1
|
Li Z, Lu S, Yi S, Mo S, Yu X, Yin J, Zhang C. Physiological and transcriptomic comparisons shed light on the cold stress response mechanisms of Dendrobium spp. BMC PLANT BIOLOGY 2024; 24:230. [PMID: 38561687 PMCID: PMC10985946 DOI: 10.1186/s12870-024-04903-1] [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: 11/13/2023] [Accepted: 03/13/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND Dendrobium spp. comprise a group of tropical orchids with ornamental and medicinal value. Dendrobium spp. are sensitive to low temperature, and the underlying cold response regulatory mechanisms in this group are unclear. To understand how these plants respond to cold stress, we compared the transcriptomic responses of the cold-tolerant cultivar 'Hongxing' (HX) and the cold-sensitive cultivar 'Sonia Hiasakul' (SH) to cold stress. RESULTS Chemometric results showed that the physiological response of SH in the later stages of cold stress is similar to that of HX throughout the cold treatment. Orthogonal partial least squares discriminant analysis (OPLS-DA) revealed that soluble protein content and peroxidase activity are key physiological parameters for assessing the cold tolerance of these two Dendrobium spp. cultivars. Additionally, weighted gene co-expression network analysis (WGCNA) results showed that many cold response genes and metabolic pathways significantly associated with the physiological indices were enriched in the 12 detected modules. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) enrichment analyses of the 105 hub genes showed that Dendrobium spp. adapt to cold stress by regulating signal transduction, phytohormones, transcription factors, protein translation and modification, functional proteins, biosynthesis and metabolism, cell structure, light, and the circadian clock. Hub genes of the cold stress response network included the remorin gene pp34, the abscisic acid signaling pathway-related genes PROTEIN PHOSPATASE 2 C (PP2C), SNF1-RELATED PROTEIN KINASE 2 (SnRK2), ABRE-BINDING FACTOR 1 (ABF1) and SKI-INTERACTING PROTEIN 17 (SKIP17), the Ca2+ signaling-related GTP diphosphokinase gene CRSH1, the carbohydrate-related gene STARCH SYNTHASE 2 (SS2), the cell wall biosynthesis gene CINNAMYL ALCOHOL DEHYDROGENASE (CAD7), and the endocytosis-related gene VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 52 A (VPS52A). CONCLUSIONS The cold-responsive genes and metabolic pathways of Dendrobium spp. revealed in this study provide important insight to enable the genetic enhancement of cold tolerance in Dendrobium spp., and to facilitate cold tolerance breeding in related plants.
Collapse
Affiliation(s)
- Zhiyuan Li
- Sanya Institute of China Agricultural University, Sanya, Hainan, 572025, China
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, 100193, Beijing, China
| | - Shunjiao Lu
- Tropical Crops Genetic Resources Institute, Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Chines Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, China
- Hainan Engineering Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, 571737, Danzhou, Hainan, China
| | - Shuangshuang Yi
- Tropical Crops Genetic Resources Institute, Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Chines Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, China
- Hainan Engineering Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, 571737, Danzhou, Hainan, China
| | - Shunjin Mo
- Tropical Crops Genetic Resources Institute, Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Chines Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, China
- Hainan Engineering Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, 571737, Danzhou, Hainan, China
| | - Xiaoyun Yu
- Tropical Crops Genetic Resources Institute, Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Chines Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, China
- Hainan Engineering Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, 571737, Danzhou, Hainan, China
| | - Junmei Yin
- Tropical Crops Genetic Resources Institute, Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Chines Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, China.
- Hainan Engineering Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, 571737, Danzhou, Hainan, China.
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571101, Sanya, China.
| | - Changqing Zhang
- Sanya Institute of China Agricultural University, Sanya, Hainan, 572025, China.
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, 100193, Beijing, China.
| |
Collapse
|
2
|
Wang M, Yu W, Yang J, Hou Z, Li C, Niu Z, Zhang B, Xue Q, Liu W, Ding X. Mitochondrial genome comparison and phylogenetic analysis of Dendrobium (Orchidaceae) based on whole mitogenomes. BMC PLANT BIOLOGY 2023; 23:586. [PMID: 37993773 PMCID: PMC10666434 DOI: 10.1186/s12870-023-04618-9] [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: 02/21/2023] [Accepted: 11/17/2023] [Indexed: 11/24/2023]
Abstract
BACKGROUND Mitochondrial genomes are essential for deciphering the unique evolutionary history of seed plants. However, the rules of their extreme variation in genomic size, multi-chromosomal structure, and foreign sequences remain unresolved in most plant lineages, which further hindered the application of mitogenomes in phylogenetic analyses. RESULTS Here, we took Dendrobium (Orchidaceae) which shows the great divergence of morphology and difficulty in species taxonomy as the study focus. We first de novo assembled two complete mitogenomes of Dendrobium wilsonii and Dendrobium henanense that were 763,005 bp and 807,551 bp long with multichromosomal structures. To understand the evolution of Dendrobium mitogenomes, we compared them with those of four other orchid species. The results showed great variations of repetitive and chloroplast-derived sequences in Dendrobium mitogenomes. Moreover, the intergenic content of Dendrobium mitogenomes has undergone expansion during evolution. We also newly sequenced mitogenomes of 26 Dendrobium species and reconstructed phylogenetic relationships of Dendrobium based on genomic mitochondrial and plastid data. The results indicated that the existence of chloroplast-derived sequences made the mitochondrial phylogeny display partial characteristics of the plastid phylogeny. Additionally, the mitochondrial phylogeny provided new insights into the phylogenetic relationships of Dendrobium species. CONCLUSIONS Our study revealed the evolution of Dendrobium mitogenomes and the potential of mitogenomes in deciphering phylogenetic relationships at low taxonomic levels.
