Analysis of paralogs in target enrichment data pinpoints multiple ancient polyploidy events in Alchemilla s.l. (Rosaceae)

Target enrichment is becoming increasingly popular for phylogenomic studies. Although baits for enrichment are typically designed to target single-copy genes, paralogs are often recovered with increased sequencing depth, sometimes from a significant proportion of loci, especially in groups experiencing whole-genome duplication (WGD) events. Common approaches for processing paralogs in target enrichment data sets include random selection, manual pruning, and mainly, the removal of entire genes that show any evidence of paralogy. These approaches are prone to errors in orthology inference or removing large numbers of genes. By removing entire genes, valuable information that could be used to detect and place WGD events is discarded. Here we used an automated approach for orthology inference in a target enrichment data set of 68 species of Alchemilla s.l. (Rosaceae), a widely distributed clade of plants primarily from temperate climate regions. Previous molecular phylogenetic studies and c...

靶向富集（Target Enrichment）在系统基因组学研究中的应用愈发普及。尽管富集探针通常被设计用于靶向单拷贝基因，但随着测序深度增加，往往会回收得到旁系同源基因（paralogs）；这类情况在部分基因座中占比可观，尤其多见于经历过全基因组复制（Whole-Genome Duplication, WGD）事件的类群。目前处理靶向富集数据集中旁系同源基因的常用方法包括随机选择、手动剔除，以及最主要的——移除所有存在旁系同源迹象的完整基因。这类方法极易导致直系同源（orthology）推断出错，或是剔除大量基因。若直接移除完整基因，本可用于检测及定位全基因组复制事件的宝贵信息也会随之丢失。本研究针对涵盖68种广义羽衣草属（Alchemilla s.l.，蔷薇科Rosaceae）物种的靶向富集数据集，采用自动化方法开展直系同源推断；该类群为分布广泛的植物支系，主要生长于温带区域。此前的分子系统发育研究及……