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Complete chloroplast genomes of Chinese wild-growing Vitis species: molecular structures and comparative and adaptive radiation analysis

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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.

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Funding

This work was supported by the National Natural Science Foundation of China (31860542), the National Program for Key S & T Project (Grant number 106001000000150012), Major Science and Technology Program of Ningxia Hui Autonomous Region (Grant no. 2019BBF02022-02), and National Key Research and Development Project (Grant no. 2019YFD1002500).

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  1. School of Agronomy, Ningxia University, Yinchuan, 750021, Ningxia, People’s Republic of China

    Guangya Xu

  2. School of Food & Wine, Ningxia University, Yinchuan, 750021, Ningxia, People’s Republic of China

    Weirong Xu

  3. Engineering Research Center of Grape and Wine, Ministry of Education, Ningxia University, Yinchuan, 750021, Ningxia, People’s Republic of China

    Weirong Xu

  4. Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan, 750021, China

    Weirong Xu

  5. Chinese Wine Industry Technology Institute, Yinchuan, 750021, China

    Weirong Xu

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  1. Guangya Xu
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Xu, G., Xu, W. Complete chloroplast genomes of Chinese wild-growing Vitis species: molecular structures and comparative and adaptive radiation analysis. Protoplasma 258, 559–571 (2021). https://doi.org/10.1007/s00709-020-01585-y

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