Category Archives: research

Recent Lab Papers

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.

Desert Crust collecting, Summer edition

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.

Stajich lab sampling team: Derreck, Nat, Sawyer, and Jericho
Stajich lab sampling team: Derreck, Nat, Sawyer, and Jericho
LightLichenCrust_JTNP
Our first collection of Lichen crust from Joshua Tree National Park
SurfaceTemp_DerreckJericho
Derreck measured crust surface temperature, while Jericho was getting ready for sampling

A desert foray

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.

Mike leads the team
Mike and Derreck ahead in Hidden Valley
Nat Sampling
Nat, getting his first taste of sampling in the desert.
Claudia looking for sandtsone associated fungi
Dereck and Claudia helping to look for crusts. Claudia is researching sandstone associated fungi from a variety of habitats.
Cyano Crust
Cyanobacteria dominated crust
Moss crust
Moss & crusts

Soil crust site

New Zygomycete evolution project in lab

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.

Cryptococcus literature curation paper

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.

Papers from the lab this month

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.

W.M. Keck Foundation grant for discovery of active transposable elements in mosquitos

 

Aedes aegypti mosquitoWe 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.

transcriptomes, bioinformatics, and light regulated genes

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.