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.

IMC10 – Bangkok, Thailand

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.

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Fig1_Mucormycotinacellwall

Mucormycotina cell wall paper published

Congrats to Divya and Jason as our paper with collaborators Hugo Melida and Vincent BuloneDeciphering the uniqueness of Mucoromycotina cell walls by combining biochemical and phylogenomic approaches is now available at Environmental Microbiology. We discovered in this work that two Mucormycotina species have novel fucose sugar composition in their cell walls which is not found in other Fungi. We also identify expansions and unique subfamilies of Chitin synthase genes.

Fig1_Mucormycotinacellwall

MSA 2014 fungi-fun

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.IMG_1645

 

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.

Welcome Ousmane Cisse

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.

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.