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. 2025 Sep 26;26(1):832.
doi: 10.1186/s12864-025-11996-x.

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

Baojun Zhao #  1 , Chaofan Jin #  1 , Yuhan Jiang  1 , Chunren Huang  2 , Yuting Yang  1 , Mingjian Liu  1 , Haizhan Tang  1 , Da Zheng  1 , Zhenmin Bao  1 , Bo Wang  3 , Jingjie Hu  4
Affiliations

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

Baojun Zhao et al. BMC Genomics. .

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.

Keywords: Epinephelus corallicola; Ancestral karyotype evolution; Eupercaria; Phylogeny.

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Conflict of interest statement

Declarations. Ethics and consent to participate: This study was approved by the Institutional Animal Care and Use Committee of the College of Marine Life Sciences, Ocean University of China (Project Identification Code: 20240810A1). The animal sources were obtained with permission from Sanya Agricultural Investment Marine Industry Co., Ltd., located in Sanya, China. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Chromosomal features of the E. corallicola genome hap1. a Distribution of genomic features. I: Density of genes; II: GC content; III: Density of DNA elements; IV: Density of TE elements. b Hi-C interaction heatmap of 24 chromosomes of hap1 assembly, ordered numerically (Chr1-Chr24)
Fig. 2
Fig. 2
Phylogenetic tree and divergence time estimates of Eupercaria. Blue shaded area: Order Perciformes; Yellow shaded area: Other order of Eupercaria; Red bar: Calibration node (divergence times based on fossil/molecular clock data). Gray box: Node support value of 91%. Red/green text: Number of expanded/contracted gene families
Fig. 3
Fig. 3
Genome evolution. a Ancestral karyotype evolution of Eupercaria; b ANI of six species of Epinephelidae; c KEGG enrichment of expanded gene families of E. corallicola
See this image and copyright information in PMC

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