High‐throughput sequencing of transcriptomes and targeted genomic regions are advancing our knowledge of The Tree of Life. Building phylogenies with regions of the genome requires 1‐to‐1 orthologue resources of genes and noncoding loci. One organismal group that has received little attention in this area is the Hemiptera, the fifth largest insect order represented by ~103,590 named species. Here, we present a set of 3,872 Hemiptera 1‐to‐1 orthogroups based on tree‐based orthology inference of eight Hemiptera species with publicly available genome sequences. We also estimate a set of 406 orthologous exons with similar mRNA splice sites that can be used for Sanger sequencing and develop enrichment probes for targeted genome sequencing for phylogenomic inference. We show this novel set of orthologues is informative at the protein, coding sequence and exon molecular levels and provides robust branch support in both gene tree–species tree methods and concatenated sequence phylogenies. In addition, we demonstrate the utility of these loci to resolve relationships in whiteflies, Bemisia tabaci, a large species complex with few phylogenomic resources. Last, we compare our Hemiptera phylogeny with previously published phylogenies and other orthologue databases, while providing suggestions on further improvement to this phylogenomic resource.

中文翻译：

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半翅目系统基因组资源：基于树的直系预测和保守外显子鉴定。

转录组和靶向基因组区域的高通量测序正在推进我们对生命之树的了解。用基因组区域构建系统发育需要一对一的基因和非编码基因座的直系同源资源。在该领域很少受到关注的一个生物群是半翅目，它是第五大昆虫目，由约 103,590 个命名物种代表。在这里，我们基于具有公开可用基因组序列的八个半翅目物种的基于树的直系学推断，提出了一组 3,872 个半翅目 1 对 1 直立群。我们还估计了一组 406 个具有相似 mRNA 剪接位点的直系同源外显子，可用于 Sanger 测序，并开发富集探针用于系统发育推断的靶向基因组测序。我们展示了这组新的直向同源物对蛋白质的信息，编码序列和外显子分子水平，并在基因树 - 物种树方法和串联序列系统发育中提供强大的分支支持。此外，我们证明了这些位点在解决粉虱中的关系方面的效用，烟粉虱，一种系统发育资源很少的大型物种复合体。最后，我们将我们的半翅目系统发育与之前发表的系统发育和其他直系同源数据库进行了比较，同时提供了进一步改进该系统发育资源的建议。