Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, USA.
Department of Entomology, University of California, Riverside, CA, USA; Department Ecology and Evolutionary Biology, University of Connecticut, Hartford, CT, USA.
Mol Phylogenet Evol. 2019 Jan;130:297-303. doi: 10.1016/j.ympev.2018.10.026. Epub 2018 Oct 22.
Target enrichment of conserved genomic regions facilitates collecting sequences of many orthologous loci from non-model organisms to address phylogenetic, phylogeographic, population genetic, and molecular evolution questions. Bait sets for sequence capture can simultaneously target thousands of loci, which opens new avenues of research on speciose groups. Current phylogenetic hypotheses on the >103,000 species of Hemiptera have failed to unambiguously resolve major nodes, suggesting that alternative datasets and more thorough taxon sampling may be required to resolve relationships. We use a recently designed ultraconserved element (UCE) bait set for Hemiptera, with a focus on the suborder Heteroptera, or the true bugs, to test previously proposed relationships. We present newly generated UCE data for 36 samples representing three suborders, all seven heteropteran infraorders, 23 families, and 34 genera of Hemiptera and one thysanopteran outgroup. To improve taxon sampling, we also mined additional UCE loci in silico from published hemipteran genomic and transcriptomic data. We obtained 2271 UCE loci for newly sequenced hemipteran taxa, ranging from 265 to 1696 (average 904) per sample. These were similar in number to the data mined from transcriptomes and genomes, but with fewer loci overall. The amount of missing data correlates with greater phylogenetic divergence from taxa used to design the baits. This bait set hybridizes to a wide range of hemipteran taxa and specimens of varying quality, including dried specimens as old as 1973. Our estimated phylogeny yielded topologies consistent with other studies for most nodes and was strongly-supported. We also demonstrate that UCE loci are almost exclusively from the transcribed portion of the genome, thus data can be successfully integrated with existing genomic and transcriptomic resources for more comprehensive phylogenetic sampling, an important feature in the era of phylogenomics. UCE approaches can be used by other researchers for additional studies on hemipteran evolution and other research that requires well resolved phylogenies.
靶向富集保守基因组区域有助于从非模式生物中收集许多同源基因座的序列，以解决系统发育、系统地理、种群遗传和分子进化问题。序列捕获的诱饵集可以同时靶向数千个基因座，这为研究种类繁多的群体开辟了新的途径。目前关于半翅目超过 103000 种物种的系统发育假设未能明确解决主要节点，这表明可能需要替代数据集和更彻底的分类群采样来解决关系。我们使用最近设计的半翅目超保守元件 (UCE) 诱饵集，重点是异翅亚目，或真正的虫子，以测试以前提出的关系。我们展示了 36 个样本的新生成的 UCE 数据，代表三个亚目、所有七个半翅目亚目、23 个科和 34 个属的半翅目和一个缨翅目外群。为了改善分类群采样，我们还从已发表的半翅目基因组和转录组数据中进行了额外的 UCE 基因座的计算机挖掘。我们从新测序的半翅目分类群中获得了 2271 个 UCE 基因座，每个样本的范围从 265 到 1696（平均 904）。这些与从转录组和基因组中挖掘的数据在数量上相似，但总体上基因座较少。缺失数据的数量与从设计诱饵的分类群中发生的更大的系统发育分歧相关。这个诱饵集与广泛的半翅目分类群和不同质量的标本杂交，包括 1973 年的干标本。我们估计的系统发育树产生的拓扑结构与其他研究大多数节点一致，并且得到了强烈支持。我们还表明，UCE 基因座几乎完全来自基因组的转录部分，因此可以成功地将数据与现有的基因组和转录组资源整合，以便进行更全面的系统发育采样，这是系统基因组学时代的一个重要特征。UCE 方法可被其他研究人员用于对半翅目进化和其他需要高度分辨率系统发育的研究进行进一步研究。
