Comparison of taxon-specific versus general locus sets for targeted sequence capture for plant phylogenomics

Premise of the study: Targeted sequence capture can be used to efficiently gather sequence data for large numbers of loci, such as single-copy nuclear loci. Most published studies in plants have used taxon-specific locus sets developed individually for a clade using multiple genomic and transcriptomic resources. General locus sets can also be developed from loci that have been identified as single-copy and having orthologs in large clades of plants. Methods: We identify and compare a taxon-specific locus set and three general locus sets (COSII, APVO SSC, PPR) for targeted sequence capture in Buddleja (Scrophulariaceae) and outgroups. We evaluate their performance in terms of assembly success, sequence variability, and resolution and support of inferred phylogenetic trees. Results: The taxon-specific locus set had the most target loci. Assembly success was high for all locus sets in Buddleja samples. For outgroups, general locus sets had greater assembly success. Taxon-specific and PPR l...

研究背景：靶向序列捕获（targeted sequence capture）可用于高效获取大量基因座的序列数据，例如单拷贝核基因座（single-copy nuclear loci）。目前已发表的多数植物学研究均采用类群特异性基因座集（taxon-specific locus sets），这类基因座集通过多套基因组与转录组资源，针对单个演化支（clade）单独开发。此外，也可从已被鉴定为单拷贝且在植物大型演化支中存在直同源基因（orthologs）的基因座中开发通用基因座集。
研究方法：本研究鉴定并比较了一套类群特异性基因座集与三套通用基因座集（COSII、APVO SSC、PPR），用于醉鱼草属（Buddleja，玄参科Scrophulariaceae）及其外类群的靶向序列捕获实验。我们从组装成功率、序列变异度以及系统发育树的解析度与支持度三个维度，评估了各基因座集的实验表现。
研究结果：类群特异性基因座集的靶标基因座数量最多。醉鱼草属样本的所有基因座集均实现了较高的组装成功率。对于外类群而言，通用基因座集展现出更优的组装成功率。类群特异性基因座集与PPR……