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Transcriptomes of Saussurea (Asteraceae) Provide Insights into High-Altitude Adaptation

CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
University of Chinese Academy of Sciences, Beijing 100049, China
Section of Plant Biology and the L.H. Bailey Hortorium, School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA
BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY 14853, USA
State Key Laboratory of Rice Biology, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
School of Life Science, Yunnan Normal University, Yunnan 650500, China
Authors to whom correspondence should be addressed.
Academic Editor: Ioannis Ganopoulos
Plants 2021, 10(8), 1715;
Received: 28 July 2021 / Revised: 10 August 2021 / Accepted: 10 August 2021 / Published: 20 August 2021
Understanding how species adapt to extreme environments is an extension of the main goals of evolutionary biology. While alpine plants are an ideal system for investigating the genetic basis of high-altitude adaptation, genomic resources in these species are still limited. In the present study, we generated reference-level transcriptomic data of five Saussurea species through high-throughput sequencing and de novo assembly. Three of them are located in the highland of the Qinghai-Tibet Plateau (QTP), and the other two are close relatives distributed in the lowland. A series of comparative and evolutionary genomics analyses were conducted to explore the genetic signatures of adaptive evolution to high-altitude environments. Estimation of divergence time using single-copy orthologs revealed that Saussurea species diversified during the Miocene, a period with extensive tectonic movement and climatic fluctuation on the QTP. We characterized gene families specific to the alpine species, including genes involved in oxidoreductase activity, pectin catabolic process, lipid transport, and polysaccharide metabolic process, which may play important roles in defense of hypoxia and freezing temperatures of the QTP. Furthermore, in a phylogenetic context with the branch model, we identified hundreds of genes with signatures of positive selection. These genes are involved in DNA repair, membrane transport, response to UV-B and hypoxia, and reproductive processes, as well as some metabolic processes associated with nutrient intake, potentially responsible for Saussurea adaptation to the harsh environments of high altitude. Overall, our study provides valuable genomic resources for alpine species and gained helpful insights into the genomic basis of plants adapting to extreme environments. View Full-Text
Keywords: high-altitude adaptation; Saussurea; transcriptomes; positive selection; extreme environments; lineage-specific genes high-altitude adaptation; Saussurea; transcriptomes; positive selection; extreme environments; lineage-specific genes
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MDPI and ACS Style

Zhang, X.; Sun, Y.; Landis, J.B.; Shen, J.; Zhang, H.; Kuang, T.; Sun, W.; Sun, J.; Tiamiyu, B.B.; Deng, T.; Sun, H.; Wang, H. Transcriptomes of Saussurea (Asteraceae) Provide Insights into High-Altitude Adaptation. Plants 2021, 10, 1715.

AMA Style

Zhang X, Sun Y, Landis JB, Shen J, Zhang H, Kuang T, Sun W, Sun J, Tiamiyu BB, Deng T, Sun H, Wang H. Transcriptomes of Saussurea (Asteraceae) Provide Insights into High-Altitude Adaptation. Plants. 2021; 10(8):1715.

Chicago/Turabian Style

Zhang, Xu, Yanxia Sun, Jacob B. Landis, Jun Shen, Huajie Zhang, Tianhui Kuang, Wenguang Sun, Jiao Sun, Bashir B. Tiamiyu, Tao Deng, Hang Sun, and Hengchang Wang. 2021. "Transcriptomes of Saussurea (Asteraceae) Provide Insights into High-Altitude Adaptation" Plants 10, no. 8: 1715.

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