3.5 Gene family comparison between the M. japonicus and other species
Ortholog analysis of genes from 21 species including Danio rerio ,Ctenopharyngodon idellus , Oreochromis niloticus ,Paralichthys olivaceus , Cynoglossus semilaevis ,Litopenaeus vannamei , Penaeus monodon ,Fenneropenaeus chinensis , Portunus trituberculatus ,Procambarus virginalis , Cherax quadricarinatus ,Daphnia magna , Locusta migratoria , Aedes aegypti ,Drosophila melanogaster , Bombyx mori , Daphnia pulex , Caenorhabditis elegans , Argopecten purpuratus ,Crassostrea gigas , and Branchiostoma floridae identified 46,954 clusters of gene families. 174 single-copy orthologs were used to construct the phylogeny and then the expansion and contraction of all ortholog families were analyzed at each node (Figure S4). In theM. japonicus lineage, we observed that 126 gene families had undergone expansion. We detected significant enrichment of neuronal function-associated genes (52 families), cuticle structure and remodeling genes (34 families), and transposons (25 families) (Figure S4A and Table S5). For the most highly expanded families, the associated gene ontology (GO) terms included binding, heterocyclic compound binding, and organic cyclic compound binding (Figure S4B and Table S6). We identified 24 contracted gene families in M. japonicus , for which the three most frequently associated GO terms were transition metal ion binding, oxidation−reduction process, and electron transfer activity (Figure S4C and Table S7).
There were 4,960 single-copy homologous gene families identified in the four Penaeus shrimps. Compared with those in L. vannamei ,P. monodon and F. chinensis , we observed 586 genes that were subjected to positive selection in M. japonicus , which were mainly associated with substance metabolic process. Among them, there was a gene annotated as heme oxygenase (HO)-like, which was clustered into the GO term of heme oxygenase (decyclizing) activity and heme oxidation. The HO-like protein of M. japonicus was truncated compared with the same gene in the other three Penaeus shrimps (Figure 6A). Positive selection sites were located at the 131st and 144th amino acid, based on the likelihood-ratio test. Variations in this gene resulted in the disappearance of the kinked helix structure (Figure 6B). Moreover, the reduction in hydrophobic amino acids caused the loss of a transmembrane domain (Figure 6C).