Collapse
Grants
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
Collapse
Affiliation(s)
- Mengting Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
- Ningbo Key Laboratory of Agricultural Germplasm Resources Mining and Environmental Regulation, College of Science and Technology, Ningbo University, Cixi, China
| | - Wenhui Yu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jiapeng Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhenyu Hou
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Chao Li
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhitao Niu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Benhou Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qingyun Xue
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wei Liu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoyu Ding
- College of Life Sciences, Nanjing Normal University, Nanjing, China.
| |
Collapse
|
3
|
Du Z, Yang X, Zhou S, Jin Y, Wang W, Xia K, Chen Z. Aromatic Terpenes and Their Biosynthesis in Dendrobium, and Conjecture on the Botanical Perfumer Mechanism. Curr Issues Mol Biol 2023; 45:5305-5316. [PMID: 37504253 PMCID: PMC10378317 DOI: 10.3390/cimb45070337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 06/23/2023] [Accepted: 06/23/2023] [Indexed: 07/29/2023] Open
Abstract
This review presents a systematic analysis of the studies on volatiles in Dendrobium. Among the various components, aromatic terpenes are a crucial component in the development of the aromatic characteristics of Dendrobium and other plants. Recent advancements in detection and sequencing technology have resulted in a considerable rise in research on the biosynthetic processes of aromatic terpenes in Dendrobium and other flowering plants. Nevertheless, the inquiry into the precise means by which plants regulate the proportion of diverse aromatic terpenes in their floral scent, thereby preserving their olfactory traits, requires further investigation. A conjecture on the botanical perfumer mechanism, which condensed the findings of earlier studies, was put forward to address this area of interest. Specific transcription factors likely govern the coordinated expression of multiple key terpene synthase (TPS) genes during the flowering stage of plants, thereby regulating the proportional biosynthesis of diverse aromatic terpenes and sustaining the distinctive aromatic properties of individual plants. This review serves as a significant theoretical reference for further investigations into aromatic volatile compounds in Dendrobium.
Collapse
Affiliation(s)
- Zhihui Du
- Guizhou Horticulture Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550000, China
| | - Xiyu Yang
- Guizhou Horticulture Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550000, China
| | - Shuting Zhou
- Natural Products Research Center of Guizhou Province, Guiyang 550000, China
| | - Yuxuan Jin
- Guizhou Horticulture Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550000, China
| | - Weize Wang
- Guizhou Horticulture Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550000, China
| | - Kuaifei Xia
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Zhilin Chen
- Guizhou Horticulture Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550000, China
| |
Collapse
|
4
|
Ding X, Chen J, Dai C, Shi P, Pan H, Lin Y, Chen Y, Gong L, Chen L, Wu W, Qiu X, Xu J, Huang Z, Liao B. Developing population identification tool based on polymorphism of rDNA for traditional Chinese medicine: Artemisia annua L. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 116:154882. [PMID: 37210961 DOI: 10.1016/j.phymed.2023.154882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/29/2023] [Accepted: 05/12/2023] [Indexed: 05/23/2023]
Abstract
BACKGROUND Artemisia annua, a well-known traditional Chinese medicine, is the main source for production of artemisinin, an anti-malaria drug. A. annua is distributed globally, with great diversity of morphological characteristics and artemisinin contents. Diverse traits among A. annua populations impeded the stable production of artemisinin, which needs an efficient tool to identify strains and assess population genetic homogeneity. PURPOSE In this study, ribosomal DNA (rDNA), were characterized for A. annua for strains identification and population genetic homogeneity assessment. METHODS The ribosomal RNA (rRNA) genes were identified using cmscan and assembled using rDNA unit of LQ-9 as a reference. rDNA among Asteraceae species were compared performing with 45S rDNA. The rDNA copy number was calculated based on sequencing depth. The polymorphisms of rDNA sequences were identified with bam-readcount, and confirmed by Sanger sequencing and restriction enzyme experiment. The ITS2 amplicon sequencing was used to verify the stability of ITS2 haplotype analysis. RESULTS Different from other Asteraceae species, 45S and 5S linked-type rDNA was only found in Artemisia genus. Rich polymorphisms of copy number and sequence of rDNA were identified in A. annua population. The haplotype composition of internal transcribed spacer 2 (ITS2) region which had moderate sequence polymorphism and relative short size was significantly different among A. annua strains. A population discrimination method was developed based on ITS2 haplotype analysis with high-throughput sequencing. CONCLUSION This study provides comprehensive characteristics of rDNA and suggests that ITS2 haplotype analysis is ideal tool for A. annua strain identification and population genetic homogeneity assessment.
