Codon Usage Bias in Mitochondrial Genomes Across Three Species of Siphonaria (Mollusca: Gastropoda)

Siphonaria is a genus of false limpets belonging to the Gastropoda class. Only two species of this genus have been described with mitochondrial genomes. Moreover, the codon usage patterns and factors influencing them have not been studied. This study aims to expand the mitochondrial genome data of this genus and clarify the codon usage patterns.

The complete mitochondrial genome of Siphonaria japonica was sequenced using next-generation sequencing. The gene arrangement and phylogenetic status were compared with Siphonaria gigas and Siphonaria pectinata. The codon usage bias of the three mitochondrial genomes was analyzed based on the relative synonymous codon usage (RSCU), the effective number of codons (ENC) plot, the parity rule 2 (PR2)-bias plot, and neutrality plot analyses.

The gene arrangement and maximum-likelihood phylogenetic tree support a close relationship between S. japonica and S. pectinata. The codon usage bias analysis indicated that the codon usage bias of mitochondrial PCGs in the three species was primarily influenced by natural selection.

This study offers significant evolutionary insights into the phylogenetic relationships and molecular adaptation strategies among Siphonaria species.