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: 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.
The past few months have passed quickly but wanted to share a few updates.
Jason presented at the EMBO Eukaryotes meeting in Spain, Mexican Mycology Congress, Univ of Arizona, attended the Kavli Frontiers meeting, co-organized the Southern California Eukaryotic Pathogens meeting held again at UCR and taught graduate course on Programming and Data analyses.
The past few months we hosted Yinka Odebode from University of Lagos from August to November. He was supported by the West African Research Association. Yinka learned about ITS sequencing of fungi to identify his isolates in his work in Africa. He also explored properties of dust associated fungi in Nigeria before he returned home in November.
We also welcomed Marco Marconi from Madrid for a few months and is working on comparative genomics of fungi using the 1KFG datasets.
Starting in September we welcomed new graduate student in Plant Pathology, Nuttapon Pombubpa (right). Here he is (right) enjoying lunch along with visiting student Claudia Coleine and graduate student Sawyer.
We gathered to say goodbye to project scientist Peng Liu who returned to China in December. Here she is with postdoc Jinfeng and visiting student Zhinquan.
Undergraduates Dillon and Jericho joined us for lunch as well. They have both worked closely with Peng this Summer and Fall.
Most of the lab together for a farewell lunch for Peng including Deane on the far right.
A quick note to say congrats and good luck to postdocs and students who finished up the summer.
Graduate student Steven Ahrendt who graduated from the GGB program and is now a postdoc at the JGI / UC Berkeley.
Postdoc Ousmane Cissé finished his fellowship from the Swiss National Science Foundation and moved on to the NIH on a fellowship to work on Pneumocystis.
Postdoc Rod Olarte moved to the University of Minnesota on a NSF postdoctoral fellowship.
Undergraduates Dillon McDonald and Christina Uriarte also finished their summer projects in the HSI-STEM and MARCU programs.