3.6 Genomic comparison with other groupers
Currently, genome sequences are only available for two groupers (genus Epinephelus), including E. lanceolatus and E.akaara . To reveal the similarities and differences of the grouper genomes, we conducted functional comparative genomic analyses. TheP. leopardus and the Epinephelus grouper species have the same karyotype (2n =48), and the chromosome syntenic comparisons showed that they have a high level of genomic collinearity (Figure 5a ).
Furthermore, gene family evolution was analyzed by constructing orthologous gene families. The numbers of gene families were highly similar in the three groupers, with 18,336, 18,674 and 18,007 inP. leopardus , E. lanceolatus and E. akaara , respectively. A total of 15,497 genes were shared by the three teleost, and 4,427 genes were specific to P. leopardus (Figure 5b ). We also found that P. leopardus shared 17,375 genes withE. lanceolatus , and 16,929 genes with E. akaara , respectively. In P. leopardus , a total of 799 gene families were expanded compared to its most recent common ancestor of the Epinephelus linage (Figure 5c ), among which 126 were significantly expanded (p < 0.05). The expanded gene families were significantly enriched in a number of immune systems and immune related pathways (Figure 5d , Supplementary Table S4 ), indicating an improved capacity for resistance to diseases in P. leopardus . A total of 12 gene families were contracted, however, no enriched KEGG pathway was found.