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Data from: Seascape genomics of eastern oyster (Crassostrea virginica) along the Atlantic coast of Canada.
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Bernatchez, Simon; Xuereb, Amanda; Laporte, Martin; Benestan, Laura; Steeves, Royce; Laflamme, Mark; Bernatchez, Louis; Mallet, Martin — 2018-11-20 Interactions between environmental factors and complex life-history characteristics of marine organisms produce the genetic diversity and structure observed within species. Our main goal was to test for genetic differentiation among eastern oyster populations from the coastal region of Canadian Maritimes against expected genetic homogeneity caused by historical events, taking into account spatial and environmental (temperature, salinity, turbidity) variation. This was achieved by genotyping 486 individuals originating from 13 locations using RADSeq. A total of 11 321 filtered SNPs were used in a combination of population genomics and environmental association analyses. We revealed significant neutral genetic differentiation (mean FST= 0.009) between sampling locations, and the occurrence of six major genetic clusters within the studied system. Redundancy analyses (RDA) revealed that spatial and environmental variables explained 3.1% and 4.9% of the neutral genetic variation and 38.6% and 12.2% of the putatively adaptive genetic variation, respectively. These results indicate that these environmental factors play a role in the distribution of both neutral and putatively adaptive genetic diversity in the system. Moreover, polygenic selection was suggested by genotype–environment association analysis and significant correlations between additive polygenic scores and temperature and salinity. We discuss our results in the context of their conservation and management implications for the eastern oyster.
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Data from: Modified low-salt CTAB extraction of high-quality DNA from contaminant rich tissues
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Arseneau, Jean-Rene; Steeves, Royce; Laflamme, Mark — 2016-10-19 The increasing use of high-throughput sequencing platforms has made the isolation of pure, high molecular weight DNA a primary concern for studies of a diverse range of organisms. Purification of DNA remains a significant challenge in many tissue and sample types due to various organic and inorganic molecules that co-precipitate with nucleic acids. Molluscs, for example, contain high concentrations of polysaccharides which often co-precipitate with DNA and can inhibit downstream enzymatic reactions. We modified a low-salt CTAB (MoLSC) extraction protocol to accommodate contaminant rich animal tissues and compared this method to a standard CTAB extraction protocol and two commercially available animal tissue DNA extraction kits using oyster adductor muscle. Comparisons of purity and molecular integrity showed that our in-house protocol yielded genomic DNA generally free of contaminants and shearing, whereas the traditional CTAB method and some of the commercial kits yielded DNA unsuitable for some applications of massively parallel sequencing (MPS). Our open-source MoLSC protocol provides a cost-effective, scalable, alternative DNA extraction method that can be easily optimized and adapted for sequencing applications in other contaminant rich samples.

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(Author: Laflamme, Mark)

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