Look out for these new Genera in the Mortierellaceae!

There are some notable changes in taxonomy of  Mortierellaceae, following the publication of ‘Resolving the Mortierellaceae phylogeny through synthesis of multi-gene phylogenetics and phylogenomics’ in Fungal Diversity1. This paper, led by recent PhD graduate Natalie Vandepol from Gregory Bonito’s lab at Michigan State University, is the result of a multi-lab ZyGoLife collaboration including Jason Stajich at University of California, Riverside and Kerry O’Donnell from the USDA ARS in Peoria, IL. In this research, low coverage sequencing (~10X) phylogenomic approaches were used to provide backbone support for major clades in the Mortierellaceae, which was combined with multi-locus phylogenetics of single copy protein genes to generate a phylogeny that included 314 isolates representing at least 48 taxa in the family. A total of 13 genera are circumscribed in this paper, including 7 that are newly proposed. 

Among these are four genera named in tribute to fungal scientists and their careers. These include

  • Benniella, named in honor of the American mycologist Gerald Benny who has dedicated his career to the study of zygomyceteous fungi, and has made important contributions to the taxonomy of fungi in the Mortierellomycotina; 
  • Gryganskiella, in honor of Andrii Gryganskyi, a Ukrainian-American mycologist who has contributed to research, training and genomics of fungi in the Mucoromycota; 
  • Podila, in honor of Gopi Podila, an Indian American biologist who advanced the fields of plant-microbe interactions, plant genetics and biotechnology of bioenergy crops;
  • Linnemannia, in honor of Germaine Linnemann, a German mycologist who contributed to many early species descriptions and hypothesis on their evolutionary relationships. 

The other proposed genera, Entomortierella, Necromortierella, Lunasporangiospora are named after suggested ecology or morphology of inclusive members, respectively. The genus Mortierella was retained for the Alpina clade, which includes the type species M. polycephela, as were Dissophora, Modicella, Gamsiella, and Lobosporangium. Finally, the genera Actinomortierella and Aquamortierella were resurrected. 

Low coverage genome sequencing has become a cost-effective tool in phylogenomics. We expect to learn more about the diverse ecologies and genomic capacities that differentiate these genera of Mortierellaceae as this newly proposed taxonomy for the family becomes adopted and integrated into taxonomic sequence classifiers.  

This work was supported through the Department of Energy’s Joint Genome Institute and grants from the National Science Foundation and USDA-NIFA.

1 Natalie Vandepol, Julian Liber, Alessandro Desirò, Hyunsoo Na, Megan Kennedy, Kerrie Barry, Igor V Grigoriev, Andrew N Miller, Kerry O’Donnell, Jason E Stajich, Gregory Bonito. Resolving the Mortierellaceae phylogeny through synthesis of multi-gene phylogenetics and phylogenomics. Fungal Diversity (2020). https://doi.org/10.1007/s13225-020-00455-5 

New Zygopubs

Several recent publications out now from the Zygolife team. Good work all on the improved phylogenetic resolution of clades within the Zoopagomycota Phylum and Zoopagomycotina sub-phylum.

Davis WJ, Amses KR, Benny GL, Carter-House D, Chang Y, Grigoriev I, Smith ME, Spatafora JW, Stajich JE, James TY. Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi).  Mol Phylogenet Evol. 2019; 133:152-163. doi: 10.1016/j.ympev.2019.01.006

Benny GL, Smith ME. Notes on Syncephalis (Zoopgales, Zoopagomycota) from the Farlow Herbarium with the description of a new species, Syncephalis aethiopica. Mycologia. 2018; 110(1):192-200. doi: 10.1080/00275514.2018.1426960

Reynolds NK, Benny GL, Ho HM, Hou YH, Crous PW, Smith ME. Phylogenetic and morphological analyses of the mycoparasitic genus Piptocephalis. Mycologia. 2019;  doi: 10.1080/00275514.2018.1538439.

Chang Y, Desirò A, Na H, Sandor L, Lipzen A, Clum A, Barry K, Grigoriev IV, Martin FM, Stajich JE, Smith ME, Bonito G, Spatafora JW. Phylogenomics of Endogonaceae and evolution of mycorrhizas within Mucoromycota. New Phytol. 2018. doi: 10.1111/nph.15613

Work from the Corradi lab also recently explored and long standing mystery as to how AM Fungi produce recombinant genotypes in the absence of observable sexual reproduction through inter-nuclear genetic exchange . They are able to conclude that “AMF can generate genetic diversity via meiotic-like processes in the absence of observable mating” which provides a new way to think about these “ancient asexuals”.

