Abstract
BackgroundThe 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.ResultsWe 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.ConclusionsUnderstanding 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.
Highlights
The assembly and annotation of a genome is a valuable resource for a species, with applications ranging from conservation genomics to gene discovery
We describe the assembly and annotation of the Seriola 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
There were 49,784 transcripts corresponding to 45,251 genes, and of these, 8155 genes had reciprocal best blast hits (RBBH) to orthologs covering at least 50% of the gene sequence in Seriola and in six other fish species (Danio rerio, Lepisosteus oculatus, Oreochromis niloticus, Oryzias latipes, Takifugu rubripes and Xiphophorus maculatus) (Additional file 1)
Summary
The assembly and annotation of a genome is a valuable resource for a species, with applications ranging from conservation genomics to gene discovery. Purcell et al BMC Genomics (2018) 19:31 and livestock breeding for decades, but have only more recently been applied to select aquaculture species (e.g. Rainbow Trout, Atlantic Salmon, tilapia, catfish, flounder, Atlantic Cod) [4, 5] These resources have been used to identify genetic variation underlying phenotypic traits of economic interest for aquaculture production, for example, disease resistance, growth rate, tolerance of environmental stressors, diet/nutrition, reproduction, and general health [5,6,7,8]. Methods to develop these resources provide the best possibilities for genetic improvement of broodstock or culture practices [9]. Generation sequencing (NGS) has revolutionized this area of research through decreasing costs and increasing number of research applications [5], and this has enabled development of genetic resources for a greater number of species [7]
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