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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. Multi-omics data provide insight into the adaptation of the glasshouse plant Rheum nobile to the alpine subnival zone. Commun Biol 2023; 6:906. [PMID: 37667004 PMCID: PMC10477342 DOI: 10.1038/s42003-023-05271-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 08/22/2023] [Indexed: 09/06/2023] Open
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.
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Affiliation(s)
- Ying Li
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Zhimin Niu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Mingjia Zhu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Zhenyue Wang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Renping Xu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Minjie Li
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Zeyu Zheng
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Zhiqiang Lu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - Congcong Dong
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Hongyin Hu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Yingbo Yang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Ying Wu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Dandan Wang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Jinli Yang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Jin Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Dongshi Wan
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Richard Abbott
- School of Biology, University of St Andrews, St Andrews, Fife, KY169TH, UK
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics & Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
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Feng T, Pucker B, Kuang T, Song B, Yang Y, Lin N, Zhang H, Moore MJ, Brockington SF, Wang Q, Deng T, Wang H, Sun H. The genome of the glasshouse plant noble rhubarb (Rheum nobile) provides a window into alpine adaptation. Commun Biol 2023; 6:706. [PMID: 37429977 DOI: 10.1038/s42003-023-05044-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 06/14/2023] [Indexed: 07/12/2023] Open
Abstract
Glasshouse plants are species that trap warmth via specialized morphology and physiology, mimicking a human glasshouse. In the Himalayan alpine region, the highly specialized glasshouse morphology has independently evolved in distinct lineages to adapt to intensive UV radiation and low temperature. Here we demonstrate that the glasshouse structure - specialized cauline leaves - is highly effective in absorbing UV light but transmitting visible and infrared light, creating an optimal microclimate for the development of reproductive organs. We reveal that this glasshouse syndrome has evolved at least three times independently in the rhubarb genus Rheum. We report the genome sequence of the flagship glasshouse plant Rheum nobile and identify key genetic network modules in association with the morphological transition to specialized glasshouse leaves, including active secondary cell wall biogenesis, upregulated cuticular cutin biosynthesis, and suppression of photosynthesis and terpenoid biosynthesis. The distinct cell wall organization and cuticle development might be important for the specialized optical property of glasshouse leaves. We also find that the expansion of LTRs has likely played an important role in noble rhubarb adaptation to high elevation environments. Our study will enable additional comparative analyses to identify the genetic basis underlying the convergent occurrence of glasshouse syndrome.
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Affiliation(s)
- Tao Feng
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Boas Pucker
- Department of Plant Sciences, University of Cambridge, Tennis Court Road, Cambridge, CB2 3EA, UK
- CeBiTec & Faculty of Biology, Bielefeld University, Universitaetsstrasse, Bielefeld, 33615, Germany
- Institute of Plant Biology & BRICS, TU Braunschweig, 38106, Braunschweig, Germany
| | - Tianhui Kuang
- CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Bo Song
- CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Ya Yang
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, St. Paul, MN, 55108, USA
| | - Nan Lin
- 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, Hubei, 430074, China
| | - Huajie Zhang
- 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, Hubei, 430074, China
| | - Michael J Moore
- Department of Biology, Oberlin College, Oberlin, OH, 44074, USA
| | - Samuel F Brockington
- Department of Plant Sciences, University of Cambridge, Tennis Court Road, Cambridge, CB2 3EA, UK
| | - Qingfeng Wang
- 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, Hubei, 430074, China
| | - Tao Deng
- CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.
| | - Hengchang Wang
- 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, Hubei, 430074, China.
| | - Hang Sun
- CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.
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Hu Y, Zhang H, Sun J, Li W, Li Y. Comparative transcriptome analysis of different tissues of Rheum tanguticum Maxim. ex Balf. (Polygonaceae) reveals putative genes involved in anthraquinone biosynthesis. Genet Mol Biol 2022; 45:e20210407. [PMID: 36150022 PMCID: PMC9505757 DOI: 10.1590/1678-4685-gmb-2021-0407] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 06/03/2022] [Indexed: 11/22/2022] Open
Abstract
Rheum tanguticum is a perennial herb and an important medicinal
plant, with anthraquinones as its main bioactive compounds. However, the
specific pathway of anthraquinone biosynthesis in rhubarb is still unclear. The
accumulation of anthraquinones in different tissues (root, leaf, stem and seed)
of R. tanguticum revealed considerable variation, suggesting
possible differences in metabolite biosynthetic pathways and accumulation among
various tissues. To better illustrate the biosynthetic pathway of
anthraquinones, we assembled transcriptome sequences from the root, leaf, stem
and seed tissues yielding 157,564 transcripts and 88,142 unigenes. Putative
functions could be assigned to 56,911 unigenes (64.57%) based on BLAST searches
against annotation databases, including GO, KEGG, Swiss-Prot, NR, and Pfam. In
addition, putative genes involved in the biosynthetic pathway of anthraquinone
were identified. The expression profiles of nine unigenes involved in
anthraquinone biosynthesis were verified in different tissues of R.
tanguticum by qRT-PCR. Various transcription factors, including
bHLH, MYB_related, and C2H2, were identified by searching unigenes against
plantTFDB. This is the first transcriptome analysis of different tissues of
R. tanguticum and can be utilized to describe the genes
involved in the biosynthetic pathway of anthraquiones, understanding the
molecular mechanism of active compounds in R. tanguticum.
