Abstract
Large yellow croaker (Larimichthys crocea) has been demonstrated to be divided into three geographical stocks from south to north along the coast of China, including Nanhai, Mindong, and Daiqu. Although multiple versions of L. crocea have been published, no high-quality Nanhai and Daiqu genomes have been assembled, hampering the assessment of the fine-scale genetic structure and adversely affecting wild stock conservation, fishery management, and germplasm exploitation of large yellow croaker. To fill the gap, we sequenced the genomes of three L. crocea stocks using a combination of PacBio and Hi-C technologies. We assembled each genome (~712 Mb) into 24 chromosomes with a contig N50 of 19.46-29.71 Mb and an integration efficiency of 88.13-92.80%. Furthermore, 26,851-28,133 protein-coding genes were predicted. The reference genomes of three geographical stocks of L. crocea provide vital resources for future research on the conservation and utilization of genetic diversity.