Collapse
Affiliation(s)
- Xiaoxia Ding
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Jieting Chen
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Chunyan Dai
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Peiqi Shi
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Hengyu Pan
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Yanqi Lin
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Yikang Chen
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Lu Gong
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Linming Chen
- Guangzhou Huibiao Testing Technology Center, Guangzhou 510700, China
| | - Wenguang Wu
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Xiaohui Qiu
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Zhihai Huang
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Baosheng Liao
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| |
Collapse
|
5
|
Si C, Zeng D, da Silva JAT, Qiu S, Duan J, Bai S, He C. Genome-wide identification of Aux/IAA and ARF gene families reveal their potential roles in flower opening of Dendrobium officinale. BMC Genomics 2023; 24:199. [PMID: 37055721 PMCID: PMC10099678 DOI: 10.1186/s12864-023-09263-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/21/2023] [Indexed: 04/15/2023] Open
Abstract
BACKGROUND The auxin indole-3-acetic acid (IAA) is a vital phytohormone that influences plant growth and development. Our previous work showed that IAA content decreased during flower development in the medicinally important orchid Dendrobium officinale, while Aux/IAA genes were downregulated. However, little information about auxin-responsive genes and their roles in D. officinale flower development exists. RESULTS This study validated 14 DoIAA and 26 DoARF early auxin-responsive genes in the D. officinale genome. A phylogenetic analysis classified the DoIAA genes into two subgroups. An analysis of cis-regulatory elements indicated that they were related by phytohormones and abiotic stresses. Gene expression profiles were tissue-specific. Most DoIAA genes (except for DoIAA7) were sensitive to IAA (10 μmol/L) and were downregulated during flower development. Four DoIAA proteins (DoIAA1, DoIAA6, DoIAA10 and DoIAA13) were mainly localized in the nucleus. A yeast two-hybrid assay showed that these four DoIAA proteins interacted with three DoARF proteins (DoARF2, DoARF17, DoARF23). CONCLUSIONS The structure and molecular functions of early auxin-responsive genes in D. officinale were investigated. The DoIAA-DoARF interaction may play an important role in flower development via the auxin signaling pathway.
Collapse
Affiliation(s)
- Can Si
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
| | - Danqi Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Shengxiang Qiu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
| | - Jun Duan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
| | - Song Bai
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China.
| | - Chunmei He
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- South China National Botanical Garden, Guangzhou, 510650, China.
| |
Collapse
|
6
|
Yang YB, Yan FX, Wang LH, Tian F, Zhou FJ. The complete chloroplast genome of Dendrobium moschatum (Buch.-Ham.) Sw. 1805 (Orchidaceae). Mitochondrial DNA B Resour 2022; 7:2027-2030. [PMCID: PMC9744202 DOI: 10.1080/23802359.2022.2149249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The morphological characteristic of Dendrobium moschatum (Buch.-Ham.) Sw. 1805 is very distinctive among Dendrobium Sw. 1799, and it has high medicinal and ornamental values. Here, we reported the first complete chloroplast genome of D. moschatum. The complete genome of D. moschatum was 159,701 bp in length with 130 genes, including 38 tRNA, 8 rRNA, and 84 protein-coding genes. Phylogenetic analysis showed that D. moschatum was strongly allied with D. denneanum Kerr. 1933.
Collapse
Affiliation(s)
| | | | | | - Fan Tian
- Guizhou Academy of Forestry, Guiyang, China
| | - Feng-Jiao Zhou
- Guizhou Institute of Forestry Inventory and Planning, Guiyang, China,CONTACT Feng-Jiao Zhou Guizhou Institute of Forestry Inventory and Planning, Guiyang, China
| |
Collapse
|
7
|
Sherpa R, Devadas R, Bolbhat SN, Nikam TD, Penna S. Gamma Radiation Induced In-Vitro Mutagenesis and Isolation of Mutants for Early Flowering and Phytomorphological Variations in Dendrobium 'Emma White'. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11223168. [PMID: 36432897 PMCID: PMC9697006 DOI: 10.3390/plants11223168] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/11/2022] [Accepted: 11/15/2022] [Indexed: 05/31/2023]
Abstract
In vitro mutagenesis offers a feasible approach for developing new orchid cultivars through genetic manipulation. In the present study, protocorm-like bodies (PLBs) were exposed to gamma rays (10, 20, 40, 60, 80 Gy) to study in vitro growth responses and induction of mutants in Dendrobium ‘Emma White’. Both proliferation and regeneration of PLBs decreased progressively with increasing doses, except for a significantly enhanced growth response at 10 Gy. The optimal dose of gamma radiation for mutagenesis was found in the range 10 to 25 Gy based on the growth reduction curve. Analysis using a high-throughput cell analyzer revealed a significant reduction in nuclear DNA content at > 40 Gy doses. At 10 Gy treatment, the growth attributes, such as root length, plant height and leaf number, were significantly increased by 36%, 26% and 20%, respectively, compared to the control. This increase was significant over other tested doses as well. Testing of random amplified polymorphic DNA markers revealed the presence of detectable polymorphism among gamma mutant plantlets with a polymorphism information content value at 0.41. The gamma-ray-induced earliness in flower development was observed within 294 days post ex vitro growth of 10 Gy mutant compared to the control plants flowered after 959 days. Our results highlight the significance of gamma radiation in inducing enhanced growth, morphological variations and early floral initiation in Dendrobium, providing a basic framework for mutation breeding and improvement of orchids.
