Centromere evolution and CpG methylation during vertebrate speciation

• DOI: 10.1038/s41467-017-01982-7
• Publication Date: 2017-11-22T16:44:29Z
• Authors: Kazuki Ichikawa; Shingo Tomioka; Yuta Suzuki; Ryohei Nakamura; Koichiro Doi; Jun Yoshimura; Masahiko Kumagai; Yusuke Inoue; Yui Uchida; Naoki Irie; Hiroyuki Takeda; Shinich Morishita
• Keywords: Genetic Markers; Genetic Speciation; Science; Centromere; Oryzias; Methylation; Polymorphism, Single Nucleotide; Article; Evolution, Molecular; 03 medical and health sciences; Animals; Genetic Association Studies; Phylogeny; 0303 health sciences; Genome; Base Sequence; Q; Chromosome Mapping; Genetic Variation; Molecular Sequence Annotation; Models, Theoretical; Telomere; Mutation; Vertebrates; CpG Islands

AbstractCentromeres 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.