With Bob Schmitz at Univ of Georgia, We’re working on a project we call MycoMeth to examine evolution of methylation across Fungi. We would welcome contributions of ~2ug of DNA from diverse fungi that have a sequenced genome. Please email Jason or Bob if you would like to contribute.
Just back from another fantastic Fungal Genetics Conference at Asilomar. An amazing number of helpful tweets under the #Fungal17 hashtag. Sarah Unruh (@sau916) and I are talking about how to best archive or building a storify this so it is easier to read. Always a fun meeting to see friends and nosh at the smorgasbord of fungal genetics, epigenetics, genomics, ecology, evolution, and chemistry that is going on. Jason got to give a Plenary talk and express the utility of sequencing fungal genomes in studying their evolution. Lab Alumnus Steven Ahrendt won a poster award on his work on Cryptomycota fungi and also gave a talk.
— Jessie (@JessieUehling) March 17, 2017
Also got some good news that our paper on structural analyses of a rhodopsin-like protein in the chytrid fungi has been accepted at PeerJ after some helpful revisions – (see the preprint).
Quick post to sum up some of the news from 2016 and head into 2017.
- Six manuscripts were published and an additional two were accepted and three more were submitted or being revised in 2016
- Three graduate students survived another year in the lab: Sawyer, Nat, Derreck
- Joined by one Microbiology graduate student Jesus Pena joined in Fall 2016.
- Nine undergraduates worked in the lab Deane, Josh, Jericho, Dillon, Na, Justin, Serena, Leandra, George and Travis has been part of bioinformatics projects
- One postdoc, Jinfeng has been the bioinformatics and genomics guru from genome assembly to transposon bioinformatics
- One new assembly of a Citrus genome
- At least 15 new genomes from our work with Zygolife and 1000 Fungal Genomes project were released or material processed. More than 100 cultures of some fungi are being examined in the lab.
- One NSF grant started on systematics of anaerobic chytrid fungi and one new grant awarded as part of the UC MRPI http://ucop.edu/research-initiatives/programs/mrpi/2017-Awards.html program on the “UC Valley Fever Research Initiative” lead by UCSF and including several other UC campus.
- Jason is on sabbatical in 2017 at Oregon State University.
Some us from the lab took a trip up to Berkeley, CA for the MSA 2016 meeting. We road tripped by car from Riverside through the central valley up to Berkeley.
At the conference we had a great chance to meet with other mycologists, ecologists, and fungal enthusiasts. The meeting was fantastic from the Clark Kerr campus at UC Berkeley we had dorm life living so everyone was close by and could eat meals together. The talks and posters were really outstanding and such fun to talk about interesting research in fungi. Clearly genomics, next generation sequencing are at the forefront of tools used by the community but new approaches to visualizing communities and exploring the interactions between fungi and partners like bacteria and plants were very well explored in the meeting. Some great work on microbiomes and mycobiomes of insects and amphibians also made for some fascinating new results. There was a MSA session dedicated to some results from the ZyGoLife project and our team also had a one day meeting earlier in the week at the Joint Genome Institute to catch up on all the different team projects (a long post on this will appear on the zygolife project page soon). It was also fun to catch up with former lab member Steven Ahrendt who now works at JGI on early diverging fungi genome projects.
The meeting also featured Arturo Casadevall as the Karling lecture – an honor to bring in a scientist who is likely an outside member of the MSA community to speak about fungi. Dr Casadevall gave a lecture that covered the importance of collaboration, the impact of the pressure to publish in ‘one word journals’, and reviewed his provocative hypothesis about the link in the success of fungi, dinofall of dinosaurs, and rise of mammals. He also paid tribute to Thomas Taylor, a Zygolife collaborator who sadly passed away this Spring but who would have been the Karling lecturer this year.
Jason spoke on new population genomics work on Candida and Fusarium, while Sawyer presented a poster on Rhizopus stolonifer resequencing and population genomics; Derreck presented a poster on Bacteria-Fungi interactions on Serratia and zygomycete fungi; Nat presented his poster on data from first environmental sequencing of desert biological soil crusts from Joshua Tree National Park. On the way back we stopped for an overnight in Pinnacles National Park. Much fun, science, and discussions were had throughout the week.
We also stopped to take our first lab album cover photo while in Pinnacles. More to come!
We celebrated a few events in April and May.
- A new NSF grant was funded and started in April on rumen fungi “Phylogenomics and evolutionary history of the anaerobic fungal group, Neocallimastigomycota“. This is a collaboration with Noha Youssef and Mostafa Elshahed at Oklahoma State University and will give the opportunity to work on systematics of these anaerobic gut fungi.
- Raúl Castanera who came to the lab for a short stay last year, authored a paper that was accepted this week on transposable elements in the Pleurotus (oyster mushroom) genome and comparisons in proliferation rates and impact on gene expression. Castanera R et al. PLoS Gen doi: 10.1371/journal.pgen.1006108
- We just started to get our first microbial diversity (16S and ITS) results for rock and soil communities from California desert environments and Antarctica as part of project by visiting student Claudia Coleine and Nat Pombubpa. Claudia is a PhD student with Laura Selbmann of Tuscia University and visited for nine months, but we processed isolates the lab collected from Antartica expeditions. We are also sequencing genomes of a handful of cultured fungal species from Antarctic locations and the first assemblies look pretty good (200-400 contigs for these 25-40Mb genomes) for a MiSeq only assembly.
- Nat is collecting samples from Joshua Tree National Park and in collaboration with other desert crust researchers Paul De Ley and Nicole Pietrasiak examining fungal and bacterial distribution.
Jason was at the European Conference on Fungal Genetics in Paris this April and had a chance to deliver a lecture. It was a great meeting of science and there was a lot of social media coverage by participants.
Jason and Ousmane also attended the 1st conference on multicellular development in fungi where Ousmane presented his work on the Neolecta genome and comparative biology of the Taphrinomycotina fungi.
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.
- We said bye to Marco Marconi, visiting student from the Wilkinson Lab in Madrid, in December. He worked on some data mining from the 1KFG project and brought some new R tools for looking for enrichment across the CAZY, Interpro, and Pfam differences in species.
- We welcome Plant Pathology graduate student Derreck Carter-House to the lab in January – after spending time working on molecular biology projects in plants and plant-microbe interactions in another lab.
- Jason went across to England to serve on Ensembl Genomes SAB and give seminar at University of Exeter – he came back with more appreciation for sunny California winters.