3.4 Genomic comparison with other species
We conducted functional comparative genomic analyses with the four groupers (P. leopardus , E. akaara , E. lanceolatus and C. sonnerati ) to reveal the similarities and differences between them by constructing orthologous gene families. The results were demonstrated through the Venn diagram (Supplementary Figure S1). Specifically, the numbers of gene families were highly similar in the four groupers, with 17,125, 16,842, 17,205, and 16,674 inC. sonnerati , E. lanceolatus , P. leopardus andE. akaara , respectively. The four groupers shared 14,512 genes, and 406 genes were specific to C. sonnerati . We also found that C. sonnerati shared 15,818, 15,594, and 15,877 genes withE. lanceolatus , E. akaara and P.leopardus , respectively. In addition, we conducted functional comparative genomic analysis between the genome of C. sonneratiand the other three groupers’ genomes. We found that the four species had the same karyotype (2n = 48) with a high level of genomic collinearity revealed by the results of chromosome syntenic comparisons between them (Figure 5).
Furthermore, a total of 1224 expanded gene families and 1977 contracted gene families were identified in the C. sonnerati genome in comparison to the 15 closet species. Additionally, 112 positive selection genes were found in the C. sonnerati genome. Next, there were 18 KEGG pathways and 33 GO terms significantly enriched from the expanded gene families (Table S4). Furthermore, there were 6 KEGG pathways and 22 GO terms significantly enriched from the contracted gene families. The expanded genes families were highly enriched in the sensory system, suggesting that these genes might play an important role in sensory organs development, such as the skin of C. sonnerati (Supplementary Figure S2).