Jason presents on genomic evolution and the 1KFG project.
The zygo-elves and the JGI have been hard at work at end of 2016 and early 2017 growing and preparing samples for sequencing. Following sequencing, assembly and annotation work at JGI the following are now available genomes – most were performed with PacBio so there are 25-400 contigs for most of these.
Good work Spatafora (Ying Chang) and Stajich labs (Derreck Carterhouse and Jericho Ortanez) with support from Matt Smith‘s lab at U Florida esp the work of Nicole Reynolds and Gerald Benny who isolated and/or verified many of these strains.
Mucoromyoctina ( Mucoromycota)
- Fennellomyces sp. T-0311
- Pilaira anomala RSA1997
- Cunninghamella echinulata NRRL 1382
- Cokeromyces recurvatus NRRL 2243
- Gilbertella persicaria CBS 190.32
- Radiomyces spectabilis RSA627
- Circinella umbellata NRRL1351
- Spinellus fusiger NRRL 22323
We are preparing the Tier II of species for the Early Diverging Fungi – 1KFG CSP with another set of 50+ zygomycetes and zoosporic fungi for the next 2 years.
These are publicly available but please contact the authors for any manuscripts which make use of these data prior to their formal publication as the groups who prepared these are working on their own analyses of these data related to phylogenomics, lifestyle and genome evolution.
ZyGoLife 2016 Workshop was an all day affair. It was hosted by JGI on August the 7th and included 35 participants from 12 institutions. Each lab presented a 20-minute update on research directly related to the ZyGoLife project followed by 10 minutes of discussion. At the end of the meeting there was a 1.5 hour discussion on goals for the second year of the project. Particular discussion topics included Tier II sampling of genomes for our JGI CSP, prioritization of analyses and papers, development of Broader Impacts, and scheduling workshops for 2017. Our Tier II sampling will focus on unsampled genera of zygomycetes with particular emphasis on greater phylogenetic coverage of the Zoopagomycotina, Entomophthoromycotina and Kickxellomycotina. Our tentative plans for 2017 workshops include a collecting and bioimaging workshop at Arizona State and a teaching workshop at MSA 2017 in Athens, GA. Stay tuned for more information on these workshops.
And if we were not yet official, we took our group photos and JGI double helix.
ZyGoLife 2016 Attendees
Arizona State University: Robby Roberson, Karen Fisher
Boise State University: Merlin White, Michael McCormick
DOE Joint Genome Institute: Igor Grigoriev, Stephen Mondo, Alan Kou, Stephen Ahrendt, Asef Salamov
Duke University: Rytas Vilgalys, Jessie Uehling, Alejandro Roja
Michigan State University: Greg Bonito, Natalie Vande Pol
Oregon State University: Joey Spatafora, Ying Chang
The University of Michigan: Tim James, Kevin Amses, William Davis, Alisha Quandt
USDA ARS Peoria: Kerry O’Donnell
University of British Columbia: Mary Berbee, Benjamin Auxier, Anna Bazzicaluipo, Jaclyn Dee, Ludovic Le Renard
University of California, Riverside: Jason Stajich, Nuttapon Pombubpa, Sawyer Masonjones, Derreck Carter-House
University of Florida: Matt Smith, Nicole Reynolds, Katy Lazarus, Alija Mujic
University of Toronto: Yan Wang
Jericho Ortanez from Jason Stajich’s lab at UC Riverside is visiting the Spatafora lab this week. Jericho is an undergraduate in Biology and is working on the ZyGoLife project. We have funding as part of the ZyGoLife project for students to visit different ZyGoLife labs, learn new techniques, and build their professional network. Jericho is here this week learning our DNA and RNA extraction protocols. He is working with Ying Chang, Jeff Beard and Nick Spatafora. Great visit and we have really enjoyed having him work in the lab this week.
L-R. Ying Chang, Nick Spatafora, Jeff Beard, Jericho Ortanez
Two new zygomycete genomes were released this week at JGI: Mucor heterogamus NRRL 1489 v1. and Mycotypha africana NRRL 2978 v1.0. Both of these genomes were sequenced as part of the ZyGoLife project and the associated CSP on early diverging fungi. We are very excited about the pace of zygomycete genome sequencing and the ability to crack open the black box of zygomycete evolution.
A number of genomes have been completed recently and made public as part of our collaboration with Joint Genome Institute (JGI). These data are unpublished and are being included in phylogenomic analyses by the ZyGoLife research consortium. We are particularly interested in resolving relationships among the zygomycete fungi and using a phylogenetic framework to test hypotheses of the evolution of fungi as they transitioned onto land and adopted nutritional modes reliant on plants and plant-based ecosystems
New releases since our last post include:
A few genomes from our project were made public as part of the JGI collaboration in the past few months. Here are two recent releases of genomes from the EKZ clade (Entomophthoromycotina, Kickxellomycotina, Zoopagomycotina) and we expect several more to be public in the coming month.
