Whole-Genome Sequencing of Hexagrammos otakii Provides Insights into Its Genomic Characteristics and Population Dynamics

Hexagrammos otakii, also commonly called "Fat Greenling", is highly valued as an important commercial fish due to its extremely delicious flesh. However, the absence of a genomic resource has limited our understanding of its genetic characteristics and hindered artificial breeding efforts. In this study, we performed Illumina paired-end sequencing of H. otakii, generating a total of 73.19 Gb of clean data. Based on K-mer analysis, the genome size was estimated to be 679.23 Mb, with a heterozygosity rate of 0.68% and a repeat sequence proportion of 43.60%. De novo genome assembly using SOAPdenovo2 resulted in a draft genome size of 723.31 Mb, with the longest sequence length being 86.24 Kb. Additionally, the mitochondrial genome was also assembled, which was 16,513 bp in size, with a GC content of 47.20%. Minisatellites were the most abundant tandem repeats in the H. otakii genome, followed by microsatellites. In the phylogenetic tree, H. otakii was placed within a well-supported clade (bootstrap support = 100%) that included S. sinica, N. coibor, L. crocea, and C. lucidus. PSMC analysis revealed that H. otakii underwent a population bottleneck during the Pleistocene, peaking around 500 thousand years ago (Kya) and declining to a minimum during the Last Glacial Period (similar to 70-15 Kya), with no significant recovery observed by similar to 10 Kya. This study was a comprehensive genome survey analysis of H. otakii, providing insights into its genomic characteristics and population dynamics.