The Complete Mitochondrial Genome of the Grooved Carpet Shell, Ruditapes decussatus (Bivalvia, Veneridae).

Supplementary files of the article entitled: "<b>The Complete Mitochondrial Genome of the Grooved Carpet Shell, Ruditapes decussatus (Bivalvia, Veneridae)</b>".<br><br><b>Abstract</b>Despite a large number of animal complete mitochondrial genomes being available in public databases, the current knowledge about mitochondrial genomics in invertebrates is sketchy. This paper reports, for the first time, the complete mitochondrial genome of the grooved carpet shell,<i> Ruditapes decussatus</i>, also known as European clam. <i>R. decussatus</i> is morphologically and ecologically similar to the Manila clam <i>Ruditapes philippinarum</i>, which has been recently introduced for aquaculture in the very same habitats of<i> R. decussatus</i>, and that is replacing the native species. Currently the production of the European clam is almost insignificant, nonetheless it is considered a high value product, and therefore it is an economically important species, especially in Portugal, Spain and Italy.In this work we: i) assembled <i>R. decussatus</i> mitochondrial genome from RNA-Seq data, and validated it by Sanger sequencing, ii) analyzed and characterized <i>R. decussatus</i> mitochondrial genome, comparing its features with those of other venerid bivalves; iii) assessed mitochondrial genetic polymorphism, both from a nucleotide (SNPs) and a structural (CNV of tandem repeats) point of view, across 26 samples.Despite using high-throughput approaches we did not find evidence of sex-linked mitochondrial genomes, so it seems that <i>R. decussatus</i> does not have Doubly Uniparental Inheritance of mitochondria, a phenomenon known in ~100 bivalve species. According to our analyses, <i>R. decussatus</i> is more genetically similar to species of the Genus Paphia than to the congeneric <i>R. philippinarum</i>, a finding that bolster the already proposed need of a taxonomic revision. We also found a quite low genetic variability across the examined samples, with a very low number of SNPs and a low polymorphism of the hypervariable sequences flanking the control region (Largest Unassigned Regions, LURs). Strikingly, contrasting with the low nucleotide variability along the entire mitochondrial genome, we observed a pretty high polymorphism in LUR length due to CNV of tandem repeats, and even a LUR length heteroplasmy in two samples. It is not clear if the lack of genetic variability in the mitochondrial genome of <i>R. decussatus</i> is a cause or an effect of the ongoing replacement of <i>R. decussatus</i> with the invasive <i>R. philippinarum</i>, and more analyses, especially on nuclear sequences, are required to assess this point. <br>