Whole-genome sequencing and resequencing for genome-wide identification of candidate sex-specific markers in the camouflage grouper (Epinephelus polyphekadion)

Abstract

As an endangered reef fish, the camouflage grouper (Epinephelus polyphekadion) has been recently cultured in south China costal area. The prevalent utilization of males E. polyphekadion in distant hybridization highlights the economic and ecological importance of developing genetic methods for accurate sex identification at early developmental stages. Here, we present a 1.08-Gb chromosome-level genome assembly for E. polyphekadion by using Illumina short-read, PacBio long-read, and Hi-C sequencing technologies. Remarkably, 99.69 % of the scaffolds were anchored onto 24 chromosomes, with contig N50 and scaffold N50 values of 28.09 Mb and 45.93 Mb, respectively. The genome comprises 42.85 % repetitive sequences and is annotated with 24,067 protein-coding genes, achieving a 98.37 % functional annotation rate. BUSCO analysis confirmed 98.0 % completeness, attesting to the assembly's high quality. Importantly, through whole-genome resequencing, we identified two sex-specific markers (three SNP sites), enabling a PCR-based gender identification assay for E. polyphekadion. Comparative genomic analyses with other Perciformes reveal Epinephelinae evolutionary trajectories across chromosomes. This study not only advances our understanding of the genetic and evolutionary dynamics of E. polyphekadion but also provides a crucial resource for genetic breeding and studies on gonadal development in reef fishes.