Collapse
Affiliation(s)
- Rubina Sherpa
- Department of Botany, Annasaheb Awate College, Manchar 410503, India
- Indian Council of Agricultural Research-National Research Centre on Orchids, Pakyong 737106, India
| | - Ramgopal Devadas
- Indian Council of Agricultural Research-National Research Centre on Orchids, Pakyong 737106, India
| | | | | | - Suprasanna Penna
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India
- Amity Institute of Biotechnology, Amity University Mumbai, Mumbai 410206, India
| |
Collapse
|
8
|
Chen CY, Tan H, Chen R, Zhang FP. Characterization of the complete chloroplast genome of Dendrobium findlayanum Par. et Rchb. f. 1874 (Orchidaceae). Mitochondrial DNA B Resour 2022; 7:644-645. [PMID: 35425859 PMCID: PMC9004495 DOI: 10.1080/23802359.2022.2062264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Dendrobium findlayanum Par. et Rchb. f. 1874 has the high ornamental and medicinal value. Here, we report the first complete chloroplast genome of D. findlayanum. The complete chloroplast genome of D. findlayanum is 153,713 bp in length with 120 genes, including 75 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The total content of GC of the whole genome is 37.46%. Phylogenetic analysis indicated that D. findlayanum was closely related to other species in Dendrobium, and this study provides new genetic resources for species identification and phylogenetic analyses in Dendrobium.
Collapse
Affiliation(s)
- Cui-Ying Chen
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, China
| | - Hui Tan
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, China
| | - Rui Chen
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, China
| | - Feng-Ping Zhang
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, China
| |
Collapse
|
9
|
Li M, Trapika IGSC, Tang SYS, Cho JL, Qi Y, Li CG, Li Y, Yao M, Yang D, Liu B, Li R, Yang P, Ma G, Ren P, Huang X, Xie D, Chen S, Li M, Yang L, Leng P, Huang Y, Li GQ. Mechanisms and Active Compounds Polysaccharides and Bibenzyls of Medicinal Dendrobiums for Diabetes Management. Front Nutr 2022; 8:811870. [PMID: 35155528 PMCID: PMC8832146 DOI: 10.3389/fnut.2021.811870] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/21/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Medicinal dendrobiums are used popularly in traditional Chinese medicine for the treatment of diabetes, while their active compounds and mechanism remain unclear. This review aimed to evaluate the mechanism and active compounds of medicinal dendrobiums in diabetes management through a systematic approach. METHODS A systematic approach was conducted to search for the mechanism and active phytochemicals in Dendrobium responsible for anti-diabetic actions using databases PubMed, Embase, and SciFinder. RESULTS Current literature indicates polysaccharides, bibenzyls, phenanthrene, and alkaloids are commonly isolated in Dendrobium genusin which polysaccharides and bibenzyls are most aboundant. Many animal studies have shown that polysaccharides from the species of Dendrobium provide with antidiabetic effects by lowering glucose level and reversing chronic inflammation of T2DM taken orally at 200 mg/kg. Dendrobium polysaccharides protect pancreatic β-cell dysfunction and insulin resistance in liver. Dendrobium polysaccharides up-regulate the abundance of short-chain fatty acid to stimulate GLP-1 secretion through gut microbiota. Bibenzyls also have great potency to inhibit the progression of the chronic inflammation in cellular studies. CONCLUSION Polysaccharides and bibenzyls are the major active compounds in medicinal dendrobiums for diabetic management through the mechanisms of lowering glucose level and reversing chronic inflammation of T2DM by modulating pancreatic β-cell dysfunction and insulin resistance in liver as a result from gut microbita regulation.
