title: Degeneration of the nonrecombining regions in the mating-type chromosomes of the anther-smut fungi.
abstract: Dimorphic mating-type chromosomes in fungi are excellent models for understanding the genomic consequences of recombination suppression. Their suppressed recombination and reduced effective population size are expected to limit the efficacy of natural selection, leading to genomic degeneration. Our aim was to identify the sequences of the mating-type chromosomes (a1 and a2) of the anther-smut fungi and to investigate degeneration in their nonrecombining regions. We used the haploid a1 Microbotryum lychnidis-dioicae reference genome sequence. The a1 and a2 mating-type chromosomes were both isolated electrophoretically and sequenced. Integration with restriction-digest optical maps identified regions of recombination and nonrecombination in the mating-type chromosomes. Genome sequence data were also obtained for 12 other Microbotryum species. We found strong evidence of degeneration across the genus in the nonrecombining regions of the mating-type chromosomes, with significantly higher rates of nonsynonymous substitution (dN/dS) than in nonmating-type chromosomes or in recombining regions of the mating-type chromosomes. The nonrecombining regions of the mating-type chromosomes also showed high transposable element content, weak gene expression, and gene losses. The levels of degeneration did not differ between the a1 and a2 mating-type chromosomes, consistent with the lack of homogametic/heterogametic asymmetry between them, and contrasting with X/Y or Z/W sex chromosomes.
authors.affiliation: Ecologie, Systématique et Evolution, Bâtiment 360, Université Paris-Sud, Orsay, France CNRS, Orsay, France.
authors.forename: Eric
authors.initials: E
authors.lastname: Fontanillas
authors.affiliation: Department of Biology, Amherst College.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Hood
authors.affiliation: Ecologie, Systématique et Evolution, Bâtiment 360, Université Paris-Sud, Orsay, France CNRS, Orsay, France.
authors.forename: Hélène
authors.initials: H
authors.lastname: Badouin
authors.affiliation: Ecologie, Systématique et Evolution, Bâtiment 360, Université Paris-Sud, Orsay, France CNRS, Orsay, France Department of Biology, Amherst College.
authors.forename: Elsa
authors.initials: E
authors.lastname: Petit
authors.affiliation: Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France.
authors.forename: Valérie
authors.initials: V
authors.lastname: Barbe
authors.affiliation: INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France.
authors.forename: Jérôme
authors.initials: J
authors.lastname: Gouzy
authors.affiliation: Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Université Lyon 1, Villeurbanne, France Université de Lyon, Lyon, France Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Damien M
authors.initials: DM
authors.lastname: de Vienne
authors.affiliation: Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Gabriela
authors.initials: G
authors.lastname: Aguileta
authors.affiliation: CNRS UMR 8030, Evry, France.
authors.forename: Julie
authors.initials: J
authors.lastname: Poulain
authors.affiliation: Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France CNRS UMR 8030, Evry, France.
authors.forename: Patrick
authors.initials: P
authors.lastname: Wincker
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA.
authors.forename: Zehua
authors.initials: Z
authors.lastname: Chen
authors.affiliation: Department of Biology, Program on Disease Evolution, University of Louisville.
authors.forename: Su San
authors.initials: SS
authors.lastname: Toh
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA.
authors.forename: Christina A
authors.initials: CA
authors.lastname: Cuomo
authors.affiliation: Department of Biology, Program on Disease Evolution, University of Louisville.
authors.forename: Michael H
authors.initials: MH
authors.lastname: Perlin
authors.affiliation: Ecologie, Systématique et Evolution, Bâtiment 360, Université Paris-Sud, Orsay, France CNRS, Orsay, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Gladieux
authors.affiliation: Ecologie, Systématique et Evolution, Bâtiment 360, Université Paris-Sud, Orsay, France CNRS, Orsay, France tatiana.giraud@u-psud.fr.
authors.forename: Tatiana
authors.initials: T
authors.lastname: Giraud
mesh_terms: D001483:Base Sequence; D001487:Basidiomycota / Q000235:genetics*; D004251:DNA Transposable Elements; D017353:Gene Deletion; D049770:Genes, Mating Type, Fungal; D008969:Molecular Sequence Data; D010802:Phylogeny; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D012730:Sex Chromosomes
chemical_list: D004251:DNA Transposable Elements
keywords: Microbotryum violaceum; PAR; Silene latifolia; Y chromosome; allosomes; autosomes; evolutionary strata; genetic map