J Integr Plant Biol. ›› 2023, Vol. 65 ›› Issue (7): 1620-1635.DOI: 10.1111/jipb.13485

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Genomic convergence underlying high-altitude adaptation in alpine plants

Xu Zhang1,2, Tianhui Kuang3, Wenlin Dong1,2,4, Zhihao Qian1,2,4, Huajie Zhang1,2, Jacob B. Landis5,6, Tao Feng1,2, Lijuan Li1,2,4, Yanxia Sun1,2, Jinling Huang3,7,8, Tao Deng3*, Hengchang Wang1,2* and Hang Sun3*   

  1. 1. CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan 430074, China;
    2. Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan 430074, China;
    3. Yunnan International Joint Laboratory for Biodiversity of Central Asia, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming 650201, China;
    4. University of Chinese Academy of Sciences, Beijing 100049, China;
    5. School of Integrative Plant Science, Section of Plant Biology and the L. H. Bailey Hortorium, Cornell University, Ithaca, New York 14850, USA;
    6. BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, New York 14853, USA;
    7. State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China;
    8. Department of Biology, East Carolina University, Greenville, North Carolina 27858, USA
    *Correspondences: Tao Deng (dengtao@mail.kib.ac.cn); Hengchang Wang (hcwang@wbgcas.cn); Hang Sun (sunhang@mail.kib.ac.cn, Dr. Sun is fully responsible for the distributions of the materials associated with this article)
  • Received:2022-11-18 Accepted:2023-03-21 Online:2023-03-24 Published:2023-07-01

Abstract: Evolutionary convergence is one of the most striking examples of adaptation driven by natural selection. However, genomic evidence for convergent adaptation to extreme environments remains scarce. Here, we assembled reference genomes of two alpine plants, Saussurea obvallata (Asteraceae) and Rheum alexandrae (Polygonaceae), with 37,938 and 61,463 annotated protein-coding genes. By integrating an additional five alpine genomes, we elucidated genomic convergence underlying high-altitude adaptation in alpine plants. Our results detected convergent contractions of disease-resistance genes in alpine genomes, which might be an energy-saving strategy for surviving in hostile environments with only a few pathogens present. We identified signatures of positive selection on a set of genes involved in reproduction and respiration (e.g., MMD1, NBS1, and HPR), and revealed signatures of molecular convergence on genes involved in self-incompatibility, cell wall modification, DNA repair and stress resistance, which may underlie adaptation to extreme cold, high ultraviolet radiation and hypoxia environments. Incorporating transcriptomic data, we further demonstrated that genes associated with cuticular wax and flavonoid biosynthetic pathways exhibit higher expression levels in leafy bracts, shedding light on the genetic mechanisms of the adaptive “greenhouse” morphology. Our integrative data provide novel insights into convergent evolution at a high-taxonomic level, aiding in a deep understanding of genetic adaptation to complex environments.

Key words: adaptation, alpine plants, evolutionary rates, genomic convergence, “greenhouse” morphology, high altitude

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