Multi-omics data provide insight into the adaptation of the glasshouse plant Rheum nobile to the alpine subnival zone

Ying Li; Zhimin Niu; Mingjia Zhu; Zhenyue Wang; Renping Xu; Minjie Li; Zeyu Zheng; Zhiqiang Lu; Congcong Dong; Hongyin Hu; Yingbo Yang; Ying Wu; Dandan Wang; Jinli Yang; Jin Zhang; Dongshi Wan; Richard Abbott; Jianquan Liu; Yongzhi Yang

doi:10.1038/s42003-023-05271-6

Multi-omics data provide insight into the adaptation of the glasshouse plant Rheum nobile to the alpine subnival zone

Ying Li, Zhimin Niu, Mingjia Zhu, Zhenyue Wang, Renping Xu, Minjie Li, Zeyu Zheng, Zhiqiang Lu, Congcong Dong, Hongyin Hu, Yingbo Yang, Ying Wu, Dandan Wang, Jinli Yang, Jin Zhang, Dongshi Wan, Richard Abbott, Jianquan Liu^*, Yongzhi Yang^*

^*Corresponding author for this work

School of Biology

Research output: Contribution to journal › Article › peer-review

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Abstract

Subnival glasshouse plants provide a text-book example of high-altitude adaptation with reproductive organs enclosed in specialized semi-translucent bracts, monocarpic reproduction and continuous survival under stress. Here, we present genomic, transcriptomic and metabolomic analyses for one such plant, the Noble rhubarb (Rheum nobile). Comparative genomic analyses show that an expanded number of genes and retained genes from two recent whole-genome duplication events are both relevant to subnival adaptation of this species. Most photosynthesis genes are downregulated within bracts compared to within leaves, and indeed bracts exhibit a sharp reduction in photosynthetic pigments, indicating that the bracts no longer perform photosynthesis. Contrastingly, genes related to flavonol synthesis are upregulated, providing enhanced defense against UV irradiation damage. Additionally, anatomically abnormal mesophyll combined with the downregulation of genes related to mesophyll differentiation in bracts illustrates the innovation and specification of the glass-like bracts. We further detect substantial accumulation of antifreeze proteins (e.g. AFPs, LEAs) and various metabolites (e.g. Proline, Protective sugars, procyanidins) in over-wintering roots. These findings provide new insights into subnival adaptation and the evolution of glasshouse alpine plants.

Original language	English
Article number	906
Number of pages	13
Journal	Communications Biology
Volume	6
DOIs	https://doi.org/10.1038/s42003-023-05271-6
Publication status	Published - 4 Sept 2023

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Li, Y., Niu, Z., Zhu, M., Wang, Z., Xu, R., Li, M., Zheng, Z., Lu, Z., Dong, C., Hu, H., Yang, Y., Wu, Y., Wang, D., Yang, J., Zhang, J., Wan, D., Abbott, R., Liu, J., & Yang, Y. (2023). Multi-omics data provide insight into the adaptation of the glasshouse plant Rheum nobile to the alpine subnival zone. Communications Biology, 6, Article 906. https://doi.org/10.1038/s42003-023-05271-6

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title = "Multi-omics data provide insight into the adaptation of the glasshouse plant Rheum nobile to the alpine subnival zone",

abstract = "Subnival glasshouse plants provide a text-book example of high-altitude adaptation with reproductive organs enclosed in specialized semi-translucent bracts, monocarpic reproduction and continuous survival under stress. Here, we present genomic, transcriptomic and metabolomic analyses for one such plant, the Noble rhubarb (Rheum nobile). Comparative genomic analyses show that an expanded number of genes and retained genes from two recent whole-genome duplication events are both relevant to subnival adaptation of this species. Most photosynthesis genes are downregulated within bracts compared to within leaves, and indeed bracts exhibit a sharp reduction in photosynthetic pigments, indicating that the bracts no longer perform photosynthesis. Contrastingly, genes related to flavonol synthesis are upregulated, providing enhanced defense against UV irradiation damage. Additionally, anatomically abnormal mesophyll combined with the downregulation of genes related to mesophyll differentiation in bracts illustrates the innovation and specification of the glass-like bracts. We further detect substantial accumulation of antifreeze proteins (e.g. AFPs, LEAs) and various metabolites (e.g. Proline, Protective sugars, procyanidins) in over-wintering roots. These findings provide new insights into subnival adaptation and the evolution of glasshouse alpine plants.",

author = "Ying Li and Zhimin Niu and Mingjia Zhu and Zhenyue Wang and Renping Xu and Minjie Li and Zeyu Zheng and Zhiqiang Lu and Congcong Dong and Hongyin Hu and Yingbo Yang and Ying Wu and Dandan Wang and Jinli Yang and Jin Zhang and Dongshi Wan and Richard Abbott and Jianquan Liu and Yongzhi Yang",

note = "Financial support was equally provided by the Strategic Priority Research Program of Chinese Academy of Sciences (XDB31000000 to J.L. and Y.Y.), the Key Science & Technology Project of Gansu Province (22ZD6NA007 to Y.Y.), the Science Fund for Creative Research Groups of Gansu Province (21JR7RA533 to Y.Y.), the Young Talent Development Project of State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems (No. 2021 + 02 to Y.Y.), andInternational Collaboration 111 Programme (BP0719040).",

