Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA.
Pacific Northwest Research Station, US Department of Agriculture Forest Service, Corvallis, Oregon, USA.
Mol Ecol Resour. 2023 Nov;23(8):1880-1904. doi: 10.1111/1755-0998.13855. Epub 2023 Aug 21.
Species detection using eDNA is revolutionizing global capacity to monitor biodiversity. However, the lack of regional, vouchered, genomic sequence information-especially sequence information that includes intraspecific variation-creates a bottleneck for management agencies wanting to harness the complete power of eDNA to monitor taxa and implement eDNA analyses. eDNA studies depend upon regional databases of mitogenomic sequence information to evaluate the effectiveness of such data to detect and identify taxa. We created the Oregon Biodiversity Genome Project to create a database of complete, nearly error-free mitogenomic sequences for all of Oregon's fishes. We have successfully assembled the complete mitogenomes of 313 specimens of freshwater, anadromous and estuarine fishes representing 24 families, 55 genera and 129 species and lineages. Comparative analyses of these sequences illustrate that many regions of the mitogenome are taxonomically informative, that the short (~150 bp) mitochondrial 'barcode' regions typically used for eDNA assays do not consistently diagnose for species and that complete single or multiple genes of the mitogenome are preferable for identifying Oregon's fishes. This project provides a blueprint for other researchers to follow as they build regional databases, illustrates the taxonomic value and limits of complete mitogenomic sequences and offers clues as to how current eDNA assays and environmental genomics methods of the future can best leverage this information.
利用 eDNA 进行物种检测正在彻底改变全球监测生物多样性的能力。然而，缺乏区域的、有凭证的、基因组序列信息，尤其是包括种内变异的序列信息，这为希望利用 eDNA 的全部力量来监测分类群并实施 eDNA 分析的管理机构制造了一个瓶颈。eDNA 研究依赖于线粒体基因组序列信息的区域数据库，以评估这些数据检测和识别分类群的有效性。我们创建了俄勒冈生物多样性基因组计划（Oregon Biodiversity Genome Project），以创建一个包含俄勒冈州所有鱼类完整、几乎无错误的线粒体基因组序列的数据库。我们已经成功组装了 313 个淡水、洄游和河口鱼类标本的完整线粒体基因组，这些标本代表了 24 个科、55 个属和 129 个物种和谱系。对这些序列的比较分析表明，线粒体基因组的许多区域在分类学上是有信息的，短的 (~150bp) 线粒体“条形码”区域通常用于 eDNA 分析，但不能始终诊断物种，而线粒体基因组的单个或多个完整基因更适合识别俄勒冈州的鱼类。该项目为其他研究人员构建区域数据库提供了蓝图，说明了完整线粒体基因组序列的分类价值和局限性，并提供了线索，说明当前的 eDNA 分析和未来环境基因组学方法如何最好地利用这些信息。
