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.
JST CREST （http://www.jst.go.jp/kisoken/crest/en/）
Research Area “Creation of Fundamental Technologies for Understanding and Control of Biosystem Dynamics”
Research Theme “Understanding and Predicting 3D Chromatin Dynamics”
Ichikawa K, Tomioka S, Suzuki Y, Nakamura R, Doi K, Yoshimura J, Kumagai M, Inoue Y, Uchida Y, Irie N, Takeda H, and Morishita S. “Centromere evolution and CpG methylation during vertebrate speciation”, Nature Communications, Published online Nov. 28, 2017, doi: 10.1038/s41467-017-01982-7.
Professor, Graduate School of Frontier Sciences, The University of Tokyo
Life Innovation Group, Department of Innovation Research, JST