fungi focused meeting, but lots of genome comparisons of yeasts and molds were presented.  It will be held again in 2 years so mark your calendars as it is a great scientific exchange and a beautiful location.

Our primer on the Fungi is available (currently free) on the Current Biology website.  A version with extra refs inserted is available in pre-print format here. In this primer we provide a broad overview of the major evolutionary defined groups within Fungal kingdom. Our intention is make the kingdom a little less mysterious for non-mycologists and introduce some open areas of research that require integrating evolutionary, morphological, and molecular research. This was joint work with Mary Berbee, Meredith Blackwell, David Hibbett, Tim James, Joey Spatafora, & John Taylor.Also thanks to several people for access to images: Jeffrey Rollins, Sabine Huhndorf, David McLaughlin & lab,George L Barron, Greg Jedd and Michelle Momany.  

Making some signs for the doors to offices.  Here’s a Wordle plot from abstracts of last 7 years of papers. Tip the hat to M. Dunham for the idea to make it part of the lab signs.      

Well, the doors have been opened and things are moving into the new Genomics building. Since we are so new, no things to really move into the lab as they will come from vendors directly. I got into my new office with furniture installed and everything. We have ordered some of the big equipment for the lab and started getting supplies. Will be some adjustment as we all learn the new space for the labs on the same floor as we start sharing space, supplies, and also ideas and collaborations.  An exciting time and with any luck some fun and productive ways of doing science will emerge.

To the newly finished Genomics building on campus.  Our (well only me still ) move date in mid-September or when the office furniture is installed.

My presentation from BSA/MSA 2009 on early fungal evolution inferred from the chytrid genome is available here.  The conference was great for the time I could be there and the interaction with mycologists and botanists at the meeting seemed to be really helpful (I caught a few botany talks) and catching up with new and old friends is a great bonus at these meetings.

I will be at the Botany & Mycology conference (mainly to see the MSA members) and present a talk on Tuesday morning of the meeting. Hope to run into some old friends and meet new people at the meeting which will see Botanists and Mycologists mixing (oh my).  I get to stop by Univ of Utah a few days early and give a quick talk and visit with some friends at the Eccles institute at the U and maybe will get to see a few more Salt Lake City sites.

Went from CA to OR to ID, MT, and WY for work (Bioinformatics symposium at Oregon State) and a little vacation.

Saw this beauty while on our hike in Pt Reyes before the Miller Institute Annual Symposium

RT @NikonSmallWorld: 1 week to enter the competition! Submit yr best photomicrographs at http://www.nikonsmallworld.com #microscope #science # Save the Frogs day is April 29th http://savethefrogs.com/day/ #

Word on the street is we will be moving into the new Genomics building at the end of the summer.

RT @hyphaltip: Lichen named for Pres Obama by UCR herbarium curator Kerry Knudsen http://is.gd/sMwk #

git archiving code from my thesis http://github.com/hyphaltip/thesis/tree/master #

Adding some OrthoMCL processing scripts to github to convert FASTA processed genome-pair search results for proper input http://is.gd/qOoM #

Live blogging JGI User meeting where the talks range from application of sequencing to problems in biofuels, comparative genomics and evolution, and the discussion of new sequencing technologies.Here are some links from Day 1. We’ll probably have the rest of the days’ coverage in the Friend Feed Room.- Friend Feed Room Jonathan Eisen’s page with some aggregated links for coverage A few of the posts I wrote are on another site, Mike Mendez, Cameron Currie on Ant farming of fungi Joe Ecker on Arabidopsis quick wrap-up from day 1.

Setting up lab pages #

I will be at Asilomar for the Fungal Genetics 2009 meeting presenting some work on the transcriptional landscape in Neurospora and collaborative work on Coccidioides, Neurospora tetrasperma, and Coprinopsis cinerea.

The lab will open in July 2009 at UC Riverside and be housed in the new genomics building on campus.