Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA, 16802, USA.
Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China.
Nat Commun. 2024 Apr 17;15(1):3305. doi: 10.1038/s41467-024-47428-9.
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.
禾本科成员共享了一次全基因组加倍，称为 rho。然而，关于 rho 衍生的重复在禾本科谱系中的进化模式及其在适应性进化中的意义，我们知之甚少。在这里，我们对涵盖所有 12 个亚科的 363 种禾本科植物进行了基因组/转录组分析，并报告了 9 个以前未知的全基因组加倍。此外，来自单个全基因组加倍的重复被映射到物种系统发育树上的多个节点；木本竹子可能与草本竹子共享全基因组加倍，并且可能存在基因流；四倍体稻的最近的旁系同源物与耐海水淹没有关。此外，在亚科间表现出差异保留的 rho 重复包括那些具有环境适应或形态发生功能的重复，包括水生环境的 ACOT（稻亚科）、冷反应的 CK2β（Pooidae）、快速细胞伸长的 SPIRAL1（竹亚科）和干旱/冷反应的 PAI1（Panicoideae）。本研究展示了禾本科全基因组加倍的概况，并提供了多种进化机制的证据，这些机制有助于基因的保留和丢失。
