Abstract
Despite the large number of animal complete mitochondrial genomes currently available in public databases, knowledge about mitochondrial genomics in invertebrates is uneven. This paper reports, for the first time, the complete mitochondrial genome of the grooved carpet shell, Ruditapes decussatus, also known as the European clam. Ruditapes decussatus is morphologically and ecologically similar to the Manila clam Ruditapes philippinarum, which has been recently introduced for aquaculture in the very same habitats of Ruditapes decussatus, 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 Ruditapes decussatus mitochondrial genome from RNA-Seq data, and validated it by Sanger sequencing; (ii) analyzed and characterized the Ruditapes decussatus mitochondrial genome, comparing its features with those of other venerid bivalves; (iii) assessed mitochondrial sequence polymorphism (SP) and copy number variation (CNV) of tandem repeats across 26 samples. Despite using high-throughput approaches we did not find evidence for the presence of two sex-linked mitochondrial genomes, typical of the doubly uniparental inheritance of mitochondria, a phenomenon known in ∼100 bivalve species. According to our analyses, Ruditapes decussatus is more genetically similar to species of the Genus Paphia than to the congeneric Ruditapes philippinarum, a finding that bolsters the already-proposed need of a taxonomic revision. We also found a quite low genetic variability across the examined samples, with few SPs and little variability of the sequences flanking the control region (Largest Unassigned Regions (LURs). Strikingly, although we found low nucleotide variability along the entire mitochondrial genome, we observed high levels of length polymorphism in the LUR 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 Ruditapes decussatus is a cause or an effect of the ongoing replacement of Ruditapes decussatus with the invasive Ruditapes philippinarum, and more analyses, especially on nuclear sequences, are required to assess this point.
Highlights
Despite a large number of animal complete mitochondrial genomes being available in public databases (>55,000 in GenBank), up to now sequencing has been focused mostly on vertebrates (∼50,000 in GenBank), and the current knowledge about mitochondrial genomics in invertebrates—with the notable exception of few model organisms (e.g., Drosophila and Caenorhabditis elegans)—is uneven
Ruditapes decussatus lives in warm coastal waters, especially in lagoons, and it is morphologically and ecologically similar to the Manila clam Ruditapes philippinarum, which has been recently introduced for aquaculture in the very same habitats of Ruditapes decussatus
The gonadal liquid was checked under a light microscope to assess the sex of the individual, and to make sure that the sample consisted of mature gametes
Summary
Despite a large number of animal complete mitochondrial genomes (mtDNAs) being available in public databases (>55,000 in GenBank), up to now sequencing has been focused mostly on vertebrates (∼50,000 in GenBank), and the current knowledge about mitochondrial genomics in invertebrates—with the notable exception of few model organisms (e.g., Drosophila and Caenorhabditis elegans)—is uneven. Despite maintaining its core features in terms of genetic content, mtDNA in Metazoa shows a wide range of variation in some other traits such as, for example, genome architecture, abundance of unassigned regions (URs)—namely regions with no assigned product (protein, RNA)—repeat content, gene duplications, introns, UTRs, and even additional coding genes (see Breton et al, 2014 for a review) or genetic elements (e.g., small RNAs, see Pozzi et al, 2017). All this emerging diversity is in sharp contrast with the—at this point outdated—textbook notion about mtDNAs role being limited to the production of a few subunits of the protein complexes involved in oxidative phosphorylation. The grooved carpet shell is considered a high value product, and it is an economically important species, especially in Portugal, Spain and Italy (Gosling, 2003; Leite et al, 2013; de Sousa et al, 2014)
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