Category Archives: news

Congrats to Yan!

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.

Helping Yan celebrate his acceptance of offer at UTSC.

Spring papers news

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.

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).

Congrats Derreck on CCSTS fellowship

Derreck Carter-HouseCongrats 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.

Fall lab news

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.

ZyGoLife visitors

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.

Zygolife team photo, minus Jason, in the UC James Reserve, San Jacinto Mountains, California

Lost in a forest? Or finding fungi? in the James Reserve, San Jacinto Mountains

bees love the water near a wash that had a little bit of moisture in Mojave, in Granite Mountain Desert Research Center

Jessie and Derreck bonded over fungi and bacteria

Lichens and mosses on granite rocks in Granite Mountain Desert Research Center

Sunset over Kelso Dunes in Mojave National Preserve

Lizards in Mojave National Preserve

Blooms among Lava in Mojave National Preserve

Sweeny Granite Mountain Desert Research Center, a University of California, Natural Reserve.

Kelso Dunes, Mojave National Preserve

The Joshua Tree Album

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

StajichLab-1-5 StajichLab-1-6
StajichLab-1-11
StajichLab-1-10 StajichLab-1-16
StajichLab-1-22 StajichLab-1-29
IMG_0453 IMG_0837
StajichLab-1-3

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.
StajichLab-1-33

Derreck is excited to collect some dung samples that may recover some zygomycete isolates for the Zygolife project. StajichLab-1-31

The rest of pictures from the day are in this flickr album.

Welcome new graduate students Tania and Julia

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 Nat on passing qualifying exam

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.

Biological Crust
Cross section of crust. Image by N. Pietrasiak

 

Chytrid Opsin structure paper published

Great work by former graduate 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 Chia-en Chang in Chemistry Dept at UCR who helped mentor Steven on homology modeling and docking analyses. I also learned a lot through this project and was excited to be able to merge evolutionary and computational approaches. The project lead to the surprising findings of a gene important for light sensing that is shared among just the zoosporic (fungi with a flagellate life stage) and animals.

This project has been going for a while … Edgar and I discovered this protein in ~2008 when we started independently analyzing the Batrachochytrium genome, the first chytrid fungus sequenced. Based on sequence similarity we realized it looked like an animal rhodopsin, a 7 transmembrane G-protein coupled receptor (GPCR). These rhodopsins are called type II opsins and typically respond to green light.  We went looking for this in the first place because of work published in 1997 from Ken Foster’s lab which showed that zoosporic chytrid fungi respond to green light and that likely this behavior is due to a rhodopsin or rhodopsin-like GPCR  We found longer intact copy in the genome of the chytrid S. punctatus, so decided to focus on that copy – though we later discovered additional modifications of the predicted gene structure appeared necessary. We decided to do some homology modeling with the solved structure of a squid rhodopsin as shown in Figure 1. This confirmed that the sequence was compatible with the Type II Opsin structure. The paper documents several other computational simulations to test for the likely binding chromophore and hypothesis testing about the stability of the protein structure. Overall this work provides confidence that the sequence encoded in the genome of the zoosporic fungus can fold into a structure compatible with an opsin.

fig-1A
Figure 1A: Structural alignment of S. punctatus homology model (grey) with T. pacificus crystal structure (light purple)

It still remains to be tested if this opsin-like gene can biochemically function in this way. We hope to explore more of that with some additional work in the future. We have also nearly completed our manuscript analyzing the evolutionary history of this protein in fungi and related species to give a better picture of the timing of the emergence of this receptor-like protein. This project has helped advance some ideas about how zoosporic fungi interact with their environment based on genomic and computational analyses. This gene is a good candidate for future investigations into environmental sensing and signaling in zoosporic fungi.