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Zhang T, Zhou L, Pu Y, Tang Y, Liu J, Yang L, Zhou T, Feng L, Wang X. A chromosome-level genome reveals genome evolution and molecular basis of anthraquinone biosynthesis in Rheum palmatum. BMC PLANT BIOLOGY 2024; 24:261. [PMID: 38594606 PMCID: PMC11005207 DOI: 10.1186/s12870-024-04972-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 04/01/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND Rhubarb is one of common traditional Chinese medicine with a diverse array of therapeutic efficacies. Despite its widespread use, molecular research into rhubarb remains limited, constraining our comprehension of the geoherbalism. RESULTS We assembled the genome of Rheum palmatum L., one of the source plants of rhubarb, to elucidate its genome evolution and unpack the biosynthetic pathways of its bioactive compounds using a combination of PacBio HiFi, Oxford Nanopore, Illumina, and Hi-C scaffolding approaches. Around 2.8 Gb genome was obtained after assembly with more than 99.9% sequences anchored to 11 pseudochromosomes (scaffold N50 = 259.19 Mb). Transposable elements (TE) with a continuous expansion of long terminal repeat retrotransposons (LTRs) is predominant in genome size, contributing to the genome expansion of R. palmatum. Totally 30,480 genes were predicted to be protein-coding genes with 473 significantly expanded gene families enriched in diverse pathways associated with high-altitude adaptation for this species. Two successive rounds of whole genome duplication event (WGD) shared by Fagopyrum tataricum and R. palmatum were confirmed. We also identified 54 genes involved in anthraquinone biosynthesis and other 97 genes entangled in flavonoid biosynthesis. Notably, RpALS emerged as a compelling candidate gene for the octaketide biosynthesis after the key residual screening. CONCLUSION Overall, our findings offer not only an enhanced understanding of this remarkable medicinal plant but also pave the way for future innovations in its genetic breeding, molecular design, and functional genomic studies.
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Affiliation(s)
- Tianyi Zhang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Lipan Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yang Pu
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yadi Tang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jie Liu
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Li Yang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Li Feng
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
| | - Xumei Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
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Zhou T, Tang Y, Zhou L, Liu J, Pu Y, Jiang F, Wang J, Wang X. Transcriptomic divergence of the Rheum palmatum complex derived from top-geoherb and non-geoherb areas provides the insights into geoherbalism properties of rhubarb. BMC Genomics 2024; 25:212. [PMID: 38408895 PMCID: PMC10898026 DOI: 10.1186/s12864-024-10142-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/19/2024] [Indexed: 02/28/2024] Open
Abstract
Geoherb usually represents high-quality medicinal herbs with better clinical therapeutic effects, and elucidating the geoherbalism is essential for the quality improvement of traditional Chinese Medicine. However, few researches were conducted to clarify the geoherbalism based on a large scale of transcriptomics. In the present study, we compared the transcriptomes of Rheum palmatum complex derived from top-geoherb and non-geoherb areas to show the geoherbalism properties of rhubarb. A total of 412.32 Gb clean reads were obtained with unigene numbers of 100,615 after assembly. Based on the obtained transcriptome datasets, key enzyme-encoding genes involved in the anthraquinones biosynthesis were also obtained. We also found that 21 anthraquinone-related unigenes were differentially expressed between two different groups, and some of these DEGs were correlated to the content accumulation of five free anthraquinones, indicating that the gene expression profiles may promote the geoherbalism formation of rhubarb. In addition, the selective pressure analyses indicated that most paired orthologous genes between these two groups were subject to negative selection, and only a low proportion of orthologs under positive selection were detected. Functional annotation analyses indicated that these positive-selected genes related to the functions such as gene expression, substance transport, stress response and metabolism, indicating that discrepant environment also enhanced the formation of geoherbalism. Our study not only provided insights for the genetic mechanism of geoherbalism of rhubarb, but also laid more genetic cues for the future rhubarb germplasms improvement and utilization.