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doi = "10.1038/s42003-023-05271-6",

language = "English",

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T1 - Multi-omics data provide insight into the adaptation of the glasshouse plant Rheum nobile to the alpine subnival zone

AU - Li, Ying

AU - Niu, Zhimin

AU - Zhu, Mingjia

AU - Wang, Zhenyue

AU - Xu, Renping

AU - Li, Minjie

AU - Zheng, Zeyu

AU - Lu, Zhiqiang

AU - Dong, Congcong

AU - Hu, Hongyin

AU - Yang, Yingbo

AU - Wu, Ying

AU - Wang, Dandan

AU - Yang, Jinli

AU - Zhang, Jin

AU - Wan, Dongshi

AU - Abbott, Richard

AU - Liu, Jianquan

AU - Yang, Yongzhi

N1 - Financial support was equally provided by the Strategic Priority Research Program of Chinese Academy of Sciences (XDB31000000 to J.L. and Y.Y.), the Key Science & Technology Project of Gansu Province (22ZD6NA007 to Y.Y.), the Science Fund for Creative Research Groups of Gansu Province (21JR7RA533 to Y.Y.), the Young Talent Development Project of State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems (No. 2021 + 02 to Y.Y.), andInternational Collaboration 111 Programme (BP0719040).

PY - 2023/9/4

Y1 - 2023/9/4

N2 - Subnival glasshouse plants provide a text-book example of high-altitude adaptation with reproductive organs enclosed in specialized semi-translucent bracts, monocarpic reproduction and continuous survival under stress. Here, we present genomic, transcriptomic and metabolomic analyses for one such plant, the Noble rhubarb (Rheum nobile). Comparative genomic analyses show that an expanded number of genes and retained genes from two recent whole-genome duplication events are both relevant to subnival adaptation of this species. Most photosynthesis genes are downregulated within bracts compared to within leaves, and indeed bracts exhibit a sharp reduction in photosynthetic pigments, indicating that the bracts no longer perform photosynthesis. Contrastingly, genes related to flavonol synthesis are upregulated, providing enhanced defense against UV irradiation damage. Additionally, anatomically abnormal mesophyll combined with the downregulation of genes related to mesophyll differentiation in bracts illustrates the innovation and specification of the glass-like bracts. We further detect substantial accumulation of antifreeze proteins (e.g. AFPs, LEAs) and various metabolites (e.g. Proline, Protective sugars, procyanidins) in over-wintering roots. These findings provide new insights into subnival adaptation and the evolution of glasshouse alpine plants.

AB - Subnival glasshouse plants provide a text-book example of high-altitude adaptation with reproductive organs enclosed in specialized semi-translucent bracts, monocarpic reproduction and continuous survival under stress. Here, we present genomic, transcriptomic and metabolomic analyses for one such plant, the Noble rhubarb (Rheum nobile). Comparative genomic analyses show that an expanded number of genes and retained genes from two recent whole-genome duplication events are both relevant to subnival adaptation of this species. Most photosynthesis genes are downregulated within bracts compared to within leaves, and indeed bracts exhibit a sharp reduction in photosynthetic pigments, indicating that the bracts no longer perform photosynthesis. Contrastingly, genes related to flavonol synthesis are upregulated, providing enhanced defense against UV irradiation damage. Additionally, anatomically abnormal mesophyll combined with the downregulation of genes related to mesophyll differentiation in bracts illustrates the innovation and specification of the glass-like bracts. We further detect substantial accumulation of antifreeze proteins (e.g. AFPs, LEAs) and various metabolites (e.g. Proline, Protective sugars, procyanidins) in over-wintering roots. These findings provide new insights into subnival adaptation and the evolution of glasshouse alpine plants.

U2 - 10.1038/s42003-023-05271-6

DO - 10.1038/s42003-023-05271-6

M3 - Article

SN - 2399-3642

VL - 6

JO - Communications Biology

JF - Communications Biology

M1 - 906

ER -

Multi-omics data provide insight into the adaptation of the glasshouse plant Rheum nobile to the alpine subnival zone

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