Gustafson Grey T, Alexander Alana, Sproul John S, Pflug James M, Maddison David R, Short Andrew E Z
Department of Ecology and Evolutionary Biology University of Kansas Lawrence Kansas.
Biodiversity Institute University of Kansas Lawrence Kansas.
Ecol Evol. 2019 Jun 11;9(12):6933-6948. doi: 10.1002/ece3.5260. eCollection 2019 Jun.
Targeted capture and enrichment approaches have proven effective for phylogenetic study. Ultraconserved elements (UCEs) in particular have exhibited great utility for phylogenomic analyses, with the software package phyluce being among the most utilized pipelines for UCE phylogenomics, including probe design. Despite the success of UCEs, it is becoming increasing apparent that diverse lineages require probe sets tailored to focal taxa in order to improve locus recovery. However, factors affecting probe design and methods for optimizing probe sets to focal taxa remain underexplored. Here, we use newly available beetle (Coleoptera) genomic resources to investigate factors affecting UCE probe set design using phyluce. In particular, we explore the effects of stringency during initial design steps, as well as base genome choice on resulting probe sets and locus recovery. We found that both base genome choice and initial bait design stringency parameters greatly alter the number of resultant probes included in final probe sets and strongly affect the number of loci detected and recovered during in silico testing of these probe sets. In addition, we identify attributes of base genomes that correlated with high performance in probe design. Ultimately, we provide a recommended workflow for using phyluce to design an optimized UCE probe set that will work across a targeted lineage, and use our findings to develop a new, open-source UCE probe set for beetles of the suborder Adephaga.
靶向捕获和富集方法已被证明在系统发育研究中是有效的。特别是超保守元件（UCEs）在系统基因组分析中展现出了巨大的效用，软件包phyluce是UCE系统基因组学（包括探针设计）中使用最广泛的流程之一。尽管UCEs取得了成功，但越来越明显的是，不同的谱系需要针对目标分类群量身定制的探针集，以提高位点回收率。然而，影响探针设计的因素以及针对目标分类群优化探针集的方法仍未得到充分探索。在这里，我们利用新获得的甲虫（鞘翅目）基因组资源，使用phyluce来研究影响UCE探针集设计的因素。特别是，我们探讨了初始设计步骤中的严格性以及基础基因组选择对最终探针集和位点回收率的影响。我们发现，基础基因组选择和初始诱饵设计严格性参数都会极大地改变最终探针集中包含的所得探针数量，并强烈影响这些探针集在计算机模拟测试期间检测和回收的位点数量。此外，我们确定了与探针设计高性能相关的基础基因组属性。最终，我们提供了一个推荐的工作流程，用于使用phyluce设计一个优化的UCE探针集，该探针集将适用于目标谱系，并利用我们的研究结果为肉食亚目甲虫开发一个新的开源UCE探针集。
