RRC ID 64272
Author Ichikawa K, Tomioka S, Suzuki Y, Nakamura R, Doi K, Yoshimura J, Kumagai M, Inoue Y, Uchida Y, Irie N, Takeda H, Morishita S.
Title Centromere evolution and CpG methylation during vertebrate speciation.
Journal Nat Commun
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.
Volume 8(1)
Pages 1833
Published 2017-11-28
DOI 10.1038/s41467-017-01982-7
PII 10.1038/s41467-017-01982-7
PMID 29184138
PMC PMC5705604
MeSH Animals Base Sequence Centromere / classification Centromere / genetics* Chromosome Mapping CpG Islands* Evolution, Molecular Genetic Association Studies Genetic Markers Genetic Speciation* Genetic Variation Genome Methylation Models, Theoretical Molecular Sequence Annotation Mutation Oryzias / genetics Phylogeny Polymorphism, Single Nucleotide Telomere / genetics Vertebrates / genetics*
IF 12.121
Medaka HdrR-II1 (IB178) HNI-II (IB176) HSOK (IB183)