Mycoparasites, Gut Dwellers, and Saprotrophs: Phylogenomic Reconstructions and Comparative Analyses of Kickxellomycotina Fungi

Reynolds, Nicole K.; Stajich, Jason E.; Benny, Gerald L.; Barry, Kerrie; Mondo, Stephen; LaButti, Kurt; Lipzen, Anna; Daum, Chris; Grigoriev, Igor V.; Ho, Hsiao-Man; Crous, Pedro W.; Spatafora, Joseph W.; Smith, Matthew E.

doi:10.1093/gbe/evac185

Mycoparasites, Gut Dwellers, and Saprotrophs: Phylogenomic Reconstructions and Comparative Analyses of Kickxellomycotina Fungi

Journal Article · Fri Jan 06 23:00:00 EST 2023 · Genome Biology and Evolution

DOI:https://doi.org/10.1093/gbe/evac185· OSTI ID:1972187

^[1]; ^[2]; Benny, Gerald L. ^[1]; Barry, Kerrie ^[3]; Mondo, Stephen ^[3]; LaButti, Kurt ^[3]; Lipzen, Anna ^[3]; Daum, Chris ^[3]; ^[4]; Ho, Hsiao-Man ^[5]; Crous, Pedro W. ^[6]; Spatafora, Joseph W. ^[7]; ^[1]

Univ. of Florida, Gainesville, FL (United States)
Univ. of California, Riverside, CA (United States)
USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
University of Education, Taipei (Taiwan)
Westerdijk Fungal Biodiversity Institute, Utrecht (Netherlands)
Oregon State Univ., Corvallis, OR (United States)

Improved sequencing technologies have profoundly altered global views of fungal diversity and evolution. High-throughput sequencing methods are critical for studying fungi due to the cryptic, symbiotic nature of many species, particularly those that are difficult to culture. However, the low coverage genome sequencing (LCGS) approach to phylogenomic inference has not been widely applied to fungi. Here we analyzed 171 Kickxellomycotina fungi using LCGS methods to obtain hundreds of marker genes for robust phylogenomic reconstruction. Additionally, we mined our LCGS data for a set of nine rDNA and protein coding genes to enable analyses across species for which no LCGS data were obtained. The main goals of this study were to: 1) evaluate the quality and utility of LCGS data for both phylogenetic reconstruction and functional annotation, 2) test relationships among clades of Kickxellomycotina, and 3) perform comparative functional analyses between clades to gain insight into putative trophic modes. In opposition to previous studies, our nine-gene analyses support two clades of arthropod gut dwelling species and suggest a possible single evolutionary event leading to this symbiotic lifestyle. Furthermore, we resolve the mycoparasitic Dimargaritales as the earliest diverging clade in the subphylum and find four major clades of Coemansia species. Finally, functional analyses illustrate clear variation in predicted carbohydrate active enzymes and secondary metabolites (SM) based on ecology, that is biotroph versus saprotroph. Saprotrophic Kickxellales broadly lack many known pectinase families compared with saprotrophic Mucoromycota and are depauperate for SM but have similar numbers of predicted chitinases as mycoparasitic.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC); National Science Foundation (NSF); USDA

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1972187

Journal Information:: Genome Biology and Evolution, Journal Name: Genome Biology and Evolution Journal Issue: 1 Vol. 15; ISSN 1759-6653

Publisher:: Society for Molecular Biology and EvolutionCopyright Statement

Country of Publication:: United States

Language:: English

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