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

Humans Phylogeny Genomics / methods Genome Sordariales / genetics Base Sequence Evolution, Molecular
Chaetomiaceae Genome evolution Podosporaceae Sordariaceae Whole-genome phylogeny

Journal

Molecular phylogenetics and evolution
ISSN: 1095-9513
Titre abrégé: Mol Phylogenet Evol
Pays: United States
ID NLM: 9304400

Informations de publication

Date de publication:
Dec 2023
Historique:
received: 26 06 2023
revised: 28 09 2023
accepted: 04 10 2023
medline: 28 11 2023
pubmed: 12 10 2023
entrez: 11 10 2023
Statut: ppublish

Résumé

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.

Identifiants

DOI: 10.1016/j.ympev.2023.107938 PMID: 37820761
pubmed: 37820761
pii: S1055-7903(23)00238-5
doi: 10.1016/j.ympev.2023.107938
pii:
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

107938

Informations de copyright

Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.

Déclaration de conflit d'intérêts

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.

Auteurs

Noah Hensen (N)

Stockholm University, Department of Ecology, Environment and Plants Sciences, Stockholm, Sweden.

Lucas Bonometti (L)

University of Montpellier, PHIM Plant Health Institute, Montpellier, France.

Ivar Westerberg (I)

Stockholm University, Department of Ecology, Environment and Plants Sciences, Stockholm, Sweden.

Ioana Onut Brännström (IO)

Oslo University, Natural History Museum, Oslo, Norway; Uppsala University, Department of Ecology and Genetics, Uppsala, Sweden.

Sonia Guillou (S)

University of Montpellier, PHIM Plant Health Institute, Montpellier, France.

Sandrine Cros-Aarteil (S)

University of Montpellier, PHIM Plant Health Institute, Montpellier, France.

Sara Calhoun (S)

Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA.

Sajeet Haridas (S)

Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA.

Alan Kuo (A)

Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA.

Stephen Mondo (S)

Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA.

Jasmyn Pangilinan (J)

Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA.

Robert Riley (R)

Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA.

Kurt LaButti (K)

Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA.

Bill Andreopoulos (B)

Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA.

Anna Lipzen (A)

Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA.

Cindy Chen (C)

Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA.

Mi Yan (M)

Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA.

Chris Daum (C)

Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA.

Vivian Ng (V)

Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA.

Alicia Clum (A)

Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA.

Andrei Steindorff (A)

Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA.

Robin A Ohm (RA)

Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA.

Francis Martin (F)

Université de Lorraine, INRAE, Champenoux, France.

Philippe Silar (P)

Université de Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain, Paris, France.

Donald O Natvig (DO)

University of New Mexico, Department of Biology, Albuquerque, USA.

Christophe Lalanne (C)

Université de Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain, Paris, France.

Valérie Gautier (V)

Université de Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain, Paris, France.

Sandra Lorena Ament-Velásquez (SL)

Stockholm University, Department of Zoology, Stockholm, Sweden.

Åsa Kruys (Å)

Uppsala University, Museum of Evolution, Uppsala, Sweden.

Miriam I Hutchinson (MI)

University of New Mexico, Department of Biology, Albuquerque, USA.

Amy Jo Powell (AJ)

Sandia National Laboratories, Dept. of Systems Design and Architecture, Albuquerque, USA.

Kerrie Barry (K)

Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA.

Andrew N Miller (AN)

University of Illinois Urbana-Champaign, Illinois Natural History Survey, USA.

Igor V 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.

Robert Debuchy (R)

Université Paris-Saclay, Institute for Integrative Biology of the Cell, Gif-sur-Yvette, France.

Pierre Gladieux (P)

University of Montpellier, PHIM Plant Health Institute, Montpellier, France.

Markus Hiltunen Thorén (M)

Stockholm University, Department of Ecology, Environment and Plants Sciences, Stockholm, Sweden; The Royal Swedish Academy of Sciences, Stockholm, Sweden.

Hanna 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.

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Genome-scale phylogeny and comparative...
questionsmedicales.fr › Sciences de l'information › Phylogenèse › Genome-scale phylogeny and comparative...
questionsmedicales.fr › Disciplines des sciences naturelles › Disciplines des sciences biologiques › Biologie › Génétique › Génomique › Genome-scale phylogeny and comparative...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Genome-scale phylogeny and comparative...
questionsmedicales.fr › Eucaryotes › Champignons › Ascomycota › Sordariales › Genome-scale phylogeny and comparative...
questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Données de séquences moléculaires › Séquence nucléotidique › Genome-scale phylogeny and comparative...
questionsmedicales.fr › Phénomènes biologiques › Évolution biologique › Évolution moléculaire › Genome-scale phylogeny and comparative...