Annotation and Characterization of the <i>Zacco platypus</i> Genome

The pale chub <i>Zacco platypus</i> (Cypriniformes; Xenocyprididae; Jordan & Evermann, 1902) is widely distributed across freshwater ecosystems in East Asia and has been recognized as a potential model fish species for ecotoxicology and environmental monitoring. Here, a high-quality de novo genome assembly of <i>Z. platypus</i> was constructed through the integration of a combination of long-read Pacific Bioscience (PacBio) sequencing, short-read Illumina sequencing, and Hi-C sequencing technologies. <i>Z. platypus</i> has the smallest genome size compared to other species belonging to the order Cypriniformes. The assembled genome encompasses 41.45% repeat sequences. As shown in other fish, a positive correlation was observed between genome size and the composition of transposable elements (TE) in the genome. Among TEs, a relatively higher rate of DNA transposon was observed, which is a common pattern in the members of the order Cypriniformes. Functional annotation was processed using four representative databases, identifying a core set of 12,907 genes shared among them. Orthologous gene family analysis revealed that <i>Z. platypus</i> has experienced more gene family contraction rather than expansion compared to other Cypriniformes species. Among the uniquely expanded gene families in <i>Z. platypus</i>, detoxification and stress-related gene families were identified, suggesting that this species could represent a promising model for ecotoxicology and environmental monitoring. Taken together, the <i>Z. platypus</i> genome assembly will provide valuable data for omics-based health assessments in aquatic ecosystems, offering further insights into the environmental and ecological facets within this species.