New diagnostic SNP molecular markers for the Mytilus species complex

Abstract

The development of diagnostic markers has been a long-standing interest of population geneticists as it allows clarification of taxonomic uncertainties. Historically, there has been much debate on the taxonomic status of species belonging to the Mytilus species complex (M. edulis, M. galloprovincialis and M. trossulus), and whether they are discrete species. We analysed reference pure specimens of M. edulis, M. galloprovincialis and M. trossulus, using Restriction site associated DNA (RAD) sequencing and identified over 6,000 SNP markers separating the three species unambiguously. We developed a panel of diagnostic SNP markers for the genotyping of Mytilus species complex as well as the identification of hybrids and interspecies introgression events in Mytilus species. We validated a panel of twelve diagnostic SNP markers which can be used for species genotyping. Being able to accurately identify species and hybrids within the Mytilus species complex is important for the selective mussel stock management, the exclusion of invasive species, basic physiology and bio-diversity studies.

Unveiling the Ecological Applications of Ancient DNA From Mollusk Shells

“…As expected for mostly non-model species, the present study highlights a general paucity of published mitochondrial and nuclear genome assemblies, population-scale data, as well as geographical metadata submitted to barcode databases (BOLD, GenBank), with some mollusk populations better described at the population genomic level, i.e., Crassostrea sp., Mytilus sp., Haliotis sp., and Pecten sp. (Zbawicka et al, 2014a(Zbawicka et al, , 2018Fraïsse et al, 2016;Mathiesen et al, 2016;Wenne et al, 2016;Gutierrez et al, 2017;Harney et al, 2018;Wilson et al, 2018;El Ayari et al, 2019;Masonbrink et al, 2019;Paterno et al, 2019;Vendrami et al, 2019a,b). It is worth noting that the phylogenetically robust data reported here significantly increases the number of released complete mitochondrial genome sequences by 6-fold for R. decussatus, five-fold for R. philippinarum, three-fold for A. islandica, and D. polymorpha, and finally two-fold for H. rufescens, H. tuberculata, and P. maximus.…”

A Genome-Wide Approach to the Phylogeography of the Mussel Mytilus galloprovincialis in the Adriatic and the Black Seas

“…High resolution, hypervariable nuclear markers such as microsatellites are typically of low densities and of difficult isolation in molluscs (Cruz et al, 2005;McInerney et al, 2011) and the use of mitochondrial markers is complicated by the doubly uniparental inheritance (DUI) of these organelles in mussels (Skibinski et al, 1994;Zouros et al, 1994). To overcome these limits, single nucleotide polymorphisms (SNPs) have started to be developed as markers in Mytilus spp., and they have been successfully used to differentiate species and populations within taxa in native and non-native areas (Zbawicka et al, 2012(Zbawicka et al, , 2018Gardner et al, 2016;Larraín et al, 2018;Wilson et al, 2018).…”

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

“…Therefore, this method is the most common DNA-based technique for identifying mussel species. Of course, Me15-16 alone is not able to distinguish introgressed individuals 40 , and also, is not able to differentiate M. chilensis from the Southern Hemisphere lineage of M. galloprovincialis from New Zealand, because in both species, this fragment of genome is not cut by Aci I due to the substitution of the allele “G” by “T” in the restriction site 97 .…”

“…The development of genotyping-by-sequencing methods to affordably discover and genotype hundreds or even thousands of single-nucleotide polymorphism (SNP) markers makes it possible to apply a multi-locus approach to specimen identification 40,101 . New multi-locus SNP panels have been developed recently, allowing for species identification using only the most informative SNPs 38,40,96,102–105 . As an example of the multi-locus approach in mixed populations, hybrids and introgressed individuals were detected by a new twelve-SNP diagnostic panel in European Mytilus samples previously analyzed with PCR-RFLP Me15-16 40 .…”

“…Therefore, these patterns are regarded as diagnostic loci and are widely used for Mytilus species identification 32–34 . Nowadays, is also possible to perform a trustworthy specimen identification with highly informative SNP panels 35–40 . However, no all laboratories have access to this genomic technology and PCR-RFLP markers are still used in recently valuable studies 41–44 .…”