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Affiliation(s)
- Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
| | - Yadi Tang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Lipan Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jie Liu
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yang Pu
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Fan Jiang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jian Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Xumei Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
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3
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Zhai Y, Zhang T, Guo Y, Gao C, Zhou L, Feng L, Zhou T, Xumei W. Phylogenomics, phylogeography and germplasms authentication of the Rheum palmatum complex based on complete chloroplast genomes. JOURNAL OF PLANT RESEARCH 2023; 136:291-304. [PMID: 36808315 DOI: 10.1007/s10265-023-01440-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
As a traditional Chinese medicine, rhubarb is used to treat several diseases such as severe acute pancreatitis, sepsis and chronic renal failure. However, few studies focused on the authentication of germplasm for the Rheum palmatum complex, and no studies have been conducted to elucidate the evolutionary history of the R. palmatum complex using plastome datasets. Hence, we aim to develop the potential molecular markers to identify the elite germplasms of rhubarb and explore the divergence and biogeographic history of the R. palmatum complex based on the newly sequenced chloroplast genome datasets. Chloroplast genomes of thirty-five the R. palmatum complex germplasms were sequenced, and the length ranged from 160,858 to 161,204 bp. The structure, gene content and gene order were highly conserved across all genomes. Eight InDels and sixty-one SNPs loci could be used to authenticate the high-quality germplasms of rhubarb in specific areas. Phylogenetic analysis revealed that all rhubarb germplasms were clustered in the same clade with high bootstrap support values and Bayesian posterior probabilities. According to the molecular dating result, the intraspecific divergence of the complex occurred in the Quaternary, which might be affected by climatic fluctuation. The biogeography reconstruction indicated that the ancestor of the R. palmatum complex might originate from the Himalaya-Hengduan Mountains or/and Bashan-Qinling Mountains, and then spread to surrounding areas. Several useful molecular markers were developed to identify rhubarb germplasms, and our study will provide further understanding on speciation, divergence and biogeography of the R. palmatum complex.
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Affiliation(s)
- Yunyan Zhai
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Tianyi Zhang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yanbing Guo
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Chenxi Gao
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Lipan Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Li Feng
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
| | - Wang Xumei
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
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Zhou T, Sun J, Zhai Y, Gao C, Ruhsam M, Wang X. Transcriptome profiles of yellowish-white and fuchsia colored flowers in the Rheum palmatum complex reveal genes related to color polymorphism. PLANT MOLECULAR BIOLOGY 2022; 110:187-197. [PMID: 35943640 DOI: 10.1007/s11103-022-01299-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Flower color variation is ubiquitous in many plant species, and several studies have been conducted to elucidate the underlying molecular mechanism. There are two flower color variants (yellowish-white and fuchsia) in the Rheum palmatum complex, however, few studies have investigated this phenomenon. Here, we used transcriptome sequencing of the two color variants to shed light on the molecular and biochemical basis for these color morphs. Comparison of the two transcriptomes identified 9641 differentially expressed unigenes (DEGs), including 6477 up-regulated and 3163 down-regulated genes. Functional analyses indicated that several DEGs were related to the anthocyanin biosynthesis pathway, and the expression profiles of these DEGs were coincident with the qRT-PCR validation results, indicating that expression levels of structural genes have a profound effect on the color variation in the R. palmatum complex. Our results suggested that the interaction of transcription factors (MYB, bHLH and WRKY) also regulated the anthocyanin biosynthesis in the R. palmatum complex. Estimation of selection pressures using the dN/dS ratio showed that 1106 pairs of orthologous genes have undergone positive selection. Of these positively selected genes, 21 were involved in the anthocyanin biosynthetic pathway, indicating that they may encode the proteins for structural alteration and affect flower color in the R. palmatum complex.
