A chromosome-level genome assembly of Hemibarbus maculatus

Hemibarbus maculatus, a keystone cyprinid species widely distributed across Asian freshwater ecosystems, holds dual significance as an economically valuable food fish and an ecological regulator. In this study we present its first chromosome-level genome assembly by integrating PacBio HiFi reads and Hi-C scaffolding. The 1.08 Gb assembly achieves exceptional continuity with a scaffold N50 of 43.84 Mb, where 98.23% sequences are anchored to 25 pseudochromosomes. BUSCO assessment confirmed 99.1% completeness, with 30.02% repetitive elements and 23,892 predicted protein-coding genes. High-resolution Hi-C interaction maps and cross-species synteny analyses validated chromosomal-scale assembly accuracy. The phylogenetic reconstruction of 10 Cyprinidae species resolves the divergence time framework within the Gobioninae subfamily, revealing that H. maculatus diverged from Rhinogobio nasutus ~12.3 Mya and shares a common ancestor with Pseudorasbora parva at ~18.3 Mya during mid-Miocene freshwater habitat radiation. This resource establishes foundational infrastructure for decoding population genomics, ecological adaptations, and precision aquaculture of H. maculatus, while facilitating evolutionary studies within Cyprinidae.