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Affiliation(s)
- Yanping Hu
- Qinghai Provincial Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Huixuan Zhang
- Qinghai Provincial Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jing Sun
- Qinghai Provincial Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wenjing Li
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Key Laboratory of Adaptation and Evolution of Plateau Biota, Xining, China.,Scientific Research and Popularization Base of Qinghai-Tibet Plateau Biology, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Yi Li
- Qinghai Provincial Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
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Comparative transcriptome analysis of Rheum australe, an endangered medicinal herb, growing in its natural habitat and those grown in controlled growth chambers. Sci Rep 2021; 11:3702. [PMID: 33580100 PMCID: PMC7881009 DOI: 10.1038/s41598-020-79020-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 11/02/2020] [Indexed: 01/30/2023] Open
Abstract
Rheum australe is an endangered medicinal herb of high altitude alpine region of Himalayas and is known to possess anti-cancerous properties. Unlike many herbs of the region, R. australe has broad leaves. The species thrives well under the environmental extremes in its niche habitat, therefore an understanding of transcriptome of R. australe to environmental cues was of significance. Since, temperature is one of the major environmental variables in the niche of R. australe, transcriptome was studied in the species growing in natural habitat and those grown in growth chambers maintained at 4 °C and 25 °C to understand genes associated with different temperatures. A total of 39,136 primarily assembled transcripts were obtained from 10,17,74,336 clean read, and 21,303 unigenes could match to public databases. An analysis of transcriptome by fragments per kilobase of transcript per million, followed by validation through qRT-PCR showed 22.4% up- and 22.5% down-regulated common differentially expressed genes in the species growing under natural habitat and at 4 °C as compared to those at 25 °C. These genes largely belonged to signaling pathway, transporters, secondary metabolites, phytohormones, and those associated with cellular protection, suggesting their importance in imparting adaptive advantage to R. australe in its niche.
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Chen Y, Ma T, Zhang L, Kang M, Zhang Z, Zheng Z, Sun P, Shrestha N, Liu J, Yang Y. Genomic analyses of a “living fossil”: The endangered dove‐tree. Mol Ecol Resour 2020; 20. [DOI: 10.1111/1755-0998.13138] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 01/09/2020] [Accepted: 01/13/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Yang Chen
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education & State Key Lab of Hydraulics & Mountain River Engineering College of Life Sciences Sichuan University Chengdu China
| | - Tao Ma
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education & State Key Lab of Hydraulics & Mountain River Engineering College of Life Sciences Sichuan University Chengdu China
| | - Lushui Zhang
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education & State Key Lab of Hydraulics & Mountain River Engineering College of Life Sciences Sichuan University Chengdu China
| | - Minghui Kang
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education & State Key Lab of Hydraulics & Mountain River Engineering College of Life Sciences Sichuan University Chengdu China
| | - Zhiyang Zhang
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education & State Key Lab of Hydraulics & Mountain River Engineering College of Life Sciences Sichuan University Chengdu China
| | - Zeyu Zheng
- State Key Laboratory of Grassland Agro‐Ecosystem Institute of Innovation Ecology Lanzhou University Lanzhou China
| | - Pengchuan Sun
- School of Life Sciences North China University of Science and Technology Caofeidian, Tangshan China
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro‐Ecosystem Institute of Innovation Ecology Lanzhou University Lanzhou China
| | - Jianquan Liu
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education & State Key Lab of Hydraulics & Mountain River Engineering College of Life Sciences Sichuan University Chengdu China
- State Key Laboratory of Grassland Agro‐Ecosystem Institute of Innovation Ecology Lanzhou University Lanzhou China
| | - Yongzhi Yang
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education & State Key Lab of Hydraulics & Mountain River Engineering College of Life Sciences Sichuan University Chengdu China
- State Key Laboratory of Grassland Agro‐Ecosystem Institute of Innovation Ecology Lanzhou University Lanzhou China
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Luo X, Hu Q, Zhou P, Zhang D, Wang Q, Abbott RJ, Liu J. Chasing ghosts: allopolyploid origin ofOxyria sinensis(Polygonaceae) from its only diploid congener and an unknown ancestor. Mol Ecol 2017; 26:3037-3049. [DOI: 10.1111/mec.14097] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 03/02/2017] [Accepted: 03/02/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Xin Luo
- MOE Key Laboratory for Bio-resources and Eco-environment; College of Life Science; Sichuan University; Chengdu China
| | - Quanjun Hu
- MOE Key Laboratory for Bio-resources and Eco-environment; College of Life Science; Sichuan University; Chengdu China
- State Key Laboratory of Grassland Agro-Ecosystem; College of Life Science; Lanzhou University; Lanzhou China
| | - Pingping Zhou
- MOE Key Laboratory for Bio-resources and Eco-environment; College of Life Science; Sichuan University; Chengdu China
| | - Dan Zhang
- MOE Key Laboratory for Bio-resources and Eco-environment; College of Life Science; Sichuan University; Chengdu China
| | - Qian Wang
- MOE Key Laboratory for Bio-resources and Eco-environment; College of Life Science; Sichuan University; Chengdu China
- Research Center for Medicine and Biology; Zunyi Medical University; Zunyi China
| | - Richard J. Abbott
- School of Biology; University of St Andrews; St Andrews Fife KY16 9TH UK
| | - Jianquan Liu
- MOE Key Laboratory for Bio-resources and Eco-environment; College of Life Science; Sichuan University; Chengdu China
- State Key Laboratory of Grassland Agro-Ecosystem; College of Life Science; Lanzhou University; Lanzhou China
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