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.
Lian et al. (Thu,) studied this question.