Recent Lab Papers

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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 [1].  Former postdoc Ousmane Cissé published his work on Pneumocystis at the NIH in his current postdoc [2]. 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 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!

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.

Figure 6 – Overview of the timing and evolution of Pneumocystis and their mammalian hosts.

ZyGoLife visitors

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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

Desert Adventures, 2018

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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.

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Kelso Dunes
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Crusts symbioses of algae and cyanobacteria with fungi, bacteria, and many uncounted single celled organisms.

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Lichen Crusts galore across from the Kelso dunes
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Moss Crusts are also rich symbioses with a predominant moss.
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Old volcanic flow in the Cima area also has cacti and crusts
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Colorful lichens found on the granite faces. On closer looks, these are often 3 or more species competing for space on the same surface.

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The Joshua Tree Album

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

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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.
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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

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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

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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

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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.

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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.