Data from: Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera

Gaining a genomic perspective on phylogeny requires the collection of data from many putatively independent loci across the genome. Among insects, an increasingly common approach to collecting this class of data involves transcriptome sequencing, because few insects have high-quality genome sequences available; assembling new genomes remains a limiting factor; the transcribed portion of the genome is a reasonable, reduced subset of the genome to target; and the data collected from transcribed portions of the genome are similar in composition to the types of data with which biologists have traditionally worked (e.g. exons). However, molecular techniques requiring RNA as a template, including transcriptome sequencing, are limited to using very high-quality source materials, which are often unavailable from a large proportion of biologically important insect samples. Recent research suggests that DNA-based target enrichment of conserved genomic elements offers another path to collecting phylogenomic data across insect taxa, provided that conserved elements are present in and can be collected from insect genomes. Here, we identify a large set (n = 1510) of ultraconserved elements (UCEs) shared among the insect order Hymenoptera. We used in silico analyses to show that these loci accurately reconstruct relationships among genome-enabled hymenoptera, and we designed a set of RNA baits (n = 2749) for enriching these loci that researchers can use with DNA templates extracted from a variety of sources. We used our UCE bait set to enrich an average of 721 UCE loci from 30 hymenopteran taxa, and we used these UCE loci to reconstruct phylogenetic relationships spanning very old (≥220 Ma) to very young (≤1 Ma) divergences among hymenopteran lineages. In contrast to a recent study addressing hymenopteran phylogeny using transcriptome data, we found ants to be sister to all remaining aculeate lineages with complete support, although this result could be explained by factors such as taxon sampling. We discuss this approach and our results in the context of elucidating the evolutionary history of one of the most diverse and speciose animal orders.

要从基因组视角开展系统发育研究，需收集基因组内多个推定独立基因座的数据。在昆虫类群中，转录组测序（transcriptome sequencing）已成为获取此类数据的日益主流的手段，原因在于：目前仅有少量昆虫拥有高质量基因组序列；全新基因组组装仍为研究的限制瓶颈；基因组的转录区域是一个规模合理且已简化的靶向测序目标子集；且从转录区域获取的数据，其组成与生物学家传统研究中常用的数据（如外显子）类型相似。然而，以RNA为模板的分子技术（包括转录组测序）仅适用于极高质量的起始材料，而这类材料在多数具有生物学重要性的昆虫样本中往往难以获取。近期研究表明，若保守基因组元件存在于昆虫基因组中且可从中获取，基于DNA的保守基因组元件靶向富集技术，可为跨昆虫类群获取系统基因组数据提供另一途径。本研究鉴定出膜翅目（Hymenoptera）昆虫中共享的一套大规模超保守元件（ultraconserved elements, UCEs）集（n=1510）。我们通过计算机分析（in silico analyses）证实，这些基因座可准确重构已完成基因组测序的膜翅目类群间的系统发育关系；并设计了一套可用于富集这些基因座的RNA诱饵探针（RNA baits）集（n=2749），可供研究人员利用从多种来源提取的DNA模板开展实验。我们利用该UCE诱饵探针集，从30个膜翅目类群中平均富集得到721个UCE基因座，并借助这些基因座重构了膜翅目类群间跨度极大的系统发育关系——从极为古老（≥220 Ma）到极为新近（≤1 Ma）的分化事件。与近期一项利用转录组数据解析膜翅目系统发育的研究不同，我们的结果显示蚂蚁为所有其余针尾亚目类群的姐妹群，且得到完全支持——尽管这一结果可能受类群取样等因素影响。我们在阐明这一物种多样性与物种丰富度均位居前列的动物目类群的演化历史这一背景下，讨论了本研究的方法与结果。