Complete chloroplast genomes of Chinese wild-growing Vitis species: molecular structures and comparative and adaptive radiation analysis
Complete chloroplast genomes of Chinese wild-growing Vitis species: molecular structures and comparative and adaptive radiation analysis
复制标题
中国野生葡萄种的完整叶绿体基因组：分子结构以及比较和适应性辐射分析
DOI：
10.1007/s00709-020-01585-y
复制
发表时间：
2020-11-23
期刊：
影响因子：
2.9
通讯作者：
Xu, Weirong
中科院分区：
文献类型：
--
作者：
Xu, Guangya;Xu, Weirong
作为葡萄科的一个矮科，中国野生葡萄品种为葡萄的人口统计学历史提供了重要的见解。在本研究中，我们基于我们的全基因组重测序数据，获得了中国野生葡萄属植物的10个完整叶绿体（cp）基因组。这些叶绿体基因组的大小在160,838 ~ 232,020 bp之间，具有典型的四部结构。比较分析表明，倒置重复序列（IR）区域特别丰富，并有助于cp基因组排列。全基因组的系统发育分析支持三个明确的主要起源，与地理分布一致，其中来自中国的东亚种与欧亚葡萄属有亲缘关系，但与北美葡萄属有明显的差异。在中国野生葡萄种中观察到两个支持良好的亚群。其中，葡萄（Vitis piasezkii）与白花葡萄（Vitis betulifolia）亲缘关系较近，支持率为100%。基于分子钟的分化时间表明，最早的分裂亚种是葡萄树（Vitis pseudoreticulata），这进一步表明葡萄树的起源和初始基因库位于中国南方（葡萄树的栖息地位于该地区）。巧合的是，分化时间为更新世时期（2.6 ~ 0.1 Ma）。由于冰期/间冰期温度的波动，适应冷的亚种，如葡萄，可以重新定居在新的栖息地。本研究结果有助于阐明中国野生葡萄在不同环境下的适应性辐射。
As a basalmost family of Vitaceae, Chinese wild Vitis species offer key insights into the demographic history of grapes. In this study, we obtained 10 complete chloroplast (cp) genomes from Chinese wild-growing Vitis species based on our whole genome re-sequencing data. These chloroplast genomes ranged from 160,838 to 232,020 bp in size and exhibited typical quadripartite structures. Comparative analyses revealed that inverted repeat (IR) regions are especially abundant and contribute to cp genome arrangements. Phylogenetic analysis of the whole Vitis cp genomes supported three clearly partitioned main origins, in keeping with their geographic distributions, among which East Asian species from China were found to be sister species with Eurasian Vitis species but exhibited significant divergence from the North American group. Two well-supported subgroups were observed within the Chinese wild-growing Vitis species. Among these species, Vitis piasezkii and Vitis betulifolia were closely related species, exhibiting a support rate of 100%. The molecular clock-based divergence time suggested that the earliest split subspecies was Vitis pseudoreticulata, which further indicated that the origin and initial gene pool are located in southern China (the habitat of V. pseudoreticulata is located in the region). Coincidentally, the divergence time was during the Pleistocene period (2.6-0.1 Ma). Due to glacial/interglacial temperature fluctuations, cold-adapted subspecies, e.g., Vitis amurensis, could re-colonize new habitats. Our results may help to elucidate the adaptive radiation of Chinese wild Vitis species in different environments.