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Genome of Crucihimalaya himalaica, a close relative of Arabidopsis, shows ecological adaptation to high altitude

Ticao Zhang, Qin Qiao, Polina Novikova (UGent) , Qia Wang, Jipei Yue, Yanlong Guan, Shengping Ming, Tianmeng Liu, Ji De, Yixuan Liu, et al.
(2019) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 116(14). p.7137-7146
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Abstract
Crucihimalaya himalaica, a close relative of Arabidopsis and Capsella, grows on the Qinghai–Tibet Plateau (QTP) about 4,000 m above sea level and represents an attractive model system for studying speciation and ecological adaptation in extreme environments. We assembled a draft genome sequence of 234.72 Mb encoding 27,019 genes and investigated its origin and adaptive evolutionary mechanisms. Phylogenomic analyses based on 4,586 single-copy genes revealed that C. himalaica is most closely related to Capsella (estimated divergence 8.8 to 12.2 Mya), whereas both species form a sister clade to Arabidopsis thaliana and Arabidopsis lyrata, from which they diverged between 12.7 and 17.2 Mya. LTR retrotransposons in C. himalaica proliferated shortly after the dramatic uplift and climatic change of the Himalayas from the Late Pliocene to Pleistocene. Compared with closely related species, C. himalaica showed significant contraction and pseudogenization in gene families associated with disease resistance and also significant expansion in gene families associated with ubiquitin-mediated proteolysis and DNA repair. We identified hundreds of genes involved in DNA repair, ubiquitin-mediated proteolysis, and reproductive processes with signs of positive selection. Gene families showing dramatic changes in size and genes showing signs of positive selection are likely candidates for C. himalaica’s adaptation to intense radiation, low temperature, and pathogen-depauperate environments in the QTP. Loss of function at the S-locus, the reason for the transition to self-fertilization of C. himalaica, might have enabled its QTP occupation. Overall, the genome sequence of C. himalaica provides insights into the mechanisms of plant adaptation to extreme environments.
Keywords
adaptive evolution, natural selection, extreme environment, Qinghai-Tibet Plateau, S-locus, MULTIPLE SEQUENCE ALIGNMENT, SELF-INCOMPATIBILITY, BRASSICACEAE PHYLOGENY, TRANSPOSABLE ELEMENTS, TIBETAN PLATEAU, DRAFT GENOME, S-LOCUS, EVOLUTION, SELECTION, ANNOTATION

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MLA
Zhang, Ticao, et al. “Genome of Crucihimalaya Himalaica, a Close Relative of Arabidopsis, Shows Ecological Adaptation to High Altitude.” PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 116, no. 14, 2019, pp. 7137–46, doi:10.1073/pnas.1817580116.
APA
Zhang, T., Qiao, Q., Novikova, P., Wang, Q., Yue, J., Guan, Y., … Qiong, L. (2019). Genome of Crucihimalaya himalaica, a close relative of Arabidopsis, shows ecological adaptation to high altitude. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 116(14), 7137–7146. https://doi.org/10.1073/pnas.1817580116
Chicago author-date
Zhang, Ticao, Qin Qiao, Polina Novikova, Qia Wang, Jipei Yue, Yanlong Guan, Shengping Ming, et al. 2019. “Genome of Crucihimalaya Himalaica, a Close Relative of Arabidopsis, Shows Ecological Adaptation to High Altitude.” PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 116 (14): 7137–46. https://doi.org/10.1073/pnas.1817580116.
Chicago author-date (all authors)
Zhang, Ticao, Qin Qiao, Polina Novikova, Qia Wang, Jipei Yue, Yanlong Guan, Shengping Ming, Tianmeng Liu, Ji De, Yixuan Liu, Ihsan A Al-Shehbaz, Hang Sun, Marc Van Montagu, Jinling Huang, Yves Van de Peer, and La Qiong. 2019. “Genome of Crucihimalaya Himalaica, a Close Relative of Arabidopsis, Shows Ecological Adaptation to High Altitude.” PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 116 (14): 7137–7146. doi:10.1073/pnas.1817580116.
Vancouver
1.
Zhang T, Qiao Q, Novikova P, Wang Q, Yue J, Guan Y, et al. Genome of Crucihimalaya himalaica, a close relative of Arabidopsis, shows ecological adaptation to high altitude. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2019;116(14):7137–46.
IEEE
[1]
T. Zhang et al., “Genome of Crucihimalaya himalaica, a close relative of Arabidopsis, shows ecological adaptation to high altitude,” PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 116, no. 14, pp. 7137–7146, 2019.
@article{8611161,
  abstract     = {{Crucihimalaya himalaica, a close relative of Arabidopsis and Capsella, grows on the Qinghai–Tibet Plateau (QTP) about 4,000 m above sea level and represents an attractive model system for studying speciation and ecological adaptation in extreme environments. We assembled a draft genome sequence of 234.72 Mb encoding 27,019 genes and investigated its origin and adaptive evolutionary mechanisms. Phylogenomic analyses based on 4,586 single-copy genes revealed that C. himalaica is most closely related to Capsella (estimated divergence 8.8 to 12.2 Mya), whereas both species form a sister clade to Arabidopsis thaliana and Arabidopsis lyrata, from which they diverged between 12.7 and 17.2 Mya. LTR retrotransposons in C. himalaica proliferated shortly after the dramatic uplift and climatic change of the Himalayas from the Late Pliocene to Pleistocene. Compared with closely related species, C. himalaica showed significant contraction and pseudogenization in gene families associated with disease resistance and also significant expansion in gene families associated with ubiquitin-mediated proteolysis and DNA repair. We identified hundreds of genes involved in DNA repair, ubiquitin-mediated proteolysis, and reproductive processes with signs of positive selection. Gene families showing dramatic changes in size and genes showing signs of positive selection are likely candidates for C. himalaica’s adaptation to intense radiation, low temperature, and pathogen-depauperate environments in the QTP. Loss of function at the S-locus, the reason for the transition to self-fertilization of C. himalaica, might have enabled its QTP occupation. Overall, the genome sequence of C. himalaica provides insights into the mechanisms of plant adaptation to extreme environments.}},
  author       = {{Zhang, Ticao and Qiao, Qin and Novikova, Polina and Wang, Qia and Yue, Jipei and Guan, Yanlong and Ming, Shengping and Liu, Tianmeng and De, Ji and Liu, Yixuan and Al-Shehbaz, Ihsan A and Sun, Hang and Van Montagu, Marc and Huang, Jinling and Van de Peer, Yves and Qiong, La}},
  issn         = {{0027-8424}},
  journal      = {{PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}},
  keywords     = {{adaptive evolution,natural selection,extreme environment,Qinghai-Tibet Plateau,S-locus,MULTIPLE SEQUENCE ALIGNMENT,SELF-INCOMPATIBILITY,BRASSICACEAE PHYLOGENY,TRANSPOSABLE ELEMENTS,TIBETAN PLATEAU,DRAFT GENOME,S-LOCUS,EVOLUTION,SELECTION,ANNOTATION}},
  language     = {{eng}},
  number       = {{14}},
  pages        = {{7137--7146}},
  title        = {{Genome of Crucihimalaya himalaica, a close relative of Arabidopsis, shows ecological adaptation to high altitude}},
  url          = {{http://doi.org/10.1073/pnas.1817580116}},
  volume       = {{116}},
  year         = {{2019}},
}
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