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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
agricultural and biological sciences
Mycoparasites, Gut Dwellers, and Saprotrophs: Phylogenomic Reconstructions and Comparative Analyses of Kickxellomycotina Fungi
Genome biology and evolution, Volume 15, No. 1, Year 2023
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Description
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. © The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.
Available Materials
https://efashare.b-cdn.net/share/pmc/articles/PMC9866270/bin/evac185_supplementary_data.zip
Authors & Co-Authors
Reynolds, Nicole K.
United States, Gainesville
University of Florida
Stajich, Jason E.
United States, Riverside
University of California, Riverside
Benny, Gerald L.
United States, Gainesville
University of Florida
Barry, Kerrie W.
United States, Berkeley
Lawrence Berkeley National Laboratory
Mondo, Stephen J.
United States, Berkeley
Lawrence Berkeley National Laboratory
LaButti, Kurt M.
United States, Berkeley
Lawrence Berkeley National Laboratory
Lipzen, Anna M.
United States, Berkeley
Lawrence Berkeley National Laboratory
Daum, Chris G.
United States, Berkeley
Lawrence Berkeley National Laboratory
Grigoriev, Igor V.
United States, Berkeley
Lawrence Berkeley National Laboratory
United States, Berkeley
University of California, Berkeley
Ho, Hsiaoman
Unknown Affiliation
Crous, Pedro Willem
Netherlands, Utrecht
Westerdijk Fungal Biodiversity Institute - Knaw
Spatafora, Joseph W.
United States, Corvallis
Oregon State University
Smith, Matthew E.
United States, Gainesville
University of Florida
Statistics
Citations: 2
Authors: 13
Affiliations: 6
Identifiers
Doi:
10.1093/gbe/evac185
ISSN:
17596653
Research Areas
Genetics And Genomics
Health System And Policy