RRC ID |
64272
|
著者 |
Ichikawa K, Tomioka S, Suzuki Y, Nakamura R, Doi K, Yoshimura J, Kumagai M, Inoue Y, Uchida Y, Irie N, Takeda H, Morishita S.
|
タイトル |
Centromere evolution and CpG methylation during vertebrate speciation.
|
ジャーナル |
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.
|
巻・号 |
8(1)
|
ページ |
1833
|
公開日 |
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
|
リソース情報 |
メダカ |
HdrR-II1 (IB178)
HNI-II (IB176)
HSOK (IB183) |