J Integr Plant Biol.

• Research Article • Previous Articles    

Plastid and nuclear phylogenomics of Cyphostemma (Vitaceae) provide new insights into genome size evolution across sub-Saharan Africa

Rindra M. Ranaivoson1,2,3,4†, Romer N. Rabarijaona1,2†, Jin-Ren Yu1,2,3, Yi-Chen You1,2,3, Russell L. Barrett5,6, Ju Zhou1,2,3, Bing Liu1,2,7, Wyckliffe Omondi Omollo1,2, Chuan-Yu Du1,2,3, Da-Ming Zhang1,2, Mijoro Rakotoarinivo4, Jie Cheng1,2,8, Chao-Bin Li1,2, Yang Dong1,2, Ilia J. Leitch9, Alexandre Antonelli9,10,11,12, Jun Wen13, Zhi-Duan Chen1,2,7* and Li-Min Lu1,2*   

  1. 1. State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
    2. China National Botanical Garden, Beijing 100093, China
    3. University of Chinese Academy of Sciences, Beijing 100049, China
    4. Department of Plant Biology and Ecology, Faculty of Sciences, University of Antananarivo, Antananarivo BP 906, Madagascar
    5. National Herbarium of New South Wales, Australian Botanic Garden, Mount Annan 6002, Australia
    6. Evolution and Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, University of New South Wales, Kensington 2052, Australia
    7. Sino-Africa Joint Research Center, The Chinese Academy of Sciences, Wuhan 430074, China
    8. Department of Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, UK
    9. Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
    10. Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg SE-41319, Sweden
    11. Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan 430074, China
    12. Department of Biology, University of Oxford, Oxford OX1 3RB, UK
    13. Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA
    These authors contributed equally to this work.
    *Correspondences: Zhi-Duan Chen (zhiduan@ibcas.ac.cn); Li-Min Lu (liminlu@ibcas.ac.cn, Dr. Lu is fully responsible for the distribution of all materials associated with this article)
  • Received:2025-06-15 Accepted:2025-11-20 Online:2026-01-08
  • Supported by:
    This study was supported by the National Natural Science Foundation of China (32221001, 32270230), the National Key Research Development Program of China (2022YFC2601200, 2023YFF0805800), the International Partnership Program of CAS (063GJHZ2024053FN, 151853 KYSB20190027), the Youth Innovation Promotion Association CAS (2020080), and the Sino-Africa Joint Research Center, CAS International Research and Education Development Program (SAJC202527ZD01).

Abstract: Genome size, the total amount of DNA content in the cell nucleus, varies greatly among flowering plants. One factor underlying this variation is the environment under which plants evolve. Given this premise, harsh environmental conditions in arid regions may profoundly influence genome evolution. However, the specific impact of aridification on genome size evolution, particularly for African lineages, remains largely unexplored. Here, we investigate linkages between genome size evolution and ecological adaptation using the genus Cyphostemma in the grape family (Vitaceae) as a model. Cyphostemma species exhibit genome size expansion and remarkable morphological traits in arid environments, including succulent stems or leaves and loss of tendrils. Our biogeographic reconstruction, based on substantial taxon sampling (112 of 200 species), reveals that Cyphostemma originated in continental Africa during the late Eocene to Oligocene and has undergone rapid radiation since the middle Miocene, coinciding with intensified aridification and geological activity in eastern Africa. Incorporating extensive data on traits, habitats, genome size, and chromosome numbers, we show that Cyphostemma species with the largest genomes are succulent polyploids restricted to nutrient-rich limestone outcrops. Broad-scale analyses across eudicots further confirm that larger genomes are significantly associated with both succulence and arid habitats. Our findings reveal a strong association between genome size expansion, polyploidy, and adaptive traits, indicating that genome size is a hitherto neglected trait associated with the radiation of succulent plants during the African aridification in the Cenozoic.

Key words: aridification, Cyphostemma, diversification, ecological adaptation, genome size

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