Collapse
Affiliation(s)
- Mingjian Li
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - I. Gusti Surya Chandra Trapika
- Faculty of Medicine and Health, The University of Sydney School of Pharmacy, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine, Department of Pharmacology and Therapy, Udayana University, Jimbaran, Indonesia
| | - Suet Yee Sara Tang
- Faculty of Medicine and Health, The University of Sydney School of Pharmacy, The University of Sydney, Sydney, NSW, Australia
| | - Jun-Lae Cho
- Faculty of Medicine and Health, The University of Sydney School of Pharmacy, The University of Sydney, Sydney, NSW, Australia
- Faculty of Engineering and Information Technologies, Centre for Advanced Food Enginomics, The University of Sydney, Sydney, NSW, Australia
| | - Yanfei Qi
- Centenary Institute of Cancer Medicine and Cell Biology, The University of Sydney, Sydney, NSW, Australia
| | - Chun Guang Li
- NICM Health Research Institute, Western Sydney University, Penrith, NSW, Australia
| | - Yujuan Li
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Meicun Yao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Depo Yang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Bowen Liu
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Rong Li
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ping Yang
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Guoyi Ma
- The National Center for Natural Products Research, The University of Mississippi, Oxford, MS, United States
| | - Ping Ren
- Institute of TCM-related Comorbidity, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xi Huang
- Institute of TCM-related Comorbidity, Nanjing University of Chinese Medicine, Nanjing, China
| | - Deshan Xie
- Chengdu Tepu Biotech Co., Ltd., Chengdu, China
| | | | - Min Li
- College of Fundamental Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Lan Yang
- College of Fundamental Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ping Leng
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yong Huang
- Chengdu Tepu Biotech Co., Ltd., Chengdu, China
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - George Q. Li
- Faculty of Medicine and Health, The University of Sydney School of Pharmacy, The University of Sydney, Sydney, NSW, Australia
- NICM Health Research Institute, Western Sydney University, Penrith, NSW, Australia
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| |
Collapse
|
10
|
Zhang FP, Yin ZL, He HP. Characterization of the complete chloroplast genome of Dendrobium christyanum and its phylogenetic analysis. Mitochondrial DNA B Resour 2021; 6:2605-2606. [PMID: 34395891 PMCID: PMC8354162 DOI: 10.1080/23802359.2021.1961629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Dendrobium christyanum H.G. Reichenbach (Orchidaceae) is used as a source of the Chinese traditional medicine. Here, we report that the complete chloroplast (cp) genome sequence of D. christyanum is 157972 bp in length with134 genes, of which 114 are unique genes (80 protein-coding genes, 30 tRNAs, and 4 rRNAs). Phylogenetic analysis indicated that D. christyanum was closely related to D. strongylanthum, and D. longicornu. The newly sequenced cp genome will be useful for the phylogenetic and genetic conservation studies of Dendrobium.
Collapse
Affiliation(s)
- Feng-Ping Zhang
- Yunnan Key Laboratory of Dai and Yi Medicines, College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Zi-Li Yin
- Yunnan Key Laboratory of Dai and Yi Medicines, College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Hong-Ping He
- Yunnan Key Laboratory of Dai and Yi Medicines, College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| |
Collapse
|
11
|
Chen Z, Li J, Hou N, Zhang Y, Qiao Y. TCM-Blast for traditional Chinese medicine genome alignment with integrated resources. BMC PLANT BIOLOGY 2021; 21:339. [PMID: 34273956 PMCID: PMC8285853 DOI: 10.1186/s12870-021-03096-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
The traditional Chinese medicine (TCM) genome project aims to reveal the genetic information and regulatory network of herbal medicines, and to clarify their molecular mechanisms in the prevention and treatment of human diseases. Moreover, the TCM genome could provide the basis for the discovery of the functional genes of active ingredients in TCM, and for the breeding and improvement of TCM. The traditional Chinese Medicine Basic Local Alignment Search Tool (TCM-Blast) is a web interface for TCM protein and DNA sequence similarity searches. It contains approximately 40G of genome data on TCMs, including protein and DNA sequence for 36 TCMs with high medical value.The development of a publicly accessible TCM genome alignment database hosted on the TCM-Blast website ( http://viroblast.pungentdb.org.cn/TCM-Blast/viroblast.php ) has expanded to query multiple sequence databases to obtain TCM genome data, and provide user-friendly output for easy analysis and browsing of BLAST results. The genome sequencing of TCMs helps to elucidate the biosynthetic pathways of important secondary metabolites and provides an essential resource for gene discovery studies and molecular breeding. The TCMs genome provides a valuable resource for the investigation of novel bioactive compounds and drugs from these TCMs under the guidance of TCM clinical practice. Our database could be expanded to other TCMs after the determination of their genome data.
