1State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China 2China National Botanical Garden, Beijing 100093, China 3University of Chinese Academy of Sciences, Beijing 100049, China 4Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China 5PubBio-Tech Services Corporation, Wuhan 430070, China 6Biology Department, Hope College, Holland, MI 49423, USA 7College of Life Sciences, Northwest Normal University, Lanzhou 730070, China 8School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China 9Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China 10Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China 11School of Life Science, Shanxi Normal University, Taiyuan 030031, China 12Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China 13Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA 14Department of Biology, University of Florida, Gainesville, FL 32611-7800, USA *Corresponding author. E-mail: dsoltis@ufl.edu,zhiduan@ibcas.ac.cn †Jian Zhang,Kai-Lin Dong,, Miao-Zhen Ren,Zhi-Wen Wang contributed equally to the study.
Received: 15 Oct 2023 Accepted: 08 Mar 2024 Published online: 01 May 2024
Abstract
How plants find a way to thrive in alpine habitats remains largely unknown. Here we present a chromosome-level genome assembly for an alpine medicinal herb, Triplostegia glandulifera (Caprifoliaceae), and 13 transcriptomes from other species of Dipsacales. We detected a whole-genome duplication event in T. glandulifera that occurred prior to the diversification of Dipsacales. Preferential gene retention after whole-genome duplication was found to contribute to increasing cold-related genes in T. glandulifera. A series of genes putatively associated with alpine adaptation (e.g. CBFs, ERF-VIIs, and RAD51C) exhibited higher expression levels in T. glandulifera than in its low-elevation relative, Lonicera japonica. Comparative genomic analysis among five pairs of high- vs low-elevation species, including a comparison of T. glandulifera and L. japonica, indicated that the gene families related to disease resistance experienced a significantly convergent contraction in alpine plants compared with their lowland relatives. The reduction in gene repertory size was largely concentrated in clades of genes for pathogen recognition (e.g. CNLs, prRLPs, and XII RLKs), while the clades for signal transduction and development remained nearly unchanged. This finding reflects an energy-saving strategy for survival in hostile alpine areas, where there is a tradeoff with less challenge from pathogens and limited resources for growth. We also identified candidate genes for alpine adaptation (e.g. RAD1, DMC1, and MSH3) that were under convergent positive selection or that exhibited a convergent acceleration in evolutionary rate in the investigated alpine plants. Overall, our study provides novel insights into the high-elevation adaptation strategies of this and other alpine plants.
, Zhi-Duan Chen,1,2,9 ,
