New diagnostic SNP molecular markers for the Mytilus species complex

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

Molecular epidemiological study on Infectious Pancreatic Necrosis Virus isolates from aquafarms in Scotland over three decades

In order to obtain an insight into genomic changes and associated evolution and adaptation of Infectious Pancreatic Necrosis Virus (IPNV) the complete coding genomes of 57 IPNV isolates collected from Scottish aquafarms from 1982-2014 were sequenced and analysed. Phylogenetic analysis of the sequenced IPNV strains showed separate clustering of genogroups I, II, III and V. IPNV isolates with genetic reassortment of segment A/B of genogroup III/II were determined. About 59% of the IPNV isolates belonged to the persistent type and 32% to the low virulent type and only one highly pathogenic strain0 (1.79%) was identified. Codon adaptation index calculations indicated that the IPNV major capsid protein VP2 has adapted to its salmonid host. Underrepresentation of CpG dinucleotides in the IPNV genome to minimise detection by the innate immunity receptors, and observed positive selection in the virulence determination sites of VP2 embedded in the variable region of the main antigenic region, suggest an immune escape mechanism driving virulence evolution. The prevalence of mostly persistent genotypes together with the assumption of adaptation and immune escape indicates that IPNV is evolving with the host

Environmental DNA Based Surveillance for the Highly Invasive Carpet Sea Squirt Didemnum vexillum : A Targeted Single-Species Approach

Funding Information: The authors would like to thank the site operators, owners and Solway Firth Partnership for allowing access and sample collection at studied sites visited during this study. Thanks also to Frank Armstrong, Katy Beaton, Maria Campbell, Pablo Dias, James Dooley, Judith Horrill, Nial McLeod, Warren Murray, Andrea Taylor, Joe Triscott, and Bill Turrell for contributing to field work and sample collection. The authors thank National Museums Scotland and particularly Fiona Ware for the loan of reference material (specimen register number NMS.Z.2015.82.8, 9 and 14 and NMS.Z.2018.2.2) which was used in the present study. KS thank the Japan Society for the Promotion of Science for post-doctoral fellowship funding.Peer reviewedPublisher PD

Development of eDNA tools for the detection of marine invasive non-native species to support European flat oyster (Ostrea edulis) restoration projects.

The European flat oyster (Ostrea edulis) is an important keystone species in Scottish coastal waters. However due to anthropogenic pressures, significant reductions to oyster beds have been observed across Europe. In Scotland, several projects are currently aiming to restore European flat oyster habitats through the translocation of juvenile oysters from various sources including hatcheries and aquaculture. However, translocation of shellfish is not risk free and can increase the risk of accidental translocation of invasive non-native species (INNS). If INNS become established outside of their native range they can cause irreversible harm to native organisms and habitats. This study aims to develop molecular tools to detect environmental DNA of INNS which can be potentially associated with the translocation of live shellfish stocks. We have developed a species-specific real-time PCR assay for detection of Pacific oyster (Crassostrea gigas) and tested its sensitivity in a large-scale replicated mesocosm based experiment with varying densities of C.gigas. A secondary objective of the experiment was to assess the detection of another invasive species, the carpet sea squirt Didemnum vexillum which was cohabited with C. gigas. We aim to quantify the detection probability of increasing densities of C. gigas from repeat water samples and qPCR replicates. This project also aims to investigate the feasibility of using portable, real-time sequencing technologies such as the Oxford Nanopore MinION to develop robust tools to support native oyster restoration programmes