Zhang Ren-Gang, Zhao Hang, Conover Justin L, Shang Hong-Yun, Liu De-Tuan, Zhou Min-Jie, Liu Xiong-Fang, Jia Kai-Hua, Shao Shi-Cheng, Li Meng-Meng, Jin Chong-Yang, Liu Yi-Hui, Shen Xiao-Yi, Li Da-Wei, Lysak Martin A, Wendel Jonathan F, Ge Xiao-Yang, Ma Yong-Peng
Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
University of Chinese Academy of Sciences, Beijing, 101408, China.
Nat Commun. 2025 Aug 12;16(1):7480. doi: 10.1038/s41467-025-62644-7.
Polyploidy and subsequent post-polyploid diploidization (PPD) are key drivers of plant genome evolution, yet their contributions to evolutionary success remain debated. Here, we analyze the Malvaceae family as an exemplary system for elucidating the evolutionary role of polyploidy and PPD in angiosperms, leveraging 11 high-quality chromosome-scale genomes from all nine subfamilies, including newly sequenced, near telomere-to-telomere assemblies from four of these subfamilies. Our findings reveal a complex reticulate paleoallopolyploidy history early in the diversification of the Malvadendrina clade, characterized by multiple rounds of species radiation punctuated by ancient allotetraploidization (Mal-β) and allodecaploidization (Mal-α) events around the Cretaceous-Paleogene (K-Pg) boundary. We further reconstruct the evolutionary dynamics of PPD and find a strong correlation between dysploidy rate and taxonomic richness of the paleopolyploid subfamilies (R ≥ 0.90, P < 1e-4), supporting the "polyploidy for survival and PPD for success" hypothesis. Overall, our study provides a comprehensive reconstruction of the evolutionary history of the Malvaceae and underscores the crucial role of polyploidy-dysploidy waves in shaping plant biodiversity.
多倍体以及随后的多倍体后二倍体化（PPD）是植物基因组进化的关键驱动力，但其对进化成功的贡献仍存在争议。在这里，我们以锦葵科为典范系统，利用来自所有九个亚科的11个高质量染色体水平基因组，包括其中四个亚科新测序的、近乎端粒到端粒的组装序列，来阐明多倍体和PPD在被子植物中的进化作用。我们的研究结果揭示了锦葵亚科分支多样化早期复杂的网状古多倍体历史，其特征是在白垩纪-古近纪（K-Pg）边界附近发生了多轮物种辐射，并穿插着古代异源四倍体化（Mal-β）和异源十聚体化（Mal-α）事件。我们进一步重建了PPD的进化动态，发现古多倍体亚科的染色体数变异率与分类丰富度之间存在很强的相关性（R≥0.90，P<1e-4），支持“多倍体求生存，PPD促成功”假说。总体而言，我们的研究全面重建了锦葵科的进化历史，并强调了多倍体-染色体数变异浪潮在塑造植物生物多样性中的关键作用。
