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
Zygomycetes comprise ancient lineages of Fungi that include plant symbionts, animal and human pathogens, and decomposers of a wide variety of organic compounds. Zygomycetes are thought to be among the first terrestrial organisms and symbiotic associations with zygomycetes apparently facilitated the origin of land plants. They represent one of the earliest origins of multicellularity and the filamentous body plan and polar cell growth that characterize most species of fungi. Zygomycete fungi are also used in numerous industrial processes (e.g., organic acid production) and fermentation of foods (e.g., tempeh, soy sauce). Despite these critical ecological roles, key morphological innovations, and importance to human civilization, this group of fungi remains understudied and little is understood about their evolutionary relationships. ZyGoLife will resolve the evolutionary relationships through integration of numerous types of data, including genome sequencing and analyses, discovery and description of zygomycete fossils, development of enhanced tools for detecting zygomycetes in the environment, and elucidation of novel morphological characteristics through state-of-the-art bioimaging. In addition, the project will develop educational resources for schools and the general public in order to highlight the importance of this poorly known group of Fungi.