Comparison between single and multi-locus approaches for specimen identification in Mytilus mussels

Abstract

Mytilus mussels have been the object of much research given their sentinel role in coastal ecosystems and significant value as an aquaculture resource appreciated for both, its flavour and nutritional content. Some of the most-studied Mytilus species are M. edulis, M. galloprovincialis, M. chilensis and M. trossulus. As species identification based on morphological characteristics of Mytilus specimens is difficult, molecular markers are often used. Single-locus markers can give conflicting results when used independently; not all markers differentiate among all species, and the markers target genomic regions with different evolutionary histories. We evaluated the concordance between the PCR-RFLP markers most commonly-used for species identification in mussels within the Mytilus genus (Me15-16, ITS, mac-1, 16S rRNA and COI) when used alone (mono-locus approach) or together (multi-locus approach). In this study, multi-locus strategy outperformed the mono-locus methods, clearly identifying all four species and also showed similar specimen identification performance than a 49 SNPs panel. We hope that these findings will contribute to a better understanding of DNA marker-based analysis of Mytilus taxa. These results support the use of a multi-locus approach when studying this important marine resource, including research on food quality and safety, sustainable production and conservation.

First description of a widespread Mytilus trossulus-derived bivalve transmissible cancer lineage in M. trossulus itself

“…According to a recent survey 60 , the blue mussel populations in the SOJ are overwhelmingly dominated by M. trossulus, but the presence of a "cryptic" species, M. galloprovincialis and its hybrids with M. trossulus cannot be entirely ruled out. Mussels from the "J" sample (N = 21), including four target mussels with DN, were genotyped for three nuclear markers routinely used for discriminating M. trossulus and M. galloprovincialis 61 , ME15/16 62 , ITS 63 and MAL-I 64 , using the primers and protocols in the original articles. The DNA extracted from the hemolymph and from the mantle of each mussel were analyzed in parallel.…”

Mussel biology: from the byssus to ecology and physiology, including microplastic ingestion and deep-sea adaptations

“…For this purpose, a convenient polymerase chain reaction (PCR) marker to distinguish the three species was designed using the sequence of a byssal protein gene (Fp-1) (Inoue et al 1995b). This marker has been utilized for more than 25 years, but is still robust (Larraín et al 2019), perhaps because it is based on a 12-or 54-bp insertion/deletion site, which may be less variable than nucleotide substitutions. However, species identification using single markers is not infallible, especially for specimens containing introgressed sequences (Larraín et al 2019;Vendrami et al 2020).…”

Improving quantification of bivalve larvae in mixed plankton samples using qPCR: A case study on Mytilus edulis

“…The primers selected for this study offer an added advantage of being able to detect alleles belonging to all members within the Mytilus edulis complex; M. edulis, M. galloprovincialis and M. trossulus (Inoue et al, 1995). The nuclear Me15/16 DNA marker follows a Mendelian inheritance pattern and is the most commonly used for routine identification of Mytilus mussels due its robustness and reliability (Larraín et al, 2019). Whilst single locus genotyping using this marker has limited potential for analysing patterns of hybridisation or genome introgression (Wilson et al, 2018;Beaumont et al, 2008) and can underestimate levels of hybridisation in populations (Larraín et al, 2019;Kijewski et al, 2011), it can be used to identify size-specific gene fragments unique to each of the Mytilus species (Wilson et al, 2018;Kijewski et al, 2006).…”

“…The implications for this are the possibility of concurrently amplifying M and F DNA when targeting mitochondrial gene regions during PCR, which depends on sequence divergence between M and F types; average sequence divergence in the 3 Mytilus species is ~8.3% but levels can be >20% (Śmietanka et al, 2016;Schizas, 2012). Both DUI and non-DUI heteroplasmy have been observed in crossings between blue mussels (Kijewski et al 2006), and this along with other issues inherent in DNA barcoding/ metabarcoding, some of which are mentioned above, can have significant implications for accurate taxonomic classification and ultimate barcoding success (Larraín et al 2019).…”