Genetic mechanism of body size variation in groupers: Insights from phylotranscriptomics

Abstract

Animal body size variation is of particular interest in evolutionary biology, but the genetic basis remains largely unknown. Previous studies have shown the presence of two parallel evolutionary genetic clusters within the fish genus Epinephelus with evident divergence in body size, providing an excellent opportunity to investigate the genetic basis of body size variation in vertebrates. Herein, we performed phylotranscriptomic analysis and reconstructed the phylogeny of 13 epinephelids originating from the South China Sea. Two genetic clades with an estimated divergence time of approximately 15.4 million years ago were correlated with large and small body size, respectively. A total of 180 rapidly evolving genes and two positively selected genes were identified between the two groups. Functional enrichment analyses of these candidate genes revealed distinct enrichment categories between the two groups. These pathways and genes may play important roles in body size variation in groupers through complex regulatory networks. Based on our results, we speculate that the ancestors of the two divergent groups of groupers may have adapted to different environments through habitat selection, leading to genetic variations in metabolic patterns, organ development, and lifespan, resulting in body size divergence between the two locally adapted populations. These findings provide important insights into the genetic mechanisms underlying body size variation in groupers and species differentiation.

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

“…Notably, yellow grouper is one of the few grouper species capable of inhabiting higher latitudes, approximately around the 40th parallel north (40 °N). It is worth noting that the yellow grouper is a protogynous hermaphroditic fish 23 , belongs to the small-sized clade of Epinephelus species in the western Pacific Ocean 20 , 21 . It serves as valuable material for exploring sex change and body size differentiation in groupers.…”

“…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. 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.…”