Comparative mitochondrial genomic analyses of three chemosynthetic vesicomyid clams from deep‐sea habitats

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.

The complete mitochondrial genome of Calyptogena marissinica (Heterodonta: Veneroida: Vesicomyidae): Insight into the deep-sea adaptive evolution of vesicomyids

“…In the present study, most of the tRNA genes had the typical secondary structure, except for tRNA His , tRNA Thr , tRNA Tyr , tRNA Ser(UCA) and tRNA Ser(AGA) . In tRNA His , tRNA Thr and tRNA Tyr , the TψC loops are incomplete, which is not observed in other vesicomyid bivalves [34–36], and this feature might be a specific character in the C . marissinica mitogenome.…”

“…In the present study, with the exception of the atp8 gene, which had the alternate initiation codon GTG, all the PCGs were initiated by typical ATN codons: 6 genes ( atp6 , cob , cox1 , cox2 , cox3 , and nad4 ) were initiated by ATG, 4 genes ( nad2 , nad3 , nad4l , and nad6 ) were initiated by ATT, and 2 genes ( nad1 and nad5 ) were initiated by ATA. Notably, genes are commonly initiated by GTG in vesicomyid bivalves [34], and the amino acid encoded by GTG is valine, which belongs to the nonpolar amino acids, such as methionine and isoleucine encoded by ATN. Moreover, in eight other vesicomyid bivalves ( Archivesica sp., Archivesica gigas , Archivesica pacifica , C .…”

“…magnifica , Abyssogena mariana , Ab . phaseoliformis , Isorropodon fossajaponicum , and Phreagena okutanii ), cox3 had a truncated termination codon, TA [34]. Previous studies have shown that the truncated stop codon is common in the metazoan mitogenome and might be corrected by posttranscriptional polyadenylation [59–60].…”

Size does matter: Parallel evolution of adaptive thermal tolerance and body size facilitates adaptation to climate change in domestic cattle

“…Mitochondria integrate environmental stimuli to modify gene expression patterns through mitonuclear communication and act as a controlling pivot in metabolism as well as during stress response (Harbauer, Zahedi, Sickmann, Pfanner, & Meisinger, ). In addition, mitochondrial diversity is also used to analyze the phylogenetic origin of breeds/populations (Liu, Cai, Liu, & Zhang, ; Marinov, Teofanova, Radoslavov, & Hristov, ). In domestic cattle, mitogenome analysis provides information regarding how functional traits like body size and tolerance are evolved in different lineages over temporal and spatial scales (Achilli et al, ).…”

“…In addition, mitochondrial diversity is also used to analyze the phylogenetic origin of breeds/populations (Liu, Cai, Liu, & Zhang, 2018;Marinov, Teofanova, Radoslavov, & Hristov, 2018). In domestic cattle, mitogenome analysis provides information regarding how functional traits like body size and tolerance are evolved in different lineages over temporal and spatial scales (Achilli et al, 2009(Achilli et al, , 2008 ).…”