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

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 g...

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Autores principales: Zhang, Xu, Sun, Yanxia, Landis, Jacob B., Shen, Jun, Zhang, Huajie, Kuang, Tianhui, Sun, Wenguang, Sun, Jiao, Tiamiyu, Bashir B., Deng, Tao, Sun, Hang, Wang, Hengchang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8402177/
https://www.ncbi.nlm.nih.gov/pubmed/34451759
http://dx.doi.org/10.3390/plants10081715
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author Zhang, Xu
Sun, Yanxia
Landis, Jacob B.
Shen, Jun
Zhang, Huajie
Kuang, Tianhui
Sun, Wenguang
Sun, Jiao
Tiamiyu, Bashir B.
Deng, Tao
Sun, Hang
Wang, Hengchang
author_facet Zhang, Xu
Sun, Yanxia
Landis, Jacob B.
Shen, Jun
Zhang, Huajie
Kuang, Tianhui
Sun, Wenguang
Sun, Jiao
Tiamiyu, Bashir B.
Deng, Tao
Sun, Hang
Wang, Hengchang
author_sort Zhang, Xu
collection PubMed
description 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.
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spelling pubmed-84021772021-08-29 Transcriptomes of Saussurea (Asteraceae) Provide Insights into High-Altitude Adaptation Zhang, Xu Sun, Yanxia Landis, Jacob B. Shen, Jun Zhang, Huajie Kuang, Tianhui Sun, Wenguang Sun, Jiao Tiamiyu, Bashir B. Deng, Tao Sun, Hang Wang, Hengchang Plants (Basel) Article 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. MDPI 2021-08-20 /pmc/articles/PMC8402177/ /pubmed/34451759 http://dx.doi.org/10.3390/plants10081715 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Zhang, Xu
Sun, Yanxia
Landis, Jacob B.
Shen, Jun
Zhang, Huajie
Kuang, Tianhui
Sun, Wenguang
Sun, Jiao
Tiamiyu, Bashir B.
Deng, Tao
Sun, Hang
Wang, Hengchang
Transcriptomes of Saussurea (Asteraceae) Provide Insights into High-Altitude Adaptation
title Transcriptomes of Saussurea (Asteraceae) Provide Insights into High-Altitude Adaptation
title_full Transcriptomes of Saussurea (Asteraceae) Provide Insights into High-Altitude Adaptation
title_fullStr Transcriptomes of Saussurea (Asteraceae) Provide Insights into High-Altitude Adaptation
title_full_unstemmed Transcriptomes of Saussurea (Asteraceae) Provide Insights into High-Altitude Adaptation
title_short Transcriptomes of Saussurea (Asteraceae) Provide Insights into High-Altitude Adaptation
title_sort transcriptomes of saussurea (asteraceae) provide insights into high-altitude adaptation
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8402177/
https://www.ncbi.nlm.nih.gov/pubmed/34451759
http://dx.doi.org/10.3390/plants10081715
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