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

Autor: Hensen N; Stockholm University, Department of Ecology, Environment and Plants Sciences, Stockholm, Sweden., Bonometti L; University of Montpellier, PHIM Plant Health Institute, Montpellier, France., Westerberg I; Stockholm University, Department of Ecology, Environment and Plants Sciences, Stockholm, Sweden., Brännström IO; Oslo University, Natural History Museum, Oslo, Norway; Uppsala University, Department of Ecology and Genetics, Uppsala, Sweden., Guillou S; University of Montpellier, PHIM Plant Health Institute, Montpellier, France., Cros-Aarteil S; University of Montpellier, PHIM Plant Health Institute, Montpellier, France., Calhoun S; Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA., Haridas S; Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA., Kuo A; Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA., Mondo S; Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA., Pangilinan J; Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA., Riley R; Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA., LaButti K; Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA., Andreopoulos B; Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA., Lipzen A; Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA., Chen C; Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA., Yan M; Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA., Daum C; Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA., Ng V; Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA., Clum A; Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA., Steindorff A; Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA., Ohm RA; Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA., Martin F; Université de Lorraine, INRAE, Champenoux, France., Silar P; Université de Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain, Paris, France., Natvig DO; University of New Mexico, Department of Biology, Albuquerque, USA., Lalanne C; Université de Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain, Paris, France., Gautier V; Université de Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain, Paris, France., Ament-Velásquez SL; Stockholm University, Department of Zoology, Stockholm, Sweden., Kruys Å; Uppsala University, Museum of Evolution, Uppsala, Sweden., Hutchinson MI; University of New Mexico, Department of Biology, Albuquerque, USA., Powell AJ; Sandia National Laboratories, Dept. of Systems Design and Architecture, Albuquerque, USA., Barry K; Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA., Miller AN; University of Illinois Urbana-Champaign, Illinois Natural History Survey, USA., Grigoriev IV; Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA; University of California Berkeley, Department of Plant and Microbial Biology, Berkeley, CA, USA., Debuchy R; Université Paris-Saclay, Institute for Integrative Biology of the Cell, Gif-sur-Yvette, France., Gladieux P; University of Montpellier, PHIM Plant Health Institute, Montpellier, France., Hiltunen Thorén M; Stockholm University, Department of Ecology, Environment and Plants Sciences, Stockholm, Sweden; The Royal Swedish Academy of Sciences, Stockholm, Sweden., Johannesson H; Stockholm University, Department of Ecology, Environment and Plants Sciences, Stockholm, Sweden; The Royal Swedish Academy of Sciences, Stockholm, Sweden. Electronic address: hanna.johannesson@su.se.
Jazyk: angličtina
Zdroj: Molecular phylogenetics and evolution [Mol Phylogenet Evol] 2023 Dec; Vol. 189, pp. 107938. Date of Electronic Publication: 2023 Oct 10.
DOI: 10.1016/j.ympev.2023.107938
Abstrakt: 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.
Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
(Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)
Databáze: MEDLINE
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