Genetic Adaptation of Giant Lobelias (Lobelia aberdarica and Lobelia telekii) to Different Altitudes in East African Mountains
Identifieur interne : 002015 ( Ncbi/Curation ); précédent : 002014; suivant : 002016Genetic Adaptation of Giant Lobelias (Lobelia aberdarica and Lobelia telekii) to Different Altitudes in East African Mountains
Auteurs : Shu-Ying Zhao [République populaire de Chine] ; Ling-Yun Chen [République populaire de Chine] ; John K. Muchuku [République populaire de Chine] ; Guang-Wan Hu [République populaire de Chine] ; Qing-Feng Wang [République populaire de Chine]Source :
- Frontiers in Plant Science [ 1664-462X ] ; 2016.
Abstract
The giant lobelias in East African mountains are good models for studying molecular mechanisms of adaptation to different altitudes. In this study, we generated RNA-seq data of a middle-altitude species
Url:
DOI: 10.3389/fpls.2016.00488
PubMed: 27148313
PubMed Central: 4828460
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genetic Adaptation of Giant Lobelias (<italic>Lobelia aberdaric</italic>a and <italic>Lobelia telekii</italic>) to Different Altitudes in East African Mountains</title><author><name sortKey="Zhao, Shu Ying" sort="Zhao, Shu Ying" uniqKey="Zhao S" first="Shu-Ying" last="Zhao">Shu-Ying Zhao</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences</institution><country>Wuhan, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Sino-Africa Joint Research Centre, Chinese Academy of Sciences</institution><country>Wuhan, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Chen, Ling Yun" sort="Chen, Ling Yun" uniqKey="Chen L" first="Ling-Yun" last="Chen">Ling-Yun Chen</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences</institution><country>Wuhan, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Sino-Africa Joint Research Centre, Chinese Academy of Sciences</institution><country>Wuhan, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Muchuku, John K" sort="Muchuku, John K" uniqKey="Muchuku J" first="John K." last="Muchuku">John K. Muchuku</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences</institution><country>Wuhan, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Sino-Africa Joint Research Centre, Chinese Academy of Sciences</institution><country>Wuhan, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Hu, Guang Wan" sort="Hu, Guang Wan" uniqKey="Hu G" first="Guang-Wan" last="Hu">Guang-Wan Hu</name><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Sino-Africa Joint Research Centre, Chinese Academy of Sciences</institution><country>Wuhan, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Wang, Qing Feng" sort="Wang, Qing Feng" uniqKey="Wang Q" first="Qing-Feng" last="Wang">Qing-Feng Wang</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences</institution><country>Wuhan, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Sino-Africa Joint Research Centre, Chinese Academy of Sciences</institution><country>Wuhan, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27148313</idno><idno type="pmc">4828460</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4828460</idno><idno type="RBID">PMC:4828460</idno><idno type="doi">10.3389/fpls.2016.00488</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000320</idno><idno type="wicri:Area/Pmc/Curation">000319</idno><idno type="wicri:Area/Pmc/Checkpoint">000170</idno><idno type="wicri:Area/Ncbi/Merge">002015</idno><idno type="wicri:Area/Ncbi/Curation">002015</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Genetic Adaptation of Giant Lobelias (<italic>Lobelia aberdaric</italic>a and <italic>Lobelia telekii</italic>) to Different Altitudes in East African Mountains</title><author><name sortKey="Zhao, Shu Ying" sort="Zhao, Shu Ying" uniqKey="Zhao S" first="Shu-Ying" last="Zhao">Shu-Ying Zhao</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences</institution><country>Wuhan, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Sino-Africa Joint Research Centre, Chinese Academy of Sciences</institution><country>Wuhan, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Chen, Ling Yun" sort="Chen, Ling Yun" uniqKey="Chen L" first="Ling-Yun" last="Chen">Ling-Yun Chen</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences</institution><country>Wuhan, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Sino-Africa Joint Research Centre, Chinese Academy of Sciences</institution><country>Wuhan, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Muchuku, John K" sort="Muchuku, John K" uniqKey="Muchuku J" first="John K." last="Muchuku">John K. Muchuku</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences</institution><country>Wuhan, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Sino-Africa Joint Research Centre, Chinese Academy of Sciences</institution><country>Wuhan, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Hu, Guang Wan" sort="Hu, Guang Wan" uniqKey="Hu G" first="Guang-Wan" last="Hu">Guang-Wan Hu</name><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Sino-Africa Joint Research Centre, Chinese Academy of Sciences</institution><country>Wuhan, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author><author><name sortKey="Wang, Qing Feng" sort="Wang, Qing Feng" uniqKey="Wang Q" first="Qing-Feng" last="Wang">Qing-Feng Wang</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences</institution><country>Wuhan, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Sino-Africa Joint Research Centre, Chinese Academy of Sciences</institution><country>Wuhan, China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea></wicri:regionArea></affiliation></author></analytic><series><title level="j">Frontiers in Plant Science</title><idno type="eISSN">1664-462X</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The giant lobelias in East African mountains are good models for studying molecular mechanisms of adaptation to different altitudes. In this study, we generated RNA-seq data of a middle-altitude species <italic>Lobelia aberdarica</italic> and a high-altitude species <italic>L. telekii</italic>, followed by selective pressure estimation of their orthologous genes. Our aim was to explore the important genes potentially involved in adaptation to different altitudes. About 9.3 Gb of clean nucleotides, 167,929–170,534 unigenes with total lengths of 159,762,099–171,138,936 bp for each of the two species were generated. OrthoMCL method identified 3,049 1:1 orthologous genes (each species was represented by one ortholog). Estimations of non-synonymous to synonymous rate were performed using an approximate method and a maximum likelihood method in PAML. Eighty-five orthologous genes were under positive selection. At least 8 of these genes are possibly involved in DNA repair, response to DNA damage and temperature stimulus, and regulation of gene expression, which hints on how giant lobelias adapt to high altitudinal environment that characterized by cold, low oxygen, and strong ultraviolet radiation. The negatively selected genes are over-represented in Gene Ontology terms of hydrolase, macromolecular complex assembly among others. This study sheds light on understanding the molecular mechanism of adaptation to different altitudes, and provides genomic resources for further studies of giant lobelias.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Agnew, A D Q" uniqKey="Agnew A">A. D. Q. Agnew</name></author><author><name sortKey=" Shirley Agnew" uniqKey=" Shirley Agnew"> Shirley-Agnew</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Beck, E" uniqKey="Beck E">E. 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