Format

Send to

Choose Destination
Mol Biol Evol. 2015 Apr;32(4):928-43. doi: 10.1093/molbev/msu396. Epub 2014 Dec 21.

Degeneration of the nonrecombining regions in the mating-type chromosomes of the anther-smut fungi.

Author information

1
Ecologie, Systématique et Evolution, Bâtiment 360, Université Paris-Sud, Orsay, France CNRS, Orsay, France.
2
Department of Biology, Amherst College.
3
Ecologie, Systématique et Evolution, Bâtiment 360, Université Paris-Sud, Orsay, France CNRS, Orsay, France Department of Biology, Amherst College.
4
Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France.
5
INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France.
6
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.
7
Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain.
8
CNRS UMR 8030, Evry, France.
9
Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France CNRS UMR 8030, Evry, France.
10
Broad Institute of MIT and Harvard, Cambridge, MA.
11
Department of Biology, Program on Disease Evolution, University of Louisville.
12
Ecologie, Systématique et Evolution, Bâtiment 360, Université Paris-Sud, Orsay, France CNRS, Orsay, France tatiana.giraud@u-psud.fr.

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.

KEYWORDS:

Microbotryum violaceum; PAR; Silene latifolia; Y chromosome; allosomes; autosomes; evolutionary strata; genetic map

PMID:
25534033
PMCID:
PMC4379399
DOI:
10.1093/molbev/msu396
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center