ArticleNature communications2024
Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed.
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- Phylogenomic profile of exon-intron organization across angiosperms, their relationships with protein domains, and functional implications.Nature communications · 2026Article
- Widespread turnover of a conserved cis-regulatory code across 589 grass species.Molecular biology and evolution · 2026Article
- Molecular characteristics and regulatory effects of dwarfing Rht genes in Triticum aestivum L.BMC plant biology · 2025Article
- The auxin gatekeepers: Evolution and diversification of the YUCCA family.The Plant journal : for cell and molecular biology · 2025Article
- SPEECHLESS duplication in grasses expands potential for environmental regulation of stomatal development.bioRxiv : the preprint server for biology · 2025Article
- Climate change and plant genomic plasticity.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Review
- The Sugar Transporter Gene Family in Colored Calla Lily: Identification, Expression Patterns, and Roles in Soft Rot Disease.Plants (Basel, Switzerland) · 2025Article
- Ancient allopolyploidy and specific subgenomic evolution drove the radiation of poplars and willows.Nature communications · 2025Article
- Learning from nature: photosynthetic traits conferring superior salt tolerance in wild ricePhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Pan-genome analysis reveals the evolution and diversity of Malus.Nature genetics · 2025Article
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Abstract
Poaceae members shared a whole-genome duplication called rho. However, little is known about the evolutionary pattern of the rho-derived duplicates among Poaceae lineages and implications in adaptive evolution. Here we present phylogenomic/phylotranscriptomic analyses of 363 grasses covering all 12 subfamilies and report nine previously unknown whole-genome duplications. Furthermore, duplications from a single whole-genome duplication were mapped to multiple nodes on the species phylogeny; a whole-genome duplication was likely shared by woody bamboos with possible gene flow from herbaceous bamboos; and recent paralogues of a tetraploid Oryza are implicated in tolerance of seawater submergence. Moreover, rho duplicates showing differential retention among subfamilies include those with functions in environmental adaptations or morphogenesis, including ACOT for aquatic environments (Oryzoideae), CK2β for cold responses (Pooideae), SPIRAL1 for rapid cell elongation (Bambusoideae), and PAI1 for drought/cold responses (Panicoideae). This study presents a Poaceae whole-genome duplication profile with evidence for multiple evolutionary mechanisms that contribute to gene retention and losses.
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