28S rDNA as an alternative marker for commercially important oyster identification

Mazón‐Suástegui, José Manuel; Fernandez, Natalia Trabal; Valencia, Ignacio; Cruz-Hernández, Pedro; Latisnere-Barragán, Hever

doi:10.1016/j.foodcont.2016.02.006

Cited by 15 publications

(10 citation statements)

References 46 publications

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“…While Magallana gigas in Alectryonella plicatula are readily distinguishable using mitochondrial (Liu et al, 2011; Crocetta et al, 2015) or nuclear markers (O’Foighil & Taylor, 2000; Salvi et al, 2014; Mazón-Suástegui et al, 2016), morphological misidentification between the two might be easy as reported by Bishop et al (2017) due the extensive degree of phenotypic plasticity of oysters. This example highlights the common difficulties encountered for identifying oysters based on shell morphology alone, and provides one more demonstration that misidentification regards not only closely related species but also taxonomic ranks as high as subfamilies (discussed in Salvi & Mariottini, 2021; see Salvi et al 2014 and Raith et al 2016 for examples regarding the subfamilies Striostreinae Harry, 1985, Ostreinae Rafinesque, 1815 and Saccostreinae Salvi & Mariottini, 2016).…”

Section: Discussionmentioning

confidence: 99%

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

Salvi

Berrilli

Garzia

et al. 2021

Preprint

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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

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Section: Discussionmentioning

confidence: 99%

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

Salvi

Berrilli

Garzia

et al. 2021

Preprint

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“…It is not uncommon that COI has variable utility even among closely related species (Sigwart & Garbett, 2018). Other studies have proposed alternative markers such as 28S fragments for separating oyster species (Mazón-Suástegui et al, 2016). There is an ongoing taxonomic problem with C.(M.) iredalei and C.(M.) madrasensis, which are both formally considered to be junior synonyms of C.(M.) bilineata, but nonetheless these names are used routinely in aquaculture literature.…”

Section: Molecular Identificationmentioning

confidence: 99%

Global controversy in oyster systematics and a newly described species from SE Asia (Bivalvia: Ostreidae: Crassostreinae)

2021

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The diversity of native oysters in many regions is overshadowed by the global dominance of a few economically important species. Here we describe the Muar Oyster, Crassostrea (Magallana) saidii sp. nov., first reported as an established local fishery renowned for exceptional and distinctive flavour over 160 years ago by British colonial officials in Malaysia, but as yet never formally named or described as a species. This new species has a subtle but clear morphological diagnosis dependent on three-dimensional characters, which has long been recognised by local fishers to differentiate the new species from co-occurring C. (M.) belcheri (G. B. Sowerby II, 1871). The Indo-Pacific clade Magallana Salvi & Mariottini, 2016 in Salvi and Mariottini 2017 is a phylogenetically distinct group that nonetheless cannot be morphologically separated from the broader genus Crassostrea Sacco, 1897. Fossils or species known only from shell specimens, though morphologically distinct species, cannot be classified as Magallana, Talonostrea Li & Qi, 1994, or Crassostrea s.s.; therefore, we revise these groups as sub-genera within Crassostrea. Our analysis of the COI barcoding fragment from previously published sequences of all available Magallana species found that gene is not sufficient to separate several economically important species, and revealed more than 5% of sequences in GenBank represent identification errors. The new species Crassostrea (Magallana) saidii sp. nov., which is genetically, morphologically, and gastronomically distinct, is known from only one population under potential threat from urbanisation. Many more global species of Magallana remain undescribed. The systematics of this group is critical to understand the diversity of global oysters, and to understand the sustainable use of species grown worldwide for centuries as our food.

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“…There are no population genetic studies for this species, but in the contribution by Cruz et al (2007) on the microsatellite loci for Crassostrea corteziensis, they mention that of the 11 loci characterized for the Cortez oyster, seven can be amplified in Saccostrea palmula, which makes them suitable for population studies. Maz´on-Su´astegui et al (2016) reported sequences of mitochondrial cytochrome c oxidase subunit 1 (COI) gene, the nuclear intertranscribed spacer 1 (ITS-1), and the nuclear 28S ribosomal gene. By means of a phylogenetic analysis with sequences of other species of ostreids, these authors concluded that the 28S gene was more reliable in correctly identifying species; thus, it can be used as an alternative marker.…”

Section: Saccostrea Palmulamentioning

confidence: 99%

“…For this species, there is only a report of the sequences of COI, ITS-1, and 28S by Maz´on-Su´astegui et al (2016).…”

Section: Crassostrea Columbiensismentioning

confidence: 99%

See 1 more Smart Citation

Tropical and Subtropical Ostreidae of the American Pacific: Taxonomy, Biology, Ecology, and Genetics

Lodeiros

Valentich-Scott

Chávez‐Villalba³

et al. 2020

Journal of Shellfish Research

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28S rDNA as an alternative marker for commercially important oyster identification

Cited by 15 publications

References 46 publications

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

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

Global controversy in oyster systematics and a newly described species from SE Asia (Bivalvia: Ostreidae: Crassostreinae)

Tropical and Subtropical Ostreidae of the American Pacific: Taxonomy, Biology, Ecology, and Genetics

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