Chen EC, Mathieu S, Hoffrichter A, Sedzielewska-Toro K, Peart M, Pelin A, Ndikumana S, Ropars J, Dreissig S, Fuchs J, Brachmann A, Corradi N. Single nucleus sequencing reveals evidence of inter-nucleus recombination in arbuscular mycorrhizal fungi. Elife. 2018 ;7. pii: e39813. doi: 10.7554/eLife.39813.

Zygolife visitors to UC Riverside

In early April the Stajich lab at UC Riverside hosted several visitors from our ZyGoLife collaborative team in sunny California. The week started with a visit from Nicole a graduate student at Univ of Florida who came to sample soils and dung on the hunt for elusive mycoparasites in the Zoopagomycotina lineage. Her graduate training with Prof Matthew Smith with input from Dr Gerald Benny is helping her become an expert in mycoparasites like Syncephalis and Piptocephalis.

One collection site was near an old spring fed trough probably built by some of the recent ranching settlements of area but likely used by the native Americans who live here well before. More on the history of the Granite Mountains.

We got to catch a desert sunset over the Kelso Dunes

A view of the Sweeny Granite Mountain Desert Center

Nicole gathered soils from the UC Reserve Sweeney Granite Mountain Desert Research Center in the Mojave National Preserve. Thanks to Jim and Tasha who manage the reserve for showing us around and helping to identify some standing water and seeps for collecting soils. Nicole used Baermann funnels to isolate nematodes from these samples to find nematophagous fungi  infecting these nematodes in these desert soils.  We trekked around to some of the places where there is standing water from springs in the mountain to try to find areas with some moisture that keep nematodes and fungi happy.

Nicole sampling standing water and soils in the Granite Mountains Desert Research Center.

In all, Nicole spent over a week of sampling in Southern California following some of the  same sampling areas established by R. K. Benjamin in his extensive discovery and classification of zygomyceteous fungi.  Thanks also to Stajich lab member Tania for helping give Nicole a place to stay and show her around Riverside. We also got help in setting up space for funnels by nematode expert at UCR Paul De Ley.


We also welcomed Javier Tabima from Joey Spatafora‘s lab at Oregon State for another week to work with Yan Wang and Jason Stajich on Basidiobolus comparative genomics.

Javier Tabima (Center) with Ying Chang (Left) and Joey Spatafora (Right) during “Zygofornia” zygolife workshop at UC James Reserve April 2018

Javier recently joined the Oregon State team after completing his PhD work with Nik Grunwald (Oregon State University and USDA ARS). He is tackling some of the comparative genomics analysis of the multiple Basidiobolus genomes and exploring ploidy, genome duplication, and metabolite diversity potential of these species.



MSA2017 ZyGoLabs

ZyGoLabs: Zygomycete Fungi in Teaching and Research – July 15, 2017

This year at the annual  Mycological Society of America meeting in Athens, GA, the ZyGoLife research team hosted the first ZyGoLabs workshop.  It was an all day affair that focused on hands-on isolation and observation laboratories that can be implemented in teaching and research.  We had a total of 25 participants including students, postdocs and professors, as well as those from industry and the general public.  The workshop was held in the Plant Pathology teaching lab in the Miller Plant Sciences Building at the University of Georgia.  A big thanks to the Department of Plant Pathology for hosting us and especially to Marin Brewer and Tina Jones for all their help.  The workshop was a big success and we plan on offering it again in the near future.  Here are a few photos of participants and the fungi we observed.

ZyGoLife workshop participants in front of Miller Plant Sciences Building.

Tim James lecturing on Stylopage, a genus of nematode destroying fungi in Zoopagomycota.

Participants busy examining zygomycete fungi.

Jason Stajich’s hand interpretation of zygospore formation.

ZyGo Sex.  ZyGoLife participant, Ton Tran, showing early stage of sexual reproduction in Phycomyces.

Poor little nematode trapped by Stylopage.

Grass roots stained to show arbuscules and hyphae of Glomeromycotina.

Germinating basidiospores of Basidiobolus shot onto agar surface from frog dung isolation.

The mycoparasitic Piptocephalis.

New Zygo genomes – March 2017 edition

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)

Zoopagomycotina (Zoopagomycota)

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

ZyGoLife 2016

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 visits the Spatafora lab.

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.

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L-R. Ying Chang, Nick Spatafora, Jeff Beard, Jericho Ortanez