A chromosomal-level genome assembly of the American shad: insights into phylogenetic relationships

American shad is an important fishery species distributed in North America. It was introduced to China in 2003 and has become one of China's most expensive aquaculture species. Here we report a high-quality, chromosomal-level genome assembly using the PacBio sequencing platform and tissue-specific transcriptomic data. The results showed the genome size is 920 Mb, with G + C content of 43.19%, contig N50 and scaffold N50 of 1.15 and 37.99 Mb. All the sequences can be successfully clustered on 24 chromosomes, with an attachment rate of 97.51%. 28,120 coding genes encoding 29,212 proteins were identified. A phylogenetic tree was constructed based on 250 single-copy orthologous genes selected from 20,706 gene families with 18 fish species, which suggests it is most closely related to European pilchard. For genome comparison, 1,017 expanded and 2,573 contracted gene families, including 81 expanded and 143 contracted ones were identified. One hundred and sixty nine unique gene families were obtained, which can explain the biological traits. Enrichment analysis of tandem duplicated genes and positively selected genes showed that terms related to biological processes for basic life activities were enriched, such as gene expression, biosynthesis, metabolism, movement, and immunization. The data can provide invaluable information to understand habitual natureo American shad.