A Complete Telomere-To-Telomere Assembly of Plectropomus leopardus and Phylogenomic Insights Into Perciformes

The leopard coral grouper, Plectropomus leopardus Lacepède, 1802, is an ecologically and economically important species in the family Epinephelidae. However, the absence of a complete reference genome has impeded advanced genetic research on this species, and the phylogenetic position of Epinephelidae within Perciformes remains unresolved. Here, we generated a complete telomere-to-telomere (T2T) genome assembly (887.20 Mb; contig N50: 39.03 Mb; QV: 67) for P. leopardus with no need for gap-filling. Leveraging this genome combined with other available genome resources, we conducted a large-scale genomic re-annotation and reconstructed a robust genome-level phylogeny of the Perciformes. Our analysis revealed that Epinephelidae and Anthiadidae form a monophyletic clade situated at the base of the Perciformes, indicating that the traditional suborder Serranoidei is non-monophyletic. Comparative genomic analysis revealed that differential expansions of transposable elements represented the primary driver of genome size variation among P. leopardus and other groupers. Furthermore, we constructed a high-density haplotype reference panel using 110 individuals and annotated 1068 loss-of-function (LoF) mutations. Enrichment analysis indicated that genes with stop-gain LoF mutations are involved in the immune response and skin color variation. This study provides an essential genomic resource for P. leopardus and offers fundamental evolutionary insights into the Epinephelidae and, more broadly, the order Perciformes.