Chromosome-level genome assembly of the coral grouper, Epinephelus corallicola and its evolutionary insights into Eupercaria

Abstract

Background: Epinephelus corallicola, also known as the coral grouper, is an economically valuable grouper species widely distributed in Southeast Asia. However, its genomic information and phylogenetic status remain unclear. Furthermore, despite substantial genomic resources accumulated for Eupercaria, integrated analyses of phylogenetic relationships and genome evolution based on these resources remain scarce. Results: In this study, we generated high-quality haplotype-solved genomes of E. corallicola, with total lengths of 1.086 Gb and 1.083 Gb for the two haplotypes, and contig N50 values of 44.94 Mb and 43.86 Mb, respectively. Phylogenomic analyses placed the Perciformes at the basal position of the Eupercaria, with an estimated divergence time of 88.55 Mya. And the phylogenetic topology supported the previous proposal to elevate Epinephelinae to the family level as Epinephelidae, distinct from Serranidae. Ancestral karyotype evolution analyses based on chromosomal genomes of 33 species revealed that E. corallicola serves as a representative model for the 24 ancestral linkage groups (ALGs) of Eupercaria, enabling the tracing of ancient chromosomal evolution across lineages. Within the Epinephelidae, the whole-genome average nucleotide identity (ANI) among species ranged from 84.16% to 96.97%. Gene family expansion and contraction analyses revealed 285 significantly expanded and 618 contracted gene families. Notably, the expanded gene families were significantly enriched in immune-related genes, including MHCIIα, MHCIIβ, and RFX5, which may contribute to the adaptive evolution of E. corallicola. Conclusions: Our results provide important genomic resources for Epinephelidae, advancing aquaculture and selective breeding programs for groupers, while offering new insights into the phylogeny and ancestral chromosomal karyotype evolution of Eupercaria.