Data from: Targeted capture of complete coding regions across divergent species

Despite continued advances in sequencing technologies, there is a need for methods that can efficiently sequence large numbers of genes from diverse species. One approach to accomplish this is targeted capture (hybrid enrichment). While these methods are well established for genome resequencing projects, cross-species capture strategies are still being developed and generally focus on the capture of conserved regions, rather than complete coding regions from specific genes of interest. The resulting data is thus useful for phylogenetic studies, but the wealth of comparative data that could be used for evolutionary and functional studies is lost. Here we design and implement a targeted capture method that enables recovery of complete coding regions across broad taxonomic scales. Capture probes were designed from multiple reference species and extensively tiled in order to facilitate cross-species capture. Using novel bioinformatics pipelines we were able to recover nearly all of the targeted genes with high completeness from species that were up to 200 myr divergent. Increased probe diversity and tiling for a subset of genes had a large positive effect on both recovery and completeness. The resulting data produced an accurate species tree, but importantly this same data can also be applied to studies of molecular evolution and function that will allow researchers to ask larger questions in broader phylogenetic contexts. Our method demonstrates the utility of cross-species approaches for the capture of full length coding sequences, and will substantially improve the ability for researchers to conduct large-scale comparative studies of molecular evolution and function.尽管测序技术不断取得进步，学界仍亟需可高效获取多样物种海量基因序列的研究方法。实现该目标的一类方法为靶向捕获（targeted capture，又称杂交富集）。尽管此类方法在基因组重测序项目中已十分成熟，但跨物种捕获策略仍处于开发阶段，且通常仅聚焦于保守区域的捕获，而非特定目的基因的完整编码区。因此，现有方法得到的数据仅适用于系统发育研究，但本可用于进化与功能研究的大量比较数据却因此丢失。本研究设计并实现了一种靶向捕获方法，可在宽泛的分类学尺度下获取完整的编码区序列。研究人员基于多个参考物种设计捕获探针，并进行高密度铺展以提升跨物种捕获效率。借助全新的生物信息学分析流程，我们可从分化时长达200百万年（myr）的物种中，近乎完整地回收全部目标基因。针对部分基因增加探针多样性与铺展密度，可显著提升目标基因的回收效率与序列完整度。该方法得到的数据不仅可构建高精度的物种树，更为关键的是，这些数据还可应用于分子进化与功能研究，使研究者能够在更宽泛的系统发育框架下探索更具广度的科学问题。本研究开发的方法证明了跨物种捕获策略在获取全长编码序列方面的实用性，将大幅提升研究者开展分子进化与功能领域大规模比较研究的能力。