Fig 1.
Complete mitogenome map of C. marissinica.
All 37 genes are encoded on the heavy (H) strand. Genes for proteins and rRNAs are shown with standard abbreviations. Genes for tRNAs are displayed by a single letter for the corresponding amino acid, with two leucine tRNAs and two serine tRNAs differentiated by numerals.
Table 1.
Mitogenome organization of C. marissinica.
Table 2.
Mitogenomes of Vesicomyidae species sequenced to date and their genomic features.
Fig 2.
Codon usage (A) and the relative synonymous codon usage (RSCU) (B) of the C. marissinica mitogenome.
Numbers to the left refer to the total number of codons (A) and the RSCU values (B). Codon families are provided on the X axis.
Fig 3.
Nucleotide sequences and stem-loop structures of the tandem repeat motifs in the control region (CR) of the C. marissinica mitogenome.
The CR is flanked by sequences encoding tRNATrp and nad6. The CR consists of certain patterns, such as special G(A)nT motifs (marked with a box), AT-rich regions and tandem repeat motifs.
Fig 4.
Mitochondrial gene arrangement of 13 species in the subclass Heterodonta (Panopea generosa, Moerella iridescens, Coelomactra antiquata, Meretrix meretrix and 9 vesicomyid bivalves).
CR indicates the control region. Genes for tRNAs are displayed by a single letter for the corresponding amino acid, with two leucine tRNAs and two serine tRNAs differentiated by numerals. Uniquely derived gene positions of individual species are depicted in red. Sequence segments are not drawn to scale.
Fig 5.
Phylogenetic tree derived from Bayesian analyses based on concatenated nucleotide sequences of 9 mitochondrial PCGs (cox1, cox2, cox3, cob, atp6, nad1, nad4, nad5, and nad6) and 2 ribosomal RNA genes (rrnS and rrnL).
Numbers on branches are Bayesian posterior probabilities (percent). Two Pectinidae species belonging to the subclass Pteriomorphia were used as outgroups.
Table 3.
CODEML analyses of selection pressure on mitochondrial genes in the Vesicomyidae lineage.
Table 4.
Possible sites under positive selection in the Vesicomyidae lineage.