- A PacBio based assembly of the Entomophthoromycotina fungus Basidiobolus meristosporus CBS 931.73. These fungi are often isolated from dung of frogs or lizards and have hyphal growth forms but the phylogenetic placement within the clade is still under investigation.
- The Kickxellomycotina soil dwelling fungus Linderina pennispora. This joins the Ramicandelaber brevisporus CBS 109374 and Martensiomyces pterosporus J.A. Mey., strain CBS 209.56 which were released earlier in 2015.
We have incorporated these data and some ongoing assemblies into updated species phylogeny and will be working to release several more of these genomes.
Species of Syncephalis (Zoopagales) are generally considered to be obligate, haustorial, biotrophic parasites of other zygomycetous fungi (Mortierellomycotina and Mucoromycotina) in nature. They can be commonly isolated from environmental soil and dung substrates and maintained in dual cultures in the lab. However, Ellis (1966) developed a medium capable of growing several Syncephalis species in pure culture without their host fungi.
The secret ingredient is beef liver. Some species of Syncephalis can be inoculated onto a cube of liver and grow as luxuriously as on their Mucoralean host fungi. Here in the Smith lab we were able to replicate Ellis’s success and grow four different species of Syncephalis on beef liver media.
Growing Syncephalis without its host is more important than ever. In the age of whole genome sequencing, acquiring enough pure tissue and DNA remains a technical limitation for many organisms, particularly when they grow biotrophically in or on a host.
Ellis, JJ. (1966) On growing Syncephalis in pure culture. Mycologia. 58: 465-469
The ZyGoLife team had our first all hands project meeting hosted by Co-PI Matthew Smith in the Department of Plant Pathology at the University of Florida in Gainesville, FL. We gathered for three days to organize several of the data collection themes and design some of the experiments we are planning. It was a great ‘kick off’ to our project where we got to interact with each other and through video chats with teams members who could not attend. The project has several foci intended to capture, analyze, and interpret the biological diversity of the early diverging fungi using genomic approaches integrated with information on the life history and ecologies of these fungi.
The project is sequencing genomes in collaboration with the JGI and 1KFG projects and in our labs in order to develop a high quality reference set of genomes from the major lineages of zygomycete fungi. This will provide confidence in the placement and branching order of these fungi, which is currently somewhat unresolved. We are also sequencing targeted markers or light draft genomes to sample the diversity of zygomycete fungi within culture collections. This includes the pioneering sampling conducted by Dr. R. K. Benjamin and continued by Dr. Gerald Benny (among others) . Dr Benny is a collaborator on this project and we are thrilled to have his expertise in the systematics, taxonomy, and biology of zygomycete fungi.
We also spent one morning at the Ordway-Swisher Biological Reserve on a “Zygoblitz” (derived from Mycoblitz, which was derived from Bioblitz) where we focused on collecting samples of soil, insects, and dung which would be likely to contain zygomycetous fungi. This provided cross-training on species collection and identification among groups where new specimens and cultures are needed. One focus was looking for Endogone species. These are small truffle-like fungi that fruit in or on soil, leaf litter, or decayed wood. Although widespread, these fungi are infrequently collected and are difficult to culture and to identify. Our team was lucky enough to find a fresh collection of Endogone cf. pisiformis at the Ordway-Swisher reserve.
Merlin White showed how to dip for aquatic insects in the lakes we visited in order to sample trichomycete fungi that inhabit the guts of insects. The techniques required to isolate these fungi are challenging, so it was great to have a master show us how to work his magic. Similarly, Gerald Benny presented an excellent overview of the major lineages in the Mucormycotina fungi and provided perspective on how much is really know the taxonomy and systematics of this lineage. Andrii Gryganskyi also entertained us with a humorous and detailed demonstration on how to culture Conidiobolus species from soil or leaf litter and Basidiobolus species from frog excrement.
Many of the team members setup EOL accounts in order to create and curate species pages about zygomycete fungi. As part of our project, herbarium staff members and students in our mycology courses will put together EOL species pages for zygomycete fungi. Although a few EOL pages have been created for select species, there are still plenty of taxa that need attention.
This first meeting will be followed up by impromptu gatherings at the upcoming Fungal Genetics 2015 meeting and MSA 2015 meeting. We also hope to run several more Zygoblitzes with additional training for students and others who want to learn to collect and identify zygomycete fungi.