The complete mitochondrial genome of the grooved carpet shell,Ruditapes decussatus(Bivalvia, Veneridae)

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.

Unveiling the Ecological Applications of Ancient DNA From Mollusk Shells

“…Interestingly, with five new R. decussatus mitochondrial genomes assembled here from ancient specimens, we could confirm a previous hypothesis based on one modern R. decussatus mitochondrial genome that R. decussatus is more closely related to the Paphia sp. than to R. philippinarum despite being named as members of the same genus (Ghiselli et al, 2017).…”

The dynamics of mito-nuclear coevolution: A perspective from bivalve species with two different mechanisms of mitochondrial inheritance

“…Is transcription level associated with the rate of protein evolution in OXPHOS genes? To address such questions, we investigated the rate of protein evolution and the transcription level of nuclear and mtDNA‐encoded OXPHOS subunits in two related bivalve species: Ruditapes decussatus , characterized by SMI of mitochondria (Ghiselli et al., ), and Ruditapes philippinarum , with DUI of mitochondria. We tested the above‐mentioned hypotheses about mito‐nuclear coevolution, focusing on nuclear compensation and E‐R correlation.…”

Lose it or keep it: (how bivalves can provide) insights into mitochondrial inheritance mechanisms

“…In the first case, DUI might be the result of a single event happened at the origin of the Autolamellibranchia superclass, more than 400 million years ago (Zouros, ). However, its distribution across the bivalve phylogenetic tree is not homogenous: for instance, within Pteriomorphia, mytilids have DUI, whereas ostreids and pectinids do not (Doucet‐Beaupré et al., ), and among Veneridae, the two lineage‐specific mtDNAs have been found in R. philippinarum (Passamonti & Scali, ) and Meretrix lamarckii (Bettinazzi, Plazzi, & Passamonti, ), whereas no evidence was found in Ruditapes decussatus (Ghiselli et al., ) and Callista chione (Plazzi, Cassano, & Passamonti, ). Besides being the result of incomplete sampling, this scattered distribution may also be imputed to false negatives due to the technical difficulties in the detection of the two different DUI mitochondrial genomes (see Theologidis, Fodelianakis, Gaspar, & Zouros, and Ghiselli et al., for a thorough discussion of this issue).…”