Orianne Tournayre, Ryan Wolfe, Hannah McCurdy-Adams, Amy A Chabot, Stephen C Lougheed
{"title":"A species-specific digital PCR assay for the endangered blue racer (<i>Coluber constrictor foxii</i>) in Canada.","authors":"Orianne Tournayre, Ryan Wolfe, Hannah McCurdy-Adams, Amy A Chabot, Stephen C Lougheed","doi":"10.1139/gen-2023-0008","DOIUrl":null,"url":null,"abstract":"<p><p>The only population of the endangered blue racer (<i>Coluber constrictor foxii</i>) in Canada occurs on Pelee Island, Ontario. The species is threatened by multiple factors, including habitat degradation and loss, road mortality, persecution, and potentially predation. We designed and evaluated the performance of an environmental DNA droplet digital PCR assay that can be used for multiple facets of conservation of this species. We tested the assay <i>in silico</i> and <i>in vitro</i> using DNA of blue racers and co-occurring snake species and estimated the LOD and LOQ using synthetic DNA. As wild turkey predation has been suggested to negatively affect racers, we tested the assay on eight wild turkey faecal samples. Our assay is specific, can detect the target species at very low levels of concentration (0.002 copies/µL), and can accurately quantify copy numbers ≥ 0.26 copies/µL. We detected no racer DNA in any wild turkey faecal sample. More faecal samples collected at strategic locations during snake peak activity on Pelee Island would enable a more thorough assessment of the possibility of turkey predation. Our assay should be effective for other environmental samples and can be used for investigating other factors negatively affecting blue racers, for example, helping to quantify blue racer habitat suitability and site occupancy.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"66 9","pages":"251-260"},"PeriodicalIF":2.3000,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genome","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1139/gen-2023-0008","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
The only population of the endangered blue racer (Coluber constrictor foxii) in Canada occurs on Pelee Island, Ontario. The species is threatened by multiple factors, including habitat degradation and loss, road mortality, persecution, and potentially predation. We designed and evaluated the performance of an environmental DNA droplet digital PCR assay that can be used for multiple facets of conservation of this species. We tested the assay in silico and in vitro using DNA of blue racers and co-occurring snake species and estimated the LOD and LOQ using synthetic DNA. As wild turkey predation has been suggested to negatively affect racers, we tested the assay on eight wild turkey faecal samples. Our assay is specific, can detect the target species at very low levels of concentration (0.002 copies/µL), and can accurately quantify copy numbers ≥ 0.26 copies/µL. We detected no racer DNA in any wild turkey faecal sample. More faecal samples collected at strategic locations during snake peak activity on Pelee Island would enable a more thorough assessment of the possibility of turkey predation. Our assay should be effective for other environmental samples and can be used for investigating other factors negatively affecting blue racers, for example, helping to quantify blue racer habitat suitability and site occupancy.
期刊介绍:
Genome is a monthly journal, established in 1959, that publishes original research articles, reviews, mini-reviews, current opinions, and commentaries. Areas of interest include general genetics and genomics, cytogenetics, molecular and evolutionary genetics, developmental genetics, population genetics, phylogenomics, molecular identification, as well as emerging areas such as ecological, comparative, and functional genomics.