The tomato hind Cephalopholis sonnerati (Valenciennes) (Serranidae), belonging to the genus Cephalopholis, is a bottom dwelling coral reef of 12–120-m depth in the Indo-Pacific and Red Sea. C. sonnerati has also been characterized by complex social structures and behavioural mechanisms. However, due to the lack of genomic resource for C. sonnerati, molecular-genetic studies and genomic breeding remain unexplored in this species. In this study, we reported the chromosome-level genome assembly of C. sonnerati using PacBio sequencing and Hi-C sequencing technologies. We obtained a total length of 1043.66 Mb with an N50 length of 2.49 Mb, containing 795 contigs assembled into 24 chromosomes. Overall 95.8% of the complete BUSCOs were identified in the assembled genome, suggesting the completeness of the genome. Then, we predicted 26,130 protein-coding genes, of which 94.26% were functionally annotated. In addition, C. sonnerati diverged from its common ancestor with E. lanceolatus and E. akaara approximately 41.7 million years ago. Finally, we found tissue-specific expression of 8,108 genes. Functional analyses showed that they mainly consisted of complement and coagulation cascades, DNA replication, synaptic vesicle cycle, long-term potentiation and other glycan degradation. Furthermore, comparative genome analyses indicated that the expanded genes families were highly enriched in the sensory system, which was different from the enrichment analysis of the tissue-specific expression genes. In brief, to our knowledge, we reported the first chromosome-level genome assembly of C. sonnerati, which will provide a valuable genome resource for studies on the genetic conservation, resistance breeding, and evolutionary of C. sonnerati.

Abstract: Most grouper species are functional protogynous hermaphrodites, but the genetic basis and the molecular mechanisms underlying regulation of this unique reproductive strategy remain enigmatic. In this study, we reported a high-quality chromosome-level genome assembly of the representative orange-spotted grouper (Epinephelus coioides). No duplication or deletion of sex differentiation related genes was found in the genome, suggesting that sex development in this grouper may be related to changes in regulatory sequences or environmental factors. Transcriptomic analyses showed that aromatase and retinoic acid are probably critical to promote ovarian fate determination, and follicle-stimulating hormone triggers the female-to-male sex change. Socially controlled sex-change studies revealed that the brain of sex-changing fish in response to social environment may be mediated by activation of phototransduction cascade and the melatonin synthesis pathway. In summary, our genomic and experimental results provide novel insights into the molecular mechanisms of sex differentiation and sex change in the protogynous grouper.

The leopard coral grouper, Plectropomus leopardus, belonging to genus Plectropomus, family Epinephelinae, is a carnivorous coral reef fish widely distributing in the tropical and subtropical water of Indo-Pacific Oceans. Due to its appealing body appearance and delicious taste, P. leopardus has become a popular commercial fish for aquaculture in many countries. However, the lack of genomic and molecular resources for P. leopardus hinders its biological studies and genomic breeding programs. Here we report the de novo sequencing and assembly of P. leopardus genome using 10× Genomics and high-throughput chromosome conformation capture (Hi-C) technologies. Using 127.36 Gb 10× Genomics we generated a 902.90 Mb genome assembly with a contig and scaffold N50 of 31.8 Kb and 33.47 Mb, respectively. The scaffolds were clustered and oriented into 24 pseudo-chromosomes with 13.39 Gb valid Hi-C data. BUSCO analysis showed that 95.3% of the conserved single-copy genes were retrieved, indicating a good entirety of the assembly. We predicted 23,234 protein-coding genes, among which 96.5% were functional annotated. The P. leopardus genome provides a valuable genomic resource for genetics, evolutionary and biological studies of this species. Particularly, it is expected to benefit the development of genomic breeding programs in the farming industry.