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 . Former postdoc Ousmane Cissé published his work on Pneumocystis at the NIH in his current postdoc . Current postdoc Yan Wang published part of his thesis work and we worked on these data a bit as part of the zygolifeproject here . 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 . 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 . Work exploring whether Transposable elements have a role in stage-specific gene expression in Coccidioides with Theo Kirkland and Anna Muszewska . 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 . 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 .
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.
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.
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 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.
Our community sequencing project at the JGI was awarded which will allow a consortium of researchers to sequence 1000 fungal genomes through the DOE’s Joint Genome Institute. The intention is to sample two species from every major lineage of Fungi.
Some press releases on the project below and we will coordinate it through several websites including a forum for discussion about potential species beyond the target list.