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.
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.
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 .
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.
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.
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!
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.
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, a ascomycete black yeast, complemented some reference genome work we published last year . Former postdoc Ousmane Cissé published his work on Pneumocystis at the NIH in his current postdoc . 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 . 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 . 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 questions . Work exploring whether Transposable elements have a role in stage-specific gene expression in Coccidioides with Theo Kirkland and Anna Muszewska . 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 . 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 .
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. We also got to host the Zygofornia Zygolife team meeting. Here are some pictures I took from the desert and mountain visits.
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.
Crusts symbioses of algae and cyanobacteria with fungi, bacteria, and many uncounted single celled organisms.
Colorful 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.
We also visited one of Julia’s field sites where she is working on a lichen biodiversity inventory and some comparison of the genetic diversity of the fungi and algae symbiont along an elevation gradient in the park.
Derreck is excited to collect some dung samples that may recover some zygomycete isolates for the Zygolife project.
The rest of pictures from the day are in this flickr album.
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.