Collapse
Affiliation(s)
- Zhao Chen
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Yangguang South Avenue, Fangshan District, Beijing, 102488 China
- Research Center of TCM-Information Engineering, State Administration of Traditional Chinese Medicine of The Peoples Republic of China, Yangguang South Avenue, Fangshan District, Beijing, 102488 China
| | - Jing Li
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Yangguang South Avenue, Fangshan District, Beijing, 102488 China
- Research Center of TCM-Information Engineering, State Administration of Traditional Chinese Medicine of The Peoples Republic of China, Yangguang South Avenue, Fangshan District, Beijing, 102488 China
| | - Ning Hou
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Yangguang South Avenue, Fangshan District, Beijing, 102488 China
- Research Center of TCM-Information Engineering, State Administration of Traditional Chinese Medicine of The Peoples Republic of China, Yangguang South Avenue, Fangshan District, Beijing, 102488 China
| | - Yanling Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Yangguang South Avenue, Fangshan District, Beijing, 102488 China
- Research Center of TCM-Information Engineering, State Administration of Traditional Chinese Medicine of The Peoples Republic of China, Yangguang South Avenue, Fangshan District, Beijing, 102488 China
| | - Yanjiang Qiao
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Yangguang South Avenue, Fangshan District, Beijing, 102488 China
- Research Center of TCM-Information Engineering, State Administration of Traditional Chinese Medicine of The Peoples Republic of China, Yangguang South Avenue, Fangshan District, Beijing, 102488 China
| |
Collapse
|
12
|
Zheng K, Cai Y, Chen W, Gao Y, Jin J, Wang H, Feng S, Lu J. Development, Identification, and Application of a Germplasm Specific SCAR Marker for Dendrobium officinale Kimura et Migo. FRONTIERS IN PLANT SCIENCE 2021; 12:669458. [PMID: 34054907 PMCID: PMC8160518 DOI: 10.3389/fpls.2021.669458] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/20/2021] [Indexed: 05/27/2023]
Abstract
The stems of Dendrobium officinale have been used as a rare and valuable Chinese tonic medicine, known as "Tiepi Fengdou", since the Qing dynasty. Because of the increased market demand and continued exploitation of this plant, the reserves of wild D. officinale resources have been depleted, and D. officinale products on the market are being increasingly adulterated. Such changes have strongly affected the sustainable utilization of this valuable medicinal plant resource and the development of related industries. In this study, a species-specific DNA marker was developed for the rapid and accurate authentication of D. officinale. In total, 36 start codon-targeted (SCoT) polymorphism primers were screened in 36 definite Dendrobium species, and a distinct species-specific DNA amplicon (SCoT13-215) for D. officinale was obtained. After the sequence was cloned and sequenced, a sequence-characterized amplified region marker was developed (named SHF/SHR) and validated through PCR amplification of all 38 Dendrobium samples. The marker's specificity for D. officinale was confirmed through the consistent amplification of a clear 197-bp band. This SCAR marker can be used to rapidly, effectively, and reliably identify D. officinale among various Dendrobium species and may play an important role in ensuring the quality of medicinal preparations and protecting the germplasm of this important medicinal species.
Collapse
Affiliation(s)
- Kaixin Zheng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Yuchen Cai
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Weijie Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yadi Gao
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Jingjing Jin
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Huizhong Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Shangguo Feng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Jiangjie Lu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| |
Collapse
|
13
|
Tang X, Yuan Y, Zhang J. How Climate Change Will Alter the Distribution of Suitable Dendrobium Habitats. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.536339] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
14
|
Chen S, Dai J, Song X, Jiang X, Zhao Q, Sun C, Chen C, Chen N, Han B. Endophytic Microbiota Comparison of Dendrobium huoshanense Root and Stem in Different Growth Years. PLANTA MEDICA 2020; 86:967-975. [PMID: 31766070 DOI: 10.1055/a-1046-1022] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The endophytic microbiome in medicinal plants is rich and diverse, but few studies have followed the endophytic microbiome of medicinal plants in different tissues with their growth. In this study, we examined the endophytic bacterial and fungal community structures associated with both the stem and root compartments of Dendrobium huoshanense at different growth years via high-throughput sequencing of 16S rRNA genes and nrDNA fragments of internal transcribed spacer regions. Results indicated that more diverse prokaryotic and fungal operational taxonomic units were detected in roots than in stems, and the alpha diversity of endophytic prokaryotic significantly differed among the 1-, 2-, and 3-year-old roots. The dominant bacterial phyla Proteobacteria Firmicutes, Actinobacteria, Bacteroidetes, and Acidobacteria, and fungal phyla Ascomycota, Basidiomycota, and Ascomycota were detected in the stems and roots with 3 growth years. Moreover, linear discriminant effect size analysis revealed 138 differentially abundant taxonomic clades in the bacterial level, and 197 in the fungal level in six groups. Our results provide evidence for endophytic microbiota communities depending on the tissues and growth years of D. huoshanense. The results from this study should be useful to better understand medicinal plant-microbe interactions.
