Genomic analysis of field pennycress (Thlaspi arvense) provides insights into mechanisms of adaptation to high elevation

BMC Biology

Ticao Zhang¹  Miao An²  La Qiong³  Qin Qiao⁴  Ji Qi⁵  Shugang Lu⁶  M. James C. Crabbe⁷  Yupeng Geng⁸  Fangqing Zhao⁹  Yabin Guan^1,10 

[1] College of Chinese Material Medica, Yunnan University of Chinese Medicine, 650500, Kunming, China;Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200001, Shanghai, China;Research Center for Ecology, College of Science, Tibet University, 850000, Lhasa, China;School of Agriculture, Yunnan University, 650504, Kunming, China;School of Life Sciences, Fudan University, 200433, Shanghai, China;School of Life Sciences, Yunnan University, 650504, Kunming, China;Wolfson College, Oxford University, OX2 6UD, Oxford, UK;Institute of Biomedical and Environmental Science & Technology, School of Life Sciences, University of Bedfordshire, Park Square, LU1 3JU, Luton, UK;School of Life Sciences, Shanxi University, 030006, Taiyuan, China;Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, School of Ecology and Environmental Sciences, Yunnan University, 650500, Kunming, China;Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, School of Ecology and Environmental Sciences, Yunnan University, 650500, Kunming, China;Beijing Institutes of Life Science, Chinese Academy of Sciences, 100101, Beijing, China;University of Chinese Academy of Sciences, 100049, Beijing, China;Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223, Kunming, China;Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, School of Ecology and Environmental Sciences, Yunnan University, 650500, Kunming, China;School of Life Sciences, Yunnan University, 650504, Kunming, China;

关键词: Adaptive evolution;    Transposable elements;    Population genomics;    FLOWERING LOCUS C;    Qinghai-Tibet Plateau;   

DOI  :  10.1186/s12915-021-01079-0

来源: Springer

【 摘 要 】

BackgroundUnderstanding how organisms evolve and adapt to extreme habitats is of crucial importance in evolutionary ecology. Altitude gradients are an important determinant of the distribution pattern and range of organisms due to distinct climate conditions at different altitudes. High-altitude regions often provide extreme environments including low temperature and oxygen concentration, poor soil, and strong levels of ultraviolet radiation, leading to very few plant species being able to populate elevation ranges greater than 4000 m. Field pennycress (Thlaspi arvense) is a valuable oilseed crop and emerging model plant distributed across an elevation range of nearly 4500 m. Here, we generate an improved genome assembly to understand how this species adapts to such different environments.ResultsWe sequenced and assembled de novo the chromosome-level pennycress genome of 527.3 Mb encoding 31,596 genes. Phylogenomic analyses based on 2495 single-copy genes revealed that pennycress is closely related to Eutrema salsugineum (estimated divergence 14.32–18.58 Mya), and both species form a sister clade to Schrenkiella parvula and genus Brassica. Field pennycress contains the highest percentage (70.19%) of transposable elements in all reported genomes of Brassicaceae, with the retrotransposon proliferation in the Middle Pleistocene being likely responsible for the expansion of genome size. Moreover, our analysis of 40 field pennycress samples in two high- and two low-elevation populations detected 1,256,971 high-quality single nucleotide polymorphisms. Using three complementary selection tests, we detected 130 candidate naturally selected genes in the Qinghai-Tibet Plateau (QTP) populations, some of which are involved in DNA repair and the ubiquitin system and potential candidates involved in high-altitude adaptation. Notably, we detected a single base mutation causing loss-of-function of the FLOWERING LOCUS C protein, responsible for the transition to early flowering in high-elevation populations.ConclusionsOur results provide a genome-wide perspective of how plants adapt to distinct environmental conditions across extreme elevation differences and the potential for further follow-up research with extensive data from additional populations and species.

【 授权许可】

CC BY