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Affiliation(s)
- Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jiangyan Sun
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yunyan Zhai
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Chenxi Gao
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Xumei Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
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5
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Hu Y, Zhang H, Qian Q, Lin G, Wang J, Sun J, Li Y, Jang JC, Li W. The Potential Roles of Unique Leaf Structure for the Adaptation of Rheum tanguticum Maxim. ex Balf. in Qinghai-Tibetan Plateau. PLANTS (BASEL, SWITZERLAND) 2022; 11:512. [PMID: 35214845 PMCID: PMC8875413 DOI: 10.3390/plants11040512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 02/08/2022] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
Leaves are essential plant organs with numerous variations in shape and size. The leaf size is generally smaller in plants that thrive in areas of higher elevation and lower annual mean temperature. The Qinghai-Tibetan Plateau is situated at an altitude of >4000 m with relatively low annual average temperatures. Most plant species found on the Qinghai-Tibetan Plateau have small leaves, with Rheum tanguticum Maxim. ex Balf. being an exception. Here, we show that the large leaves of R. tanguticum with a unique three-dimensional (3D) shape are potentially an ideal solution for thermoregulation with little energy consumption. With the increase in age, the shape of R. tanguticum leaves changed from a small oval plane to a large palmatipartite 3D shape. Therefore, R. tanguticum is a highly heteroblastic species. The leaf shape change during the transition from the juvenile to the adult phase of the development in R. tanguticum is a striking example of the manifestation of plant phenotypic plasticity. The temperature variation in different parts of the leaf was a distinct character of leaves of over-5-year-old plants. The temperature of single-plane leaves under strong solar radiation could accumulate heat rapidly and resulted in temperatures much higher than the ambient temperature. However, leaves of over-5-year-old plants could lower leaf temperature by avoiding direct exposure to solar radiation and promoting local airflow to prevent serious tissue damage by sunburn. Furthermore, the net photosynthesis rate was correlated with the heterogeneity of the leaf surface temperature. Our results demonstrate that the robust 3D shape of the leaf is a strategy that R. tanguticum has developed evolutionarily to adapt to the strong solar radiation and low temperature on the Qinghai-Tibetan Plateau.
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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 810008, China; (Y.H.); (H.Z.); (Q.Q.); (J.W.); (J.S.)
| | - Huixuan Zhang
- Qinghai Provincial Key Laboratory of Qinghai–Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (Y.H.); (H.Z.); (Q.Q.); (J.W.); (J.S.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qian Qian
- Qinghai Provincial Key Laboratory of Qinghai–Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (Y.H.); (H.Z.); (Q.Q.); (J.W.); (J.S.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gonghua Lin
- School of Life Sciences, Jinggangshan University, Ji’an 343009, China;
| | - Jun Wang
- Qinghai Provincial Key Laboratory of Qinghai–Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (Y.H.); (H.Z.); (Q.Q.); (J.W.); (J.S.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Sun
- Qinghai Provincial Key Laboratory of Qinghai–Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (Y.H.); (H.Z.); (Q.Q.); (J.W.); (J.S.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Li
- Qinghai Provincial Key Laboratory of Qinghai–Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (Y.H.); (H.Z.); (Q.Q.); (J.W.); (J.S.)
| | - Jyan-Chyun Jang
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH 43210, USA
| | - Wenjing Li
- Scientific Research and Popularization Base of Qinghai–Tibet Plateau Biology, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
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6
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Zhou T, Zhu H, Wang J, Xu Y, Xu F, Wang X. Complete chloroplast genome sequence determination of Rheum species and comparative chloroplast genomics for the members of Rumiceae. PLANT CELL REPORTS 2020; 39:811-824. [PMID: 32221666 DOI: 10.1007/s00299-020-02532-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 03/13/2020] [Indexed: 05/10/2023]
Abstract
Complete plastomes of Rheum species facilitated to clarify the phylogeny of Polygonaceae, and comparative chloroplast genomics contributed to develop genetic markers for the authentication of Rheum species. Rheum (Polygonaceae) is widely distributed throughout the temperate and subtropical areas of Asian interior. Rheum species are usually perennial herbs, and half of them are endemic to China with important medicinal properties. On account of similar morphological characteristics, species delimitation of Rheum still remains unclear. Chloroplast genomes of eight Rheum species, Rumex crispus and Oxyria digyna were characterized. Based on the comparison of genome structure of these species and the two published Rheum species, it is shown that plastome sequences of these species are relatively conserved with the same gene order, and three Sect. Palmata species remarkably showed high sequence similarities. Some hotspots could be used to discriminate the Rheum species, and 17 plastid genes were subject to positive selection. The phylogenetic analyses indicated that all the Polygonaceae species were clustered in the same group and showed that Rheum species, except for Rheum wittrockii, formed a monophyletic group with high maximum parsimony/maximum likelihood bootstrap support values and Bayesian posterior probabilities. The molecular dating based on plastomes indicated that the divergences within Polygonaceae species were dated to the Upper Cretaceous period [73.86-77.99 million years ago (Ma)]. The divergence of Sect. Palmata species was estimated to have occurred around 1.60 Ma, indicating that its diversification was affected by the repeated climatic fluctuation in the Quaternary.
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Affiliation(s)
- Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
- Key Laboratory of Qiyao Resources and Anti-Tumor Activities, Shaanxi Administration of Traditional Chinese Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Honghong Zhu
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jian Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yucan Xu
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Fusheng Xu
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Xumei Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
- Key Laboratory of Qiyao Resources and Anti-Tumor Activities, Shaanxi Administration of Traditional Chinese Medicine, Xi'an Jiaotong University, Xi'an, 710061, China.
