A dataset of whole-genome sequencing and genomic variants for the American Shad, Alosa sapidissima, from the Neuse River, North Carolina

Genetic data are critical for informing future conservation decisions for the American Shad, <i>Alosa sapidissima</i>, an economically important fish in the eastern coast of the United States. To improve genomic resources for this species, we generated more than 230 Gbp of whole-genome sequencing data from an individual American Shad collected from a hatchery with parentage from the Neuse River in North Carolina, USA. These data included 94.7 Gbp from a paired-end 500-bp insert library, 68.5 Gbp from a 5-7 Kbp insert mate-pair library, and 67.5 Gbp from a 10-12 Kbp insert mate-pair library, all of which were sequenced on an Illumina NovaSeq 6000. These sequencing data were cleaned, trimmed, and aligned to an existing American Shad reference genome. The resulting variants are described, including possible effects of variants and high-impact variants by annotated gene. A total of 3.8 million variants were identified across the genome, averaging 1 variant every 237 bp. Of these variants, 64.5% were single nucleotide polymorphisms, 35.5% were insertion-deletion polymorphisms, and a total of 11.3 million variant effects were annotated. Future analyses of specific genes outlined by these data may be valuable in research on anadromy and life history in the American Shad and other migratory fish in addition to providing useful genomic resources for the conservation and management of this ecologically and economically important species.