Abstract：
The proliferation of genomic sequencing approaches has significantly impacted the field of phylogenetics. Target capture approaches provide a cost-effective, fast and easily applied strategy for phylogenetic inference of non-model organisms. However, several existing target capture processing pipelines are incapable of incorporating whole genome sequencing (WGS). Here, we develop a new pipeline for capture and de novo assembly of the targeted regions using whole genome re-sequencing reads. This new pipeline captured targeted loci accurately, and given its unbiased nature, can be used with any target capture probe set. Moreover, due to its low computational demand, this new pipeline may be ideal for users with limited resources and when high-coverage sequencing outputs are required. We demonstrate the utility of our approach by incorporating WGS data into the first comprehensive phylogenomic reconstruction of the freshwater mussel family Margaritiferidae. We also provide a catalogue of well-curated functional annotations of these previously uncharacterized freshwater mussel-specific target regions, representing a complementary tool for scrutinizing phylogenetic inferences while expanding future applications of the probe set.
摘要：
基因组测序方法的增殖已经显著影响了系统遗传学领域。目标捕获方法提供了一种具有成本效益的，快速，易于应用的策略，用于非模型生物的系统发育推断。然而,一些现有的靶捕获处理流水线无法整合全基因组测序(WGS)。这里,我们开发了一种新的管道，用于使用全基因组重新测序读取捕获和从头组装靶向区域。这个新的管道准确地捕获了目标基因座，鉴于其不偏不倚的性质，可与任何靶捕获探针组一起使用。此外，由于其计算需求低，对于资源有限且需要高覆盖率测序输出的用户来说,这种新管道可能是理想的选择.我们通过将WGS数据纳入淡水贻贝家族Margaritiferidae的第一个全面系统基因组重建中，证明了我们方法的实用性。我们还提供了这些先前未表征的淡水贻贝特定目标区域的精心策划的功能注释目录，代表了一种补充工具，用于仔细检查系统发育推断，同时扩展了探针集的未来应用。