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Feng L, Ruhsam M, Wang YH, Li ZH, Wang XM. Using demographic model selection to untangle allopatric divergence and diversification mechanisms in the Rheum palmatum complex in the Eastern Asiatic Region. Mol Ecol 2020; 29:1791-1805. [PMID: 32306487 DOI: 10.1111/mec.15448] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 03/30/2020] [Accepted: 04/08/2020] [Indexed: 12/22/2022]
Abstract
Allopatric divergence is often initiated by geological uplift and restriction to sky-islands, climate oscillations, or river capture. However, it can be difficult to establish which mechanism was the most likely to generate the current phylogeographical structure of a species. Recently, genomic data in conjunction with a model testing framework have been applied to address this issue in animals. To test whether such an approach is also likely to be successful in plants, we used population genomic data of the Rheum palmatum complex from the Eastern Asiatic Region, in conjunction with biogeographical reconstruction and demographic model selection, to identify the potential mechanism(s) which have led to the current level of divergence. Our results indicate that the R. palmatum complex originated in the central Hengduan Mts and possibly in regions further east, and then dispersed westward and eastward resulting in genetically distinct lineages. Populations are likely to have diverged in refugia during climate oscillations followed by subsequent expansion and secondary contact. However, model simulations within the western lineage of the R. palmatum complex cannot reject a restriction to sky-islands as a possible mechanism of diversification due to the genetically ambiguous position of one population. This highlights that genetically mixed populations might introduce ambiguity regarding the best diversification model in some cases. Although it might be possible to resolve this ambiguity using other data, sometimes this could prove to be difficult in complex biogeographical areas.
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Affiliation(s)
- Li Feng
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China.,Key Laboratory of Qiyao Resources and Anti-tumor Activities, Shaanxi Administration of Traditional Chinese Medicine, School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | | | - Yi-Han Wang
- College of Life Sciences, Henan Agriculture University, Zhengzhou, China
| | - Zhong-Hu Li
- College of Life Sciences, Northwest University, Xi'an, China
| | - Xu-Mei Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China.,Key Laboratory of Qiyao Resources and Anti-tumor Activities, Shaanxi Administration of Traditional Chinese Medicine, School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
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Comparative Chloroplast Genome Analysis of Rhubarb Botanical Origins and the Development of Specific Identification Markers. Molecules 2018; 23:molecules23112811. [PMID: 30380708 PMCID: PMC6278470 DOI: 10.3390/molecules23112811] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 10/21/2018] [Accepted: 10/27/2018] [Indexed: 11/18/2022] Open
Abstract
Rhubarb is an important ingredient in traditional Chinese medicine known as Rhei radix et rhizome. However, this common name refers to three different botanical species with different pharmacological effects. To facilitate the genetic identification of these three species for their more precise application in Chinese medicine we here want to provide chloroplast sequences with specific identification sites that are easy to amplify. We therefore sequenced the complete chloroplast genomes of all three species and then screened those for suitable sequences describing the three species. The length of the three chloroplast genomes ranged from 161,053 bp to 161,541 bp, with a total of 131 encoded genes including 31 tRNA, eight rRNA and 92 protein-coding sequences. The simple repeat sequence analysis indicated the differences existed in these species, phylogenetic analyses showed the chloroplast genome can be used as an ultra-barcode to distinguish the three botanical species of rhubarb, the variation of the non-coding regions is higher than that of the protein coding regions, and the variations in single-copy region are higher than that in inverted repeat. Twenty-one specific primer pairs were designed and eight specific identification sites were experimentally confirmed that can be used as special DNA barcodes for the identification of the three species based on the highly variable regions. This study provides a molecular basis for precise medicinal plant selection, and supplies the groundwork for the next investigation of the closely related Rheum species comparing and correctly identification on these important medicinal species.
