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).