Collapse
Affiliation(s)
- Shaotong Chen
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, China
- Department of Pharmacy, Anhui University of Chinese Medicine, He'fei, China
| | - Jun Dai
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, China
- Anhui Province Traditional Chinese Medicine Resource Protection and Sustainable Utilization Engineering Laboratory, Lu'an, China
| | - Xiangwen Song
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, China
- Anhui Province Traditional Chinese Medicine Resource Protection and Sustainable Utilization Engineering Laboratory, Lu'an, China
| | - Xueping Jiang
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, China
- Anhui Province Traditional Chinese Medicine Resource Protection and Sustainable Utilization Engineering Laboratory, Lu'an, China
| | - Qun Zhao
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, China
- Anhui Province Traditional Chinese Medicine Resource Protection and Sustainable Utilization Engineering Laboratory, Lu'an, China
| | - Chuanbo Sun
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, China
- Anhui Province Traditional Chinese Medicine Resource Protection and Sustainable Utilization Engineering Laboratory, Lu'an, China
| | - Cunwu Chen
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, China
- Anhui Province Traditional Chinese Medicine Resource Protection and Sustainable Utilization Engineering Laboratory, Lu'an, China
| | - Naifu Chen
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, China
- Anhui Province Traditional Chinese Medicine Resource Protection and Sustainable Utilization Engineering Laboratory, Lu'an, China
| | - Bangxing Han
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, China
- Anhui Province Traditional Chinese Medicine Resource Protection and Sustainable Utilization Engineering Laboratory, Lu'an, China
| |
Collapse
|
15
|
Qi Y, Huang JL, Zhang SB. Correlated evolution of leaf and root anatomic traits in Dendrobium (Orchidaceae). AOB PLANTS 2020; 12:plaa034. [PMID: 32818052 PMCID: PMC7426005 DOI: 10.1093/aobpla/plaa034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 07/15/2020] [Indexed: 06/02/2023]
Abstract
The whole-plant economic spectrum concept predicts that leaf and root traits evolve in coordination to cope with environmental stresses. However, this hypothesis is difficult to test in many species because their leaves and roots are exposed to different environments, above- and below-ground. In epiphytes, both leaves and roots are exposed to the atmosphere. Thus, we suspect there are consistent water conservation strategies in leaf and root traits of epiphytes due to similar selection pressures. Here, we measured the functional traits of 21 species in the genus Dendrobium, which is one of the largest epiphytic taxa in the family Orchidaceae, and used phylogenetically independent contrasts to test the relationships among traits, and between traits and the environment. Our results demonstrate that species with a thicker velamen tended to have thicker roots, a thicker root cortex and vascular cylinder, and a larger number of vessels in the root. Correspondingly, these species also had higher leaf mass per area, and thicker leaf lower cuticles. Leaf and root traits associated with water conservation showed significantly positive relationships. The number of velamen layers, leaf density and the ratio of vascular cylinder radius to root radius were significantly affected by the species' differing environments. Thus, traits related to water conservation and transport may play an important role in helping Dendrobium cope with the cool and dry conditions found at high elevations. These findings confirmed the hypothesis that leaf and root traits have evolved in coordination, and also provide insights into trait evolution and ecological adaptation in epiphytic orchids.
Collapse
Affiliation(s)
- Ying Qi
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jia-Lin Huang
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Shi-Bao Zhang
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| |
Collapse
|
16
|
Zhang J, Li CR, Luo Y, Li QQ, Li L. The complete chloroplast genome sequence of Dendrobium chrysocrepis (Orchidaceae). Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1753590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Jin Zhang
- Department of Biodiversity Conservation, Southwest Forestry University, Kunming, China
- Department of Life Science, Southwest Forestry University, Kunming, China
| | - Chu-Ran Li
- Department of Forestry, Southwest Forestry University, Kunming, China
| | - Yan Luo
- Department of Gardening and Horticulture, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Qing-Qing Li
- Department of Life Science, Southwest Forestry University, Kunming, China
| | - Lu Li
- Department of Biodiversity Conservation, Southwest Forestry University, Kunming, China
| |
Collapse
|
17
|
An Overview of Orchid Protocorm-Like Bodies: Mass Propagation, Biotechnology, Molecular Aspects, and Breeding. Int J Mol Sci 2020; 21:ijms21030985. [PMID: 32024235 PMCID: PMC7037051 DOI: 10.3390/ijms21030985] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 01/25/2020] [Accepted: 01/28/2020] [Indexed: 12/15/2022] Open
Abstract
The process through induction, proliferation and regeneration of protocorm-like bodies (PLBs) is one of the most advantageous methods for mass propagation of orchids which applied to the world floricultural market. In addition, this method has been used as a tool to identify genes of interest associated with the production of PLBs, and also in breeding techniques that use biotechnology to produce new cultivars, such as to obtain transgenic plants. Most of the molecular studies developed have used model plants as species of Phalaenopsis, and interestingly, despite similarities to somatic embryogenesis, some molecular differences do not yet allow to characterize that PLB induction is in fact a type of somatic embryogenesis. Despite the importance of species for conservation and collection purposes, the flower market is supported by hybrid cultivars, usually polyploid, which makes more detailed molecular evaluations difficult. Studies on the effect of plant growth regulators on induction, proliferation, and regeneration of PLBs are the most numerous. However, studies of other factors and new technologies affecting PLB production such as the use of temporary immersion bioreactors and the use of lighting-emitting diodes have emerged as new tools for advancing the technique with increasing PLB production efficiency. In addition, recent studies on Phalaenopsis equestris genome sequencing have enabled more detailed molecular studies and the molecular characterization of plantlets obtained from this technique currently allow the technique to be evaluated in a more comprehensive way regarding its real applications and main limitations aiming at mass propagation, such as somaclonal variation.
