Assembly of Genome and Resequencing Provide Insights into Genetic Differentiation between Parents of Hulong Hybrid Grouper (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂)

Abstract

The Hulong hybrid grouper was bred from the brown-marbled grouper (Epinephelus fuscoguttatus) ♀ and the giant grouper (E. lanceolatus) ♂, combining the advantageous traits of both parents. Possessing an excellent performance, this hybrid’s cultivation promotes the development of the grouper industry. Its male parent, the giant grouper, possesses the fastest growth and the largest body size among all coral-reef-dwelling fish. This species is not only an economically important species in marine aquaculture, but it is also an ideal male parent in the interspecific crossing of grouper species. In the present study, a high-quality chromosome-level genome of the giant grouper was constructed with a total length of 1.06 Gb, consisting of 24 chromosomes and 69 scaffolds. To analyze the genetic differences between the parents of the Hulong hybrid grouper, the structural variations (SVs) between both parental genomes were detected, and a total of 46,643 SVs were obtained. High-quality SNPs were identified from resequencing data. There were significant differences between the two genomes, and the average FST reached 0.685. A total of 234 highly differentiated regions were detected with an FST > 0.9. The protein-coding genes involved in SVs and highly differentiated regions were significantly enriched in metabolic pathways, including fatty metabolism, carbohydrate metabolism, amino acid metabolism and the TCA cycle. These genes may be related to the differences in feeding preferences and the ability to digest carbohydrates between the two grouper species under natural conditions. In addition, protein-coding genes related to the cell cycle and p53-signaling pathway were also detected. These genes may play important roles in the regulation of body size and growth performance. This research provides genomic resources for further breeding works and evolutionary analyses.

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.…”

“…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. However, a significant limitation exists, as reference genomes are available for seven species within the large-bodied clade 5,[7][8][9][10][11][12][13]18 , whereas the small-bodied clade has an accessible reference genome for only one Library construction and sequencing. All the DNA extraction, library construction and sequencing procedures were performed by the Nextomics Biosciences (Wuhan, China) according to the manufacturer's protocols.…”