3.4 Comparative genomics
According to the gene family clustering analysis of 17 Arthropoda species, a total of 27,512 gene families were clustered, and 443 of them were single-copy genes in all species (Figure 2a). Compared withP. monodon , L. vannamei, and P. trituberculatus ,F. chinensis possessed 593 unique gene families (Figure 2b). In general, gene families unique to a species are responsible for the biological characteristics of the species. GO enrichment analysis of the 593 unique gene families indicated that they were enriched in 47 GO terms, including structural constituent of cuticle, sodium and potassium ion transport, and chitin metabolic process (Table S13). These genes were enriched in nine KEGG pathways, including RNA polymerase, Huntington’s disease, and endocrine and other factor-regulated calcium reabsorption pathways (Table S14).
Phylogenetic analysis based on the 443 single-copy homologous genes revealed that F. chinensis and P. monodon diverged approximately 44 Mya, after they diverged from L. vannamei 70 Mya (Figure 2c). The three penaeid shrimp species diverged from P. trituberculatus , which belongs to Family Portunidae , approximately 271.5 Mya. The F. chinensis genome showed 49 expanded and 51 contracted gene families in comparison with the P. monodon genome. The GO and KEGG enrichment analysis indicated that the expanded gene families were mostly related to cellular process and metabolic process, including chitin metabolism (Figure S2, Table S15-16), whereas the contracted gene families were mostly associated with infection with certain pathogens and phototransduction (Figure S3, Table S17-18). Compared with L. vannamei , P. trituberculatus and H. azteca , a total of 63 genes were subject to positive selection. These genes were mostly related to basic cellular process (Table S19). One KEGG pathway named mRNA surveillance pathway was enriched.