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Genetic and chemical differentiation characterizes top-geoherb and non-top-geoherb areas in the TCM herb rhubarb. Sci Rep 2018; 8:9424. [PMID: 29930263 PMCID: PMC6013459 DOI: 10.1038/s41598-018-27510-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 06/05/2018] [Indexed: 11/29/2022] Open
Abstract
Medicinal herbs of high quality and with significant clinical effects have been designated as top-geoherbs in traditional Chinese medicine (TCM). However, the validity of this concept using genetic markers has not been widely tested. In this study, we investigated the genetic variation within the Rheum palmatum complex (rhubarb), an important herbal remedy in TCM, using a phylogeographic (six chloroplast DNA regions, five nuclear DNA regions, and 14 nuclear microsatellite loci) and a chemical approach (anthraquinone content). Genetic and chemical data identified two distinct groups in the 38 analysed populations from the R. palmatum complex which geographically coincide with the traditional top-geoherb and non-top-geoherb areas of rhubarb. Molecular dating suggests that the two groups diverged in the Quaternary c. 2.0 million years ago, a time of repeated climate changes and uplift of the Qinghai-Tibetan Plateau. Our results show that the ancient TCM concept of top-geoherb and non-top-geoherb areas corresponds to genetically and chemically differentiated groups in rhubarb.
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10
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Morphological and genetic differences between Coptis japonica var. anemonifolia H. Ohba and Coptis japonica var. major Satake in Hokuriku area. J Nat Med 2018; 72:514-522. [DOI: 10.1007/s11418-018-1179-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 01/18/2018] [Indexed: 11/25/2022]
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11
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Zhou Y, Du XL, Zheng X, Huang M, Li Y, Wang XM. ITS2 barcode for identifying the officinal rhubarb source plants from its adulterants. BIOCHEM SYST ECOL 2017. [DOI: 10.1016/j.bse.2016.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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12
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Biot E, Cortizo M, Burguet J, Kiss A, Oughou M, Maugarny-Calès A, Gonçalves B, Adroher B, Andrey P, Boudaoud A, Laufs P. Multiscale quantification of morphodynamics: MorphoLeaf software for 2D shape analysis. Development 2016; 143:3417-28. [PMID: 27387872 DOI: 10.1242/dev.134619] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 06/13/2016] [Indexed: 01/27/2023]
Abstract
A major challenge in morphometrics is to analyse complex biological shapes formed by structures at different scales. Leaves exemplify this challenge as they combine differences in their overall shape with smaller shape variations at their margin, leading to lobes or teeth. Current methods based on contour or on landmark analysis are successful in quantifying either overall leaf shape or leaf margin dissection, but fail in combining the two. Here, we present a comprehensive strategy and its associated freely available platform for the quantitative, multiscale analysis of the morphology of leaves with different architectures. For this, biologically relevant landmarks are automatically extracted and hierarchised, and used to guide the reconstruction of accurate average contours that properly represent both global and local features. Using this method, we establish a quantitative framework of the developmental trajectory of Arabidopsis leaves of different ranks and retrace the origin of leaf heteroblasty. When applied to different mutant forms, our method can contribute to a better understanding of gene function, as we show here for the role of CUC2 during Arabidopsis leaf serration. Finally, we illustrate the wider applicability of our tool by analysing hand morphometrics.
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Affiliation(s)
- Eric Biot
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex 78026, France
| | - Millán Cortizo
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex 78026, France
| | - Jasmine Burguet
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex 78026, France
| | - Annamaria Kiss
- Laboratoire de Reproduction et de Développement des Plantes, INRA, CNRS, ENS de Lyon, UCB Lyon 1, Université de Lyon, 46 Allée d'Italie, Lyon Cedex 07 69364, France Laboratoire Joliot-Curie, CNRS, ENS de Lyon, Université de Lyon, 46 Allée d'Italie, Lyon Cedex 07 69364, France
| | - Mohamed Oughou
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex 78026, France
| | - Aude Maugarny-Calès
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex 78026, France Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay, France
| | - Beatriz Gonçalves
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex 78026, France
| | - Bernard Adroher
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex 78026, France
| | - Philippe Andrey
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex 78026, France Sorbonne Universités, UPMC Univ. Paris 06 UFR 927, 75252 Paris, France
| | - Arezki Boudaoud
- Laboratoire de Reproduction et de Développement des Plantes, INRA, CNRS, ENS de Lyon, UCB Lyon 1, Université de Lyon, 46 Allée d'Italie, Lyon Cedex 07 69364, France Laboratoire Joliot-Curie, CNRS, ENS de Lyon, Université de Lyon, 46 Allée d'Italie, Lyon Cedex 07 69364, France
| | - Patrick Laufs
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex 78026, France
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