Linkage mapping and comparative genomics of red drum (Sciaenops Ocellatus) using next-generation sequencing

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Abstract

Developments in next-generation sequencing allow genotyping of thousands of genetic markers across hundreds of individuals in a cost-effective manner. Because of this, it is now possible to rapidly produce dense genetic linkage maps for nonmodel species. Here, we report a dense genetic linkage map for red drum, a marine fish species of considerable economic importance in the southeastern United States and elsewhere. We used a prior microsatellite-based linkage map as a framework and incorporated 1794 haplotyped contigs derived from high-throughput, reduced representation DNA sequencing to produce a linkage map containing 1794 haplotyped restriction-site associated DNA (RAD) contigs, 437 anonymous microsatellites, and 44 expressed sequence-tag-linked microsatellites (EST-SSRs). A total of 274 candidate genes, identified from transcripts from a preliminary hydrocarbon exposure study, were localized to specific chromosomes, using a shared synteny approach. The linkage map will be a useful resource for red drum commercial and restoration aquaculture, and for better understanding and managing populations of red drum in the wild.

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APA

Hollenbeck, C. M., Portnoy, D. S., Wetzel, D., Sherwood, T. A., Samollow, P. B., & Gold, J. R. (2017). Linkage mapping and comparative genomics of red drum (Sciaenops Ocellatus) using next-generation sequencing. G3: Genes, Genomes, Genetics, 7(3), 843–850. https://doi.org/10.1534/g3.116.036350

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