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).