July 19, 2019  |  

Centromere evolution and CpG methylation during vertebrate speciation.

Authors: Ichikawa, Kazuki and Tomioka, Shingo and Suzuki, Yuta and Nakamura, Ryohei and Doi, Koichiro and Yoshimura, Jun and Kumagai, Masahiko and Inoue, Yusuke and Uchida, Yui and Irie, Naoki and Takeda, Hiroyuki and Morishita, Shinich

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.

Journal: Nature communications
DOI: 10.1038/s41467-017-01982-7
Year: 2017

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