Sha Li-Na, Chen Ning, Chen Shi-Yong, Zhang Yue, Cheng Yi-Ran, Wu Dan-Dan, Wang Yi, Kang Hou-Yang, Zhang Hai-Qin, Ma Xiao, Zhou Yong-Hong, Fan Xing
College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
BMC Plant Biol. 2025 Jan 9;25(1):32. doi: 10.1186/s12870-025-06051-6.
The St-genome-sharing taxa are highly complex group of the species with the St nuclear genome and monophyletic origin in maternal lineages within the Triticeae, which contains more than half of polyploid species that distributed in a wide range of ecological habitats. While high level of genetic heterogeneity in plastome DNA due to a reticulate evolutionary event has been considered to link with the richness of the St-genome-sharing taxa, the relationship between the dynamics of diversification and molecular evolution is lack of understanding.
Here, integrating 106 previously and 12 newly sequenced plastomes representing almost all previously recognized genomic types and genus of the Triticeae, this study applies phylogenetic reconstruction methods in combination with lineage diversification analyses, estimate of sequence evolution, and gene expression to investigate the dynamics of diversification in the tribe. Phylogenomic analysis confirmed previous phylogenetic relationships, with the St/E/V lineages (Pseudoroegneria/Lophopyrum + Thinopyrum/Dasypyrum) being suffered from a chloroplast capture event prior to polyploidization events. Analyses of diversification rates detected a significant acceleration approximately five million years ago in the St-genome-sharing taxa. Molecular tests of evolution and gene expression further indicated that radiation within the accelerated group has been accompanied by adaptive genetic changes in a few chloroplast-encoded genes directly or indirectly related to photosynthesis.
Our results support an important role for adaptive evolution in plastomes during accelerated diversification. In combination with plastome data, further investigations using other genomes, such as the nuclear genome, are urgently needed to enhance our understanding of the evolutionary history of the St-genome-sharing taxa, especially to determine whether adaptive changes in the nuclear genome are accelerated as well because plastome represents the maternal inheritation in angiosperms.
具有St核基因组且母系谱系单系起源的St基因组共享类群是小麦族中高度复杂的物种群体，该类群包含超过一半的多倍体物种，分布于广泛的生态栖息地。虽然由于网状进化事件导致质体基因组DNA存在高度遗传异质性被认为与St基因组共享类群的丰富性有关，但对多样化动态与分子进化之间的关系仍缺乏了解。
本研究整合了106个先前测序和12个新测序的质体基因组，这些质体基因组几乎代表了小麦族所有先前认可的基因组类型和属，应用系统发育重建方法结合谱系多样化分析、序列进化估计和基因表达来研究该族的多样化动态。系统基因组分析证实了先前的系统发育关系，即St/E/V谱系（拟鹅观草属/鹅观草属+披碱草属/厚穗草属）在多倍体化事件之前经历了叶绿体捕获事件。多样化速率分析检测到大约500万年前St基因组共享类群的多样化显著加速。进化和基因表达的分子测试进一步表明，加速类群内的辐射伴随着一些与光合作用直接或间接相关的叶绿体编码基因的适应性遗传变化。
我们的结果支持了在加速多样化过程中质体基因组适应性进化的重要作用。结合质体基因组数据，迫切需要使用其他基因组（如核基因组）进行进一步研究，以加深我们对St基因组共享类群进化历史的理解，特别是确定核基因组中的适应性变化是否也会加速，因为质体基因组代表被子植物中的母系遗传。
