Intraspecific Genome Size Variation of the Ocellate Spot Skate Okamejei kenojei Revealed Using Whole Genome Survey Sequencing

Intraspecific genome size variation has important implications in both biological evolution and population genetics. However, such pattern has scarcely been reported in marine chondrichthyans. The skate Okamejei kenojei is an economic species widely distributed in the Northwestern Pacific Ocean. In this study, whole genome resequencing data of an O. kenojei individual collected from coastal waters of Zhoushan, China were generated. The genome size was estimated as 3081.23 Mb, with a heterozygosity of 0.78% and a repeat ratio of 68.12%. The estimated genome size in our study was approximately 0.37 and 1 Gb larger than those of previous studies, suggesting high-level intraspecific genome size variation. The repeat ratios were comparatively consistent with genome sizes. When the repetitive sequences were excluded, the revised genome sizes were comparable (approximately 1 Gb). Therefore, we suggest that the observed genome size variation of O. kenojei might be due to repetitive sequence expansion. Our results provide empirical evidence to demonstrate intraspecific genome size variation of O. kenojei, which should facilitate further genome evolution and phylogenetics studies of this species.