Abstract
Vesicomyid clams of the subfamily Pliocardinae are among the dominant chemosymbiotic bivalves found in sulfide‐rich deep‐sea habitats. Plastic morphologies and present molecular data could not resolve taxonomic uncertainties. The complete mitochondrial (mt) genomes will provide more data for comparative studies on molecular phylogeny and systematics of this taxonomically uncertain group, and help to clarify generic classifications. In this study, we analyze the features and evolutionary dynamics of mt genomes from three Archivesica species (Archivesica sp., Ar. gigas and Ar. pacifica) pertaining to subfamily Pliocardinae. Sequence coverage is nearly complete for the three newly sequenced mt genomes, with only the control region and some tRNA genes missing. Gene content, base composition, and codon usage are highly conserved in these pliocardiin species. Comparative analysis revealed the vesicomyid have a relatively lower ratio of Ka/Ks, and all 13 protein‐coding genes (PGCs) are under strong purifying selection with a ratio of Ka/Ks far lower than one. Minimal changes in gene arrangement among vesicomyid species are due to the translocation trnaG in Isorropodon fossajaponicum. Additional tRNA genes were detected between trnaG and nad2 in Abyssogena mariana (trnaL3), Ab. phaseoliformis (trnaS3), and Phreagena okutanii (trnaM2), and display high similarity to other pliocardiin sequences at the same location. Single base insertion in multiple sites of this location could result in new tRNA genes, suggesting a possible tRNA arising from nongeneic sequence. Phylogenetic analysis based on 12 PCGs (excluding atp8) supports the monophyly of Pliocardiinae. These nearly complete mitogenomes provide relevant data for further comparative studies on molecular phylogeny and systematics of this taxonomically uncertain group of chemosymbiotic bivalves.
Highlights
The animal mitochondrial genome is typically a circular molecule, usually containing 37 genes: 13 protein-coding genes (PCGs) of the respiratory chain, 22 tRNA, and two rRNAs (Wolstenholme, 1992)
The three genomes examined in this study contained 13 PCGs and two rRNA (Appendix S2), all encoded on the same strand, as consistently reported for other bivalves (Ozawa, Shimamura, Takaki, Yokobori et al, 2017; Xu, Wu, & Yu, 2010)
Twenty-two tRNAs were detected for Ar. pacifica, while 20 and 21 tRNA were detected for Archivesica sp. and Ar. gigas, respectively, indicating that we have sequenced most mt genes of these three clams
Summary
The animal mitochondrial (mt) genome is typically a circular molecule, usually containing 37 genes: 13 protein-coding genes (PCGs) (cox1–cox, cytb, nad1–nad, nad4L, atp, and atp8) of the respiratory chain, 22 tRNA, and two rRNAs (rrnL and rrnS) (Wolstenholme, 1992). Vesicomyid bivalves occur globally, mostly in sulfide-rich marine substrates found at deep-sea hydrothermal vents, hydrocarbon seeps, and sites of organic enrichment such as whale carcasses (Johnson, Krylova, Audzijonyte, Sahling, & Vrijenhoek, 2017; Krylova & Sahling, 2010; Peek, Gustafson, Lutz, & Vrijenhoek, 1997; Peek et al, 2000) Most members of this family housing intracellular autotrophic sulfide-oxidizing endosymbionts that provide essentially all of their nutrients and energy supply, making them primary subjects for studying adaptive strategies for chemosynthesis-based nutrition (Krylova & Sahling, 2010), and host/symbiont coevolution (Ozawa, Shimamura, Takaki, Takishita et al, 2017; Shimamura et al, 2017). We discuss our findings in nucleotide composition, gene rearrangement patterns, and mt genome evolution at the intrafamily level
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