Chromosome-Level Genome Assembly and Transcriptome Comparison Analysis of Cephalopholis sonnerati and Its Related Grouper Species

Abstract

The tomato hind, Cephalopholis sonnerati, is a bottom-dwelling coral reef fish, which is widely distributed in the Indo-Pacific and Red Sea. C. sonnerati also features complex social structures and behaviour mechanisms. Here, we present a high-quality, chromosome-level genome assembly for C. sonnerati that was derived using PacBio sequencing and Hi-C technologies. A 1043.66 Mb genome with an N50 length of 2.49 Mb was assembled, produced containing 795 contigs assembled into 24 chromosomes. Overall, 97.2% of the complete BUSCOs were identified in the genome. A total of 26,130 protein-coding genes were predicted, of which 94.26% were functionally annotated. Evolutionary analysis revealed that C. sonnerati diverged from its common ancestor with E. lanceolatus and E. akaara approximately 41.7 million years ago. In addition, comparative genome analyses indicated that the expanded gene families were highly enriched in the sensory system. Finally, we found the tissue-specific expression of 8108 genes. We found that these tissue-specific genes were highly enriched in the brain. In brief, the high-quality, chromosome-level reference genome will provide a valuable genome resource for studies of the genetic conservation, resistance breeding, and evolution of C. sonnerati.

Mitogenomic Characterization and Phylogenetic Placement of African Hind, Cephalopholis taeniops: Shedding Light on the Evolution of Groupers (Serranidae: Epinephelinae)

“…Within the Serranidae family, focused investigations on Cephalopholis species have primarily addressed aspects such as physiology and reproductive life history [18,19], genetic connectivity, phylogeography, evolutionary implications through Pleistocene isolation [20,21], and the assembly of chromosome-level genomes alongside transcriptome comparisons [22]. Further, in conjunction with other serranid species, comprehensive examinations of the phylogenetic relationships of Cephalopholis species have involved the utilization of two mitochondrial (16S rRNA and 12S rRNA) and two nuclear (Tmo-4C4 and histone H3) genes [23,24].…”

Chromosome-level genome assembly and annotation of the yellow grouper, Epinephelus awoara

“…In conclusion, groupers hold significant ecological aimportance and commercial value. In recent years, several high-quality chromosome-level assemblies of grouper reference genomes have been assembled, including seven species of the Epinephelus genus [5][6][7][8][9][10][11][12][13] , one species of the Plectropomus genus [14][15][16][17] , one species of the Cromileptes genus 18 , and one species of the Cephalopholis genus 19 , which provide important genomic resources for evolutionary analysis, molecular-assisted breeding, and germplasm conservation of groupers. Phylogenetic studies show that Epinephelus species in the western Pacific Ocean have diverged into two genetic clades with variations in body size 20,21 , implying the potential presence of independent evolutionary trajectories during the course of adaptation.…”

Utilizing ISSRseq genotyping to assist growth selection in tomato grouper (Cephalopholis sonnerati) without broodstock information

“…The aquaculture industry has experienced tremendous growth in recent years, driven by the increasing global demand for seafood. One emerging aquaculture species is the tomato grouper ( Cephalopholis sonnerati ), a marine fish belonging to the family Serranidae (Rimmer & Glamuzina, 2019; Xie et al, 2022). This species is native to the Indo‐Pacific region and is highly valued for its delicious taste and firm texture (Morris et al, 2000; Rimmer & Glamuzina, 2019).…”

“…This species is native to the Indo‐Pacific region and is highly valued for its delicious taste and firm texture (Morris et al, 2000; Rimmer & Glamuzina, 2019). The tomato grouper has a generation cycle of at least 5 to 10 years, which poses challenges for breeding efforts in aquaculture (Rimmer & Glamuzina, 2019; Xie et al, 2022). In current aquaculture practices, it is common to employ mixed cultures of broodstock and natural mating, often without detailed broodstock information, which can lead to difficulties in controlling and optimizing the breeding process.…”