Complete chloroplast genomes of Chinese wild-growing Vitis species: molecular structures and comparative and adaptive ra
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ORIGINAL ARTICLE
Complete chloroplast genomes of Chinese wild-growing Vitis species: molecular structures and comparative and adaptive radiation analysis Guangya Xu 1 & Weirong Xu 2,3,4,5 Received: 18 May 2020 / Accepted: 11 November 2020 # Springer-Verlag GmbH Austria, part of Springer Nature 2020
Abstract 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. Keywords Chloroplast genomes . Chinese wild Vitis . Phylogenetic relationship . Adaptive radiation
Introduction As an important and basalmost family of Vitaceae, grapevine (Vitis L.) is widely viticultured and utilized worldwide, there Handling Editor: Handling Editor: Hanns H. Kassemeyer * Weirong Xu [email protected] 1
School of Agronomy, Ningxia University, Yinchuan 750021, Ningxia, People’s Republic of China
2
School of Food & Wine, Ningxia University, Yinchuan 750021, Ningxia, People’s Republic of China
3
Engineering Research Center of Grape and Wine, Ministry of Education, Ningxia University, Yinchuan 750021, Ningxia, People’s Republic of China
4
Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan 750021, China
5
Chinese Wine Industry Technology Institute, Yinchuan 750021, China
are 8000–10,000 grape varieties worldwide (Ramezani et al. 2009), most of which are distributed in the Northern Hemisphere (Wen et al. 2007; Zecca et al. 2012; Aradhya et al. 2013; Ma et al. 2016; Wen et al. 2018). Taxonomically, the genus Vitis is typical
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