Centromere evolution and CpG methylation during vertebrate speciation

Kazuki Ichikawa, Shingo Tomioka, Yuta Suzuki, Ryohei Nakamura, Koichiro Doi, Jun Yoshimura, Masahiko Kumagai, Yusuke Inoue, Yui Uchida, Naoki Irie, Hiroyuki Takeda () and Shinich Morishita ()
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Kazuki Ichikawa: The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa
Shingo Tomioka: The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa
Yuta Suzuki: The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa
Ryohei Nakamura: The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku
Koichiro Doi: The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa
Jun Yoshimura: The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa
Masahiko Kumagai: The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku
Yusuke Inoue: The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku
Yui Uchida: The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku
Naoki Irie: The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku
Hiroyuki Takeda: The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku
Shinich Morishita: The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa

Nature Communications, 2017, vol. 8, issue 1, 1-11

Abstract: 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.

Date: 2017
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DOI: 10.1038/s41467-017-01982-7

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