TY - JOUR
T1 - Genome-scale phylogeny and comparative genomics of the fungal order Sordariales
AU - Hensen, Noah
AU - Bonometti, Lucas
AU - Westerberg, Ivar
AU - Brännström, Ioana Onut
AU - Guillou, Sonia
AU - Cros-Aarteil, Sandrine
AU - Calhoun, Sara
AU - Haridas, Sajeet
AU - Kuo, Alan
AU - Mondo, Stephen
AU - Pangilinan, Jasmyn
AU - Riley, Robert
AU - LaButti, Kurt
AU - Andreopoulos, Bill
AU - Lipzen, Anna
AU - Chen, Cindy
AU - Yan, Mi
AU - Daum, Chris
AU - Ng, Vivian
AU - Clum, Alicia
AU - Steindorff, Andrei
AU - Ohm, Robin A.
AU - Martin, Francis
AU - Silar, Philippe
AU - Natvig, Donald O.
AU - Lalanne, Christophe
AU - Gautier, Valérie
AU - Ament-Velásquez, Sandra Lorena
AU - Kruys, Åsa
AU - Hutchinson, Miriam I.
AU - Powell, Amy Jo
AU - Barry, Kerrie
AU - Miller, Andrew N.
AU - Grigoriev, Igor V.
AU - Debuchy, Robert
AU - Gladieux, Pierre
AU - Hiltunen Thorén, Markus
AU - Johannesson, Hanna
N1 - Publisher Copyright:
© 2023 The Authors
PY - 2023/12
Y1 - 2023/12
N2 - 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.
AB - 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.
KW - Chaetomiaceae
KW - Genome evolution
KW - Podosporaceae
KW - Sordariaceae
KW - Whole-genome phylogeny
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U2 - 10.1016/j.ympev.2023.107938
DO - 10.1016/j.ympev.2023.107938
M3 - Article
C2 - 37820761
AN - SCOPUS:85174351665
SN - 1055-7903
VL - 189
JO - Molecular Phylogenetics and Evolution
JF - Molecular Phylogenetics and Evolution
M1 - 107938
ER -