Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China.
Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC 20013-7012, USA.
Mol Phylogenet Evol. 2018 Dec;129:258-267. doi: 10.1016/j.ympev.2018.08.021. Epub 2018 Sep 6.
The application of whole-genome resequencing based on next-generation sequencing technologies provides an unprecedented opportunity for researchers to resolve long-standing evolutionary problems. Taxa belonging to the grape genus (Vitis L.) represent important genetic resources for the improvement of cultivated grapes. However, it has been challenging to resolve the deep phylogenetic relationships within Vitis, limiting the current understanding of the evolutionary history of Vitis and preventing the use of valuable wild grape resources. In this study, we obtained whole-genome sequence data from 41 accessions representing most taxa within subgenus Vitis and aligned these sequences to the Vitis vinifera L. reference genome. We reconstructed deep phylogenetic relationships within subgenus Vitis based on 2068 single-copy orthologous genes, which led to a robust topology with bootstrap support values of 100% for almost all branches. Three main clades are recovered within subgenus Vitis reflecting their continental distribution through North America, Europe, and East Asia, respectively. Our results suggest that the most possible migration route of the East Asian Vitis is from northeastern Asia southward to South Asia and Southeast Asia. The East Asian Vitis seems to have experienced adaptive radiation during the Miocene. This study provides novel insights into the diversification history of the grape genus Vitis.
基于新一代测序技术的全基因组重测序的应用为研究人员解决长期存在的进化问题提供了前所未有的机会。属于葡萄属（Vitis L.）的物种代表了栽培葡萄改良的重要遗传资源。然而，葡萄属内的深层系统发育关系一直难以解决，限制了目前对葡萄属进化历史的理解，并阻碍了有价值的野生葡萄资源的利用。在这项研究中，我们从代表亚属葡萄属内大多数类群的 41 个样本中获得了全基因组序列数据，并将这些序列与欧亚葡萄（Vitis vinifera L.）参考基因组进行了比对。我们基于 2068 个单拷贝直系同源基因重建了葡萄属内的深层系统发育关系，得到了一个稳健的拓扑结构，几乎所有分支的自举支持值都达到 100%。在葡萄属内发现了三个主要的分支，反映了它们在北美的、欧洲的和东亚的大陆分布。我们的结果表明，东亚葡萄属最有可能的迁移路线是从东北亚向南到南亚和东南亚。东亚葡萄属似乎在中新世经历了适应性辐射。这项研究为葡萄属的多样化历史提供了新的见解。
