Chromosome-Level Genome Assembly of the Japanese Zacco platypus for Comparative Genomics

Zacco platypus is a freshwater minnow widely distributed across East Asia, noted for its high environmental adaptability, strong reproductive capacity, and ability to hybridize across genera. The type specimen was described from Japan, yet no representative genome from the Japanese lineage has been reported to date. Introduced to Taiwan in the 1980s, Z. platypus rapidly established a stable population. In this study, we assembled a chromosome-level genome from a Taiwanese population and resequenced a native Japanese individual, providing genomic evidence that the Taiwanese lineage originated from Japan. The assembly and gene annotation achieved BUSCO completeness scores of 98.9% and 96.6%, respectively, representing the highest quality reported among published Z. platypus genomes. Furthermore, we identified chromosomal structural variation among populations, and both PCA and genetic distance analyses revealed that the Japanese lineage is distinct from continental populations, indicating the importance of representative genomes across geographic lineages. This high-quality genome provides a valuable resource for future research in comparative genomics, population genetics, hybridization, speciation, and evolutionary biology.