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 - Data and materials: The computations/data handling were enabled by resources provided by the Swedish National Infrastructure for Computing (SNIC) at UPPMAX partially funded by the Swedish Research Council through grant agreement no. 2018-05973. Assemblies were produced through JGI community sequencing programs, with the additional four outgroup genomes publicly available through National Center for Biotechnology Information.
We thank Petter Madsen and Aaron Vogan for useful discussions and constructive feedback. Sabine Huhndorf is thanked for providing strains. Sandia National Laboratories is a multimission laboratory managed and operated by the National Technology and Engineering Solutions of Sandia, LLC., a wholly owned subsidiary of Honeywell International, Inc., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525. This paper describes objective technical results and analysis. Any subjective views or opinions that might be expressed in the paper do not necessarily represent the views of the U.S. Department of Energy or the U.S. Government.
We thank Petter Madsen and Aaron Vogan for useful discussions and constructive feedback. Sabine Huhndorf is thanked for providing strains. Sandia National Laboratories is a multimission laboratory managed and operated by the National Technology and Engineering Solutions of Sandia, LLC. a wholly owned subsidiary of Honeywell International, Inc. for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525. This paper describes objective technical results and analysis. Any subjective views or opinions that might be expressed in the paper do not necessarily represent the views of the U.S. Department of Energy or the U.S. Government. Data and materials: The computations/data handling were enabled by resources provided by the Swedish National Infrastructure for Computing (SNIC) at UPPMAX partially funded by the Swedish Research Council through grant agreement no. 2018-05973. Assemblies were produced through JGI community sequencing programs, with the additional four outgroup genomes publicly available through National Center for Biotechnology Information. Funding sources: This work was funded by JGI's Community Science Program grant #504394 and Marie Curie postdoctoral fellowship FP7-PEOPLE-2010-IOF-No.273086 to Pierre Gladieux. The work (proposal: 10.46936/10.25585/60000837, 10.46936/10.25585/60001060 and 10.46936/10.25585/60001199) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231. We further acknowledge funding from The Bergianus Foundation of The Royal Swedish Academy of Sciences.
Funding sources: This work was funded by JGI’s Community Science Program grant #504394 and Marie Curie postdoctoral fellowship FP7-PEOPLE-2010-IOF-No.273086 to Pierre Gladieux. The work (proposal: 10.46936/10.25585/60000837, 10.46936/10.25585/60001060 and 10.46936/10.25585/60001199) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231. We further acknowledge funding from The Bergianus Foundation of The Royal Swedish Academy of Sciences.
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 -