Genome-scale phylogeny and comparative genomics of the fungal order Sordariales

Hensen, Noah; Bonometti, Lucas; Westerberg, Ivar; Brännström, Ioana Onut; Guillou, Sonia; Cros-Aarteil, Sandrine; Calhoun, Sara; Haridas, Sajeet; Kuo, Alan; Mondo, Stephen; Pangilinan, Jasmyn; Riley, Robert; LaButti, Kurt; Andreopoulos, Bill; Lipzen, Anna; Chen, Cindy; Yan, Mi; Daum, Chris; Ng, Vivian; Clum, Alicia; Steindorff, Andrei; Ohm, Robin A.; Martin, Francis; Silar, Philippe; Natvig, Donald O.; Lalanne, Christophe; Gautier, Valérie; Ament-Velásquez, Sandra Lorena; Kruys, Åsa; Hutchinson, Miriam I.; Powell, Amy Jo; Barry, Kerrie; Miller, Andrew N.; Grigoriev, Igor V.; Debuchy, Robert; Gladieux, Pierre; Hiltunen Thorén, Markus; Johannesson, Hanna

doi:10.1016/j.ympev.2023.107938

Genome-scale phylogeny and comparative genomics of the fungal order Sordariales

Journal Article · Tue Oct 10 00:00:00 EDT 2023 · Molecular Phylogenetics and Evolution

DOI:https://doi.org/10.1016/j.ympev.2023.107938· OSTI ID:2439707

Hensen, Noah ^[1]; Bonometti, Lucas ^[2]; Westerberg, Ivar ^[1]; Brännström, Ioana Onut ^[3]; Guillou, Sonia ^[2]; Cros-Aarteil, Sandrine ^[2]; Calhoun, Sara ^[4]; Haridas, Sajeet ^[4]; Kuo, Alan ^[4]; Mondo, Stephen ^[4]; Pangilinan, Jasmyn ^[4]; Riley, Robert ^[4]; LaButti, Kurt ^[4]; Andreopoulos, Bill ^[4]; Lipzen, Anna ^[4]; Chen, Cindy ^[4]; Yan, Mi ^[4]; Daum, Chris ^[4]; Ng, Vivian ^[4]; Clum, Alicia ^[4] more »

Stockholm Univ. (Sweden)
University of Montpellier (France)
Univ. of Oslo (Norway); Uppsala Univ. (Sweden)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
Universite de Lorraine, Champenoux (France); French National Research Institute for Agriculture, Food and Environment (INRAE), Champenoux (France)
Université de Paris Cité (France)
Univ. of New Mexico, Albuquerque, NM (United States)
Uppsala Univ. (Sweden)
Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
Univ. of Illinois at Urbana-Champaign, IL (United States)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
Univ. Paris-Saclay, Gif-sur-Yvette (France)
Stockholm Univ. (Sweden); Royal Swedish Academy of Sciences, Stockholm (Sweden)

The order Sordariales is taxonomically diverse, and harbours many species with different lifestyles and large economic importance. Despite its importance, a robust genome-scale phylogeny, and associated comparative genomic analysis of the order is lacking. In this study, we examined whole-genome data from 99 Sordariales, including 52 newly sequenced genomes, and seven outgroup taxa. We inferred a comprehensive phylogeny that resolved several contentious relationships amongst families in the order, and cleared-up intrafamily relationships within the Podosporaceae. Extensive comparative genomics showed that genomes from the three largest families in the dataset (Chaetomiaceae, Podosporaceae and Sordariaceae) differ greatly in GC content, genome size, gene number, repeat percentage, evolutionary rate, and genome content affected by repeat-induced point mutations (RIP). All genomic traits showed phylogenetic signal, and ancestral state reconstruction revealed that the variation of the properties stems primarily from within-family evolution. Together, the results provide a thorough framework for understanding genome evolution in this important group of fungi.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States)

Sponsoring Organization:: USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231; NA0003525

OSTI ID:: 2439707

Journal Information:: Molecular Phylogenetics and Evolution, Journal Name: Molecular Phylogenetics and Evolution Vol. 189; ISSN 1055-7903

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
Chaetomiaceae
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Genome-scale phylogeny and comparative genomics of the fungal order Sordariales

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References (56)

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