Epinephelus cyanopodus is a coral reef-dwelling grouper with important economic and ecological value and is widely distributed in the western Pacific Ocean. The lack of genomic resources for E. cyanopodus hinders its adaptive evolution and phylogeny research. We constructed the first high-quality genome of E. cyanopodus based on DNBSEQ, PacBio, and Hic sequencing technologies, with a genome size of 998.82 Mb, contig N50 of 5.855 Mb, and scaffold N50 of 41.98 Mb. More than 99.7% of contigs were anchored to 24 pseudochromosomes, and 94.2% of BUSCO genes were found in the E. cyanopodus genome, indicating a high genome assembly completeness. A total of 26,337 protein-coding genes were predicted, of which 98.77% were functionally annotated. Phylogenetic analysis showed that E. cyanopodus separated from its closely related species Epinephelus akaara about 11.5–26.5 million years ago, and the uplift of the Indo-Australian archipelago may have provided an opportunity for its rapid radiation. Moreover, several gene families associated with innate and adaptive immunity were significantly expanded in speckled blue grouper compared to other teleost genomes. Additionally, we identified several genes associated with immunity, growth and reproduction that are under positive selection in E. cyanopodus compared to other groupers, suggesting that E. cyanopodus has evolved broad adaptability in response to complex survival environment, which may provide the genetic basis for its rapid radiation. In brief, the high-quality reference genome of the speckled blue grouper provides a foundation for research on its biological traits and adaptive evolution and will be an important genetic tool to guide aquaculture and resolve its taxonomic controversies in future studies.

The grouper Epinephelus rankini, described from the waters off Western Australia, has long been regarded as a junior synonym of Epinephelus multinotatus. However, the two species are discernible as distinct species on the basis of their morphological characteristics and genetic differences by the holotype material and non-type of specimens. In this study, Epinephelus rankini is considered as a valid species and re-described based on the examination of the holotype and additional specimens. Epinephelus rankini can be distinguished from the closely-related species E. multinotatus by the following combination of characters: body dark greyish-brown to chocolate with irregular white blotches (vs. body pale brownish-grey with irregular and small white blotches in E. multinotatus), absence of small dark brown spots (vs. numerous small dark brown spots in E. multinotatus). Furthermore, genetic differences between the two species strongly support the validity of both species based on molecular analysis (mtDNA, COI gene). In addition based on the sampling range, E. rankini was observed range from the Abrolhos Islands of Western Australia to south-eastern Indonesia, while E. multinotatus ranges from the Persian Gulf to southern Mozambique.

In this study, we identified the important contribution of frontal bone remodeling in shaping the ‘sunken head and humpback’ appearance in C. altivelis. Our investigation identified a developmental milestone at a total length of 5–6 cm, making the onset of its morphologic specialization in this species. A comparative analysis with closely related species reveals heightened activity in the frontal osteoblasts of the humpback grouper, potentially providing a physiological basis for its remodeling. Furthermore, our findings highlight that a significant upregulation in the expression levels of Ihhb, Ptch1, and Gli2a genes was seen in C. altivelis within the specified developmental stage, indicating an important involvement of the Ihhb-Ptch1-Gli2a signaling pathway in initiating the morphological specialization. We hypothesized that Ihh signaling could be attributed to shifts in mechanical stress, resulting from muscle traction on the frontal bone due to changes in swimming patterns during development. This study not only offers significant insights into unraveling the molecular mechanisms that govern phenotypic specialization and ecological adaptations in the humpback grouper but also serves as a valuable reference for studies on fishes with a controversial morphology and molecular phylogeny.