Establishing a standardized and universally applicable set of nuclear-encoded markers for genome-wide multi-locus species delimitation of metazoans

建立一套标准化且普遍适用的核编码标记，用于后生动物的全基因组多位点物种界定

• 批准号: 350964009
• 负责人: Dr. Dirk Ahrens
• 金额: --
• 依托单位: Leibniz-Institut zur Analyse des Biodiversitätswandels (LIB)
• 依托单位国家: 德国
• 项目类别: Priority Programmes
• 资助国家: 德国
• 项目状态: 未结题
• 来源: https://gepris.dfg.de/gepris/projekt/350964009?language=en
• 关键词: Establishing; standardized; universally; applicable; set

In our project funded during phase I of the DFG SPP "TaxonOmics", we established a set of markers for nuclear barcoding of Metazoa that rests on genes that almost exclusively occur in single-copy in the genomes of animals (universal single copy genes — USCOs). Using target DNA enrichment, we assess applicability and strengths of USCOs for delimiting species on the example of selected groups of arthropods. In the second phase of the SPP, we plan to assess the robustness of the USCO barcoding approach and to compare its performance with that of COI barcoding. We are particularly interested in the susceptibly of USCOs for overestimating the true species diversity, a problem that COI barcoding is known to suffer from. For this purpose, we will increase the infraspecific geographic sampling relative to that in our preceding project, focusing on groups which were already investigated by us during phase I of the SPP: butterflies, cellar spiders, centipedes, chafer beetles, and hoverflies. We additionally plan to study gene flow— something that would not be feasible with the classical barcoding approach. All bioinformatic steps required to conduct the above research will be integrated in a bioinformatics pipeline. In this context, we will plan to assess the performance of various sequence assembly and species delimitation approaches. To determine how well USCOs cover the full length of nuclear genomes and whether or not they perhaps show a tendency to cluster (the latter would have consequences for statistical analyses relying on these genes), we will apply long-read DNA sequencing techniques to determine the position of USCOs in the nuclear genomes of selected species from the investigated groups.

在 DFG SPP“TaxonOmics”第一阶段资助的项目中，我们建立了一套用于后生动物核条形码的标记，这些标记依赖于几乎完全以单拷贝出现在动物基因组中的基因（通用单拷贝基因 - USCO）。使用目标 DNA 富集，我们以选定的节肢动物群体为例，评估 USCO 在界定物种方面的适用性和优势。在 SPP 的第二阶段，我们计划评估 USCO 条形码方法的稳健性，并将其性能与 COI 条形码的性能进行比较。我们特别感兴趣的是 USCO 是否容易高估真实的物种多样性，这是众所周知的 COI 条形码所面临的问题。为此，我们将相对于之前的项目增加种下地理采样，重点关注我们在 SPP 第一阶段已经调查过的群体：蝴蝶、地窖蜘蛛、蜈蚣、金龟子甲虫和食蚜蝇。我们还计划研究基因流——这是传统条形码方法无法实现的。进行上述研究所需的所有生物信息学步骤将整合到生物信息学管道中。在这种情况下，我们将计划评估各种序列组装和物种界定方法的性能。为了确定 USCO 覆盖整个核基因组的程度以及它们是否可能表现出聚类趋势（后者会对依赖这些基因的统计分析产生影响），我们将应用长读长 DNA 测序技术来确定 USCO 在所研究群体中选定物种的核基因组中的位置。