Yet Another Mitochondrial Genome of the Pacific Cupped Oyster: The Published Mitogenome of Alectryonella plicatula (Ostreinae) Is Based on a Misidentified Magallana gigas (Crassostreinae)

The recently published mitochondrial genome of the fingerprint oyster Alectryonella plicatula (Gmelin, 1791) with GenBank accession number MW143047 was resolved in an unexpected phylogenetic position, as sister to the Pacific cupped oyster Magallana gigas (Thunberg, 1793) and share with this species three typical gene duplications that represent robust synapomorphies of the Magallana clade. In this study, we verified the identity of MW143047 using direct comparisons of single gene sequences, DNA barcoding and phylogenetic analyses. BLAST searches using as query each of the 12 protein coding genes (PCGs) and rRNA genes extracted from MW143047 retrieved M. gigas as best hit with 100% sequence identity for all genes. MW143047 is nested within the clade formed by M. gigas sequences, with virtually zero-length terminal branch, both in the cox1 gene tree (based on 3639 sequences) and in the 16S gene tree (based on 1839 sequences), as well as in the Maximum Likelihood mitogenomic tree based on concatenated sequence of 12 PCGs. Our findings suggest that the original specimen used for mitogenome sequencing was misidentified and represents an individual of M. gigas. This study reinforces the notion that morphological shell analysis alone is not sufficient for oyster identification, not even at high taxonomic ranks such as subfamilies. While it is well established that morphological identification of oysters should be validated by molecular data, this study emphasizes that also molecular data should be taxonomically verified by means of DNA barcoding and phylogenetic analyses. The implications of the publication of taxonomically misidentified sequences and mitogenomes are discussed.

Yet another mitochondrial genome of the Pacific cupped oyster: the published mitogenome of Alectryonella plicatula (Ostreinae) is based on a misidentified Magallana gigas (Crassostreinae)

The recently published mitochondrial genome of the fingerprint oyster Alectryonella plicatula (Gmelin, 1791) with GenBank accession number MW143047 was resolved in an unexpected phylogenetic position, as sister to the Pacific cupped oyster Magallana gigas (Thunberg, 1793) and share with this species three typical gene duplications that represent robust synapomorphies of the Magallana clade. In this study, we verified the identity of MW143047 using direct comparisons of single gene sequences, DNA barcoding and phylogenetic analyses. BLAST searches using each of the 12 protein coding genes and rRNA genes extracted from MW143047 as query retrieved M. gigas as best hit with 100% sequence identity. MW143047 is nested within the clade formed by M. gigas sequences, with virtually no difference between their terminal branch lengths, both in the cox1 gene tree (based on 3639 sequences) and in the 16S gene tree (based on 1839 sequences), as well as in the Maximum Likelihood mitogenomic tree based on concatenated sequence of 12 PCGs. Our findings suggest that the original specimen used for mitogenome sequencing was misidentified and represents an individual of M. gigas. This study reinforces the notion that morphological shell analysis alone is not sufficient for oyster identification, not even at high taxonomic ranks such as subfamilies. While it is well established that morphological identification of oysters should be validated by molecular data, this study emphasizes that also molecular data should be taxonomically validated by means of DNA barcoding and phylogenetic analyses. The implications of the publication of taxonomically misidentified sequences and mitogenomes are discussed

Molecular and morphological systematics of a new, reef forming, cupped oyster from the northern Arabian Gulf: Talonostrea salpinx new species

The rocky northern shores of Kuwait and those of the western, inner shores of Kuwait Bay are dominated by a small, densely encrusting oyster. The identity of this oyster has never been confirmed and was mistaken previously for a small Saccostrea. The shell morphology suggests that this species belongs to the subfamily Crassostreinae, but within that subfamily, the presence of marginal erect trumpet-shaped projections is so far unique. Phylogenetic analyses based on mitochondrial DNA sequence data confirmed that this species belongs to the Crassostreinae and has a sister position to the clade including Talonostrea talonata and T. zhanjiangensis. Genetic distance between this species and Talonostrea species is remarkably high, being ~20% for the cytochrome oxidase I gene and ~7% for the 16S rRNA gene. Based on morphological and molecular analyses, this oyster is therefore described here as Talonostrea salpinx Oliver, Salvi & Al-Kandari, sp. nov. Shell morphology is shown to be variable, and the different forms encountered are described. The wider distribution and origins of this species, whether native or introduced, are discussed.

Genetic Characterization of Cupped Oyster Resources in Europe Using Informative Single Nucleotide Polymorphism (SNP) Panels

The Pacific oyster, Crassostrea gigas, was voluntarily introduced from Japan and British Columbia into Europe in the early 1970s, mainly to replace the Portuguese oyster, Crassostrea angulata, in the French shellfish industry, following a severe disease outbreak. Since then, the two species have been in contact in southern Europe and, therefore, have the potential to exchange genes. Recent evolutionary genomic works have provided empirical evidence that C. gigas and C. angulata exhibit partial reproductive isolation. Although hybridization occurs in nature, the rate of interspecific gene flow varies across the genome, resulting in highly heterogeneous genome divergence. Taking this biological property into account is important to characterize genetic ancestry and population structure in oysters. Here, we identified a subset of ancestry-informative makers from the most differentiated regions of the genome using existing genomic resources. We developed two different panels in order to (i) easily differentiate C. gigas and C. angulata, and (ii) describe the genetic diversity and structure of the cupped oyster with a particular focus on French Atlantic populations. Our results confirm high genetic homogeneity among Pacific cupped oyster populations in France and reveal several cases of introgressions between Portuguese and Japanese oysters in France and Portugal.