All posts by stajich

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.

 

 

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.

New Zygomycete genomes

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.

We have incorporated these data and some ongoing assemblies into updated species phylogeny and will be working to release several more of these genomes.

First Zygoblitz and ZyGoLife project meeting

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.ZygoLife-for-Life-group-picture

 

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 Endogene_ORDSWISHER_1Reserve 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 lEndogone_truffle_UFooking 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 Merlinvisited 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.

ZyGoLife project launched

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.