Centromere evolution and CpG methylation during vertebrate speciation.
Nat Commun, 2017/11/28;8(1):1833.
Ichikawa K[1], Tomioka S[1], Suzuki Y[1], Nakamura R[2], Doi K[1], Yoshimura J[1], Kumagai M[2], Inoue Y[2], Uchida Y[2], Irie N[2], Takeda H[3], Morishita S[4]
Affiliations
PMID: 29184138DOI: 10.1038/s41467-017-01982-7
Impact factor: 17.694
Abstract
Centromeres and large-scale structural variants evolve and contribute to genome diversity during vertebrate speciation. Here, we perform de novo long-read genome assembly of three inbred medaka strains that are derived from geographically isolated subpopulations and undergo speciation. Using single-molecule real-time (SMRT) sequencing, we obtain three chromosome-mapped genomes of length ~734, ~678, and ~744Mbp with a resource of twenty-two centromeric regions of length 20-345kbp. Centromeres are positionally conserved among the three strains and even between four pairs of chromosomes that were duplicated by the teleost-specific whole-genome duplication 320-350 million years ago. The centromeres do not all evolve at a similar pace; rather, centromeric monomers in non-acrocentric chromosomes evolve significantly faster than those in acrocentric chromosomes. Using methylation sensitive SMRT reads, we uncover centromeres are mostly hypermethylated but have hypomethylated sub-regions that acquire unique sequence compositions independently. These findings reveal the potential of non-acrocentric centromere evolution to contribute to speciation.
MeSH terms
Animals; Base Sequence; Centromere; Chromosome Mapping; CpG Islands; Evolution, Molecular; Genetic Association Studies; Genetic Markers; Genetic Speciation; Genetic Variation; Genome; Methylation; Models, Theoretical; Molecular Sequence Annotation; Mutation; Oryzias; Phylogeny; Polymorphism, Single Nucleotide; Telomere; Vertebrates
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