Southwest Fisheries Science Center, National Marine Fisheries Service, 8901 La Jolla Shores Drive, La Jolla, CA, 92037, USA.
Genome Informatics Facility, Iowa State University, 206 Science I, Ames, IA, 50011, USA.
BMC Genomics. 2018 Jan 8;19(1):31. doi: 10.1186/s12864-017-4403-1.
The assembly and annotation of a genome is a valuable resource for a species, with applications ranging from conservation genomics to gene discovery. Genomic resource development is especially important for species in culture, such as the California Yellowtail (Seriola dorsalis), the likely candidate for the establishment of commercial offshore aquaculture production in southern California. Genomic resource development for this species will improve the understanding of sex and other phenotypic traits, and allow for rapid increases in genetic improvement for and economic gain in culture production.
We describe the assembly and annotation of the S. dorsalis genome, and present resequencing data from 45 male and 45 female wild-caught S. dorsalis used to identify a sex-determining region and marker in this species. The genome assembly captured approximately 93% of the total 685 MB genome with an average coverage depth of 180×. Using the assembled genome, resequencing data from the 90 fish were aligned to place boundaries on the sex-determining region. Sex-specific markers were developed based on a female-specific, 61 nucleotide deletion identified in that region. We hypothesize that Estradiol 17-beta-dehydrogenase is the putative sex-determining gene and propose a plausible genetic mechanism for ZW sex determination in S. dorsalis involving a female-specific deletion of a transcription factor binding motif that may be targeted by Sox3.
Understanding the mechanism of sex determination and development of assays to determine sex is critical both for management of wild fisheries and for development of efficient and sustainable aquaculture practices. In addition, this genome assembly for S. dorsalis will be a substantial resource for a variety of future research applications.
基因组的组装和注释是一个物种的宝贵资源，其应用范围从保护基因组学到基因发现。基因组资源的开发对于养殖物种尤为重要，例如加利福尼亚黄尾（Seriola dorsalis），它是在南加州建立商业近海水产养殖生产的可能候选物种。该物种的基因组资源开发将提高对性别和其他表型特征的理解，并允许快速提高遗传改良和文化生产的经济效益。
我们描述了 S. dorsalis 基因组的组装和注释，并展示了来自 45 条野生捕获的 S. dorsalis 雄性和 45 条野生捕获的 S. dorsalis 雌性的重测序数据，用于鉴定该物种中的性别决定区域和标记。基因组组装捕获了大约 93%的总 685 MB 基因组，平均覆盖深度为 180×。使用组装的基因组，将来自 90 条鱼的重测序数据与该区域的性别决定区域进行比对，以确定边界。基于在该区域中鉴定出的 61 个核苷酸缺失的雌性特异性标记，开发了性别特异性标记。我们假设雌二醇 17-β-脱氢酶是潜在的性别决定基因，并提出了 S. dorsalis 中 ZW 性别决定的合理遗传机制，涉及转录因子结合基序的雌性特异性缺失，该基序可能是 Sox3 的靶标。
了解性别决定的机制和开发用于确定性别的测定方法对于野生渔业的管理和高效可持续水产养殖实践的发展都至关重要。此外，S. dorsalis 的这个基因组组装将成为未来各种研究应用的重要资源。
