Duplication Genes in 558 Genomes across 352 Plant Species

This study presents a comprehensive analysis of gene duplication across 558 high-quality plant genomes, encompassing 352 species from 221 genera across five phyla, ranging from algae to angiosperms. A modified DupGen_finder pipeline was used to identify gene duplications. Briefly, all-versus-all BLASTP was performed via OrthoFinder to search for potential homologous gene pairs. DupGen_finder was then used to identify whole-genome duplication (WGD), proximal duplication (PD), tandem duplication (TD), transposed duplication (TRD), and dispersed duplication (DSD) gene pairs. For further analysis, we focused only on TRD and DSD genes, as WGD, PD and TD duplicates may not have been caused by TEs. Next, we filtered out gene pairs without TE evidence support (requiring cosine similarity >0.5 of TE components between the two genes of each gene pair).本研究对558个高质量植物基因组中的基因复制现象开展了全面分析，涵盖5个门下221个属的352个物种，演化跨度从藻类至被子植物。本研究采用改良版DupGen_finder分析流程识别基因复制事件：首先通过OrthoFinder完成全对全BLASTP比对，以筛选潜在同源基因对；随后借助DupGen_finder工具，鉴定出全基因组复制（whole-genome duplication, WGD）、近端复制（proximal duplication, PD）、串联复制（tandem duplication, TD）、转座复制（transposed duplication, TRD）以及分散复制（dispersed duplication, DSD）共五类基因复制对。为开展后续分析，本研究仅聚焦TRD与DSD类基因，原因在于WGD、PD及TD复制事件可能并非由转座因子（transposable element, TE）介导。本研究进一步过滤掉无转座因子证据支持的基因对，要求每对基因的转座因子组分余弦相似度需大于0.5。