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).