Collapse
|
18
|
Lv C, He Y, Kang C, Zhou L, Wang T, Yang J, Guo L. Tracing the Geographical Origins of Dendrobe ( Dendrobium spp.) by Near-Infrared Spectroscopy Sensor Combined with Porphyrin and Chemometrics. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2020; 2020:8879957. [PMID: 33005473 PMCID: PMC7503109 DOI: 10.1155/2020/8879957] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 08/19/2020] [Accepted: 08/28/2020] [Indexed: 05/03/2023]
Abstract
Dendrobe (Dendrobium spp.) is a traditional medicinal and edible food, which is rich in nutrients and contains biologically active metabolites. The quality and price of dendrobe are related to its geographical origins, and high quality dendrobe is often imitated by low quality dendrobe in the market. In this work, near-infrared (NIR) spectroscopy sensor combined with porphyrin and chemometrics was used to distinguish 360 dendrobe samples from twelve different geographical origins. Partial least squares discriminant analysis (PLSDA) was used to study the sensing performance of traditional NIR and tera-(4-methoxyphenyl)-porphyrin (TMPP)-NIR on the identification of dendrobe origin. In the PLSDA model, the recognition rate of the training and prediction set of the TMPP-NIR could reach 100%, which was higher than the 91.85% and 91.34% of traditional NIR. And the accuracy, sensitivity, and specificity of the TMPP-NIR sensor are all 1.00. The mechanism of TMPP improving the specificity of NIR spectroscopy should be related to the π-π conjugated system and the methoxy groups of TMPP interact with the chemical components of dendrobe. This study reflected that NIR spectrum with TMPP sensor was an effective approach for identifying the geographic origin of dendrobe.
Collapse
Affiliation(s)
- Chaogeng Lv
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yali He
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Chuanzhi Kang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Li Zhou
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Tielin Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jian Yang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Lanping Guo
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| |
Collapse
|
19
|
Konhar R, Debnath M, Vishwakarma S, Bhattacharjee A, Sundar D, Tandon P, Dash D, Biswal DK. The complete chloroplast genome of Dendrobium nobile, an endangered medicinal orchid from north-east India and its comparison with related Dendrobium species. PeerJ 2019; 7:e7756. [PMID: 31695964 PMCID: PMC6830405 DOI: 10.7717/peerj.7756] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 08/26/2019] [Indexed: 11/21/2022] Open
Abstract
The medicinal orchid genus Dendrobium belonging to the Orchidaceae family is a huge genus comprising about 800-1,500 species. To better illustrate the species status in the genus Dendrobium, a comparative analysis of 33 available chloroplast genomes retrieved from NCBI RefSeq database was compared with that of the first complete chloroplast genome of D. nobile from north-east India based on next-generation sequencing methods (Illumina HiSeq 2500-PE150). Our results provide comparative chloroplast genomic information for taxonomical identification, alignment-free phylogenomic inference and other statistical features of Dendrobium plastomes, which can also provide valuable information on their mutational events and sequence divergence.
Collapse
Affiliation(s)
- Ruchishree Konhar
- Bioinformatics Centre, North-Eastern Hill University, Shillong, Meghalaya, India
- Informatics and Big Data, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Manish Debnath
- Bioinformatics Centre, North-Eastern Hill University, Shillong, Meghalaya, India
| | - Santosh Vishwakarma
- Bioinformatics Centre, North-Eastern Hill University, Shillong, Meghalaya, India
| | - Atanu Bhattacharjee
- Bioinformatics Centre, North-Eastern Hill University, Shillong, Meghalaya, India
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Pramod Tandon
- Biotech Park, Kursi road, Lucknow, Uttar Pradesh, India
| | - Debasis Dash
- Informatics and Big Data, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, India
| | | |
Collapse
|
20
|
Huang ZC, Pan YY, Chen GZ, Chen LJ, Wu XY, Huang J. The complete chloroplast genome of Dendrobium harveyanum (Orchidaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:3200-3201. [PMID: 33365918 PMCID: PMC7707279 DOI: 10.1080/23802359.2019.1669088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Dendrobium harveyanum is an endangered species of Orchidaceae. Here we report the complete chloroplast (cp) genome sequence and the cp genome features of D. harveyanum. The complete cp genome sequence of D. harveyanum is 157,292 bp in length and presented a typical quadripartite structure including one large single-copy region (LSC, 86,583 bp), one small single-copy region (SSC, 19,449 bp), and two inverted repeat regions (IRs, 25,630 bp each). The cp genome encoded 138 genes, of which 120 were unique genes. The phylogenetic relationships show that D. harveyanum is closely related to other species in Dendrobium.
Collapse
Affiliation(s)
- Zhi-Cong Huang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Shenzhen, Guangdong, China.,Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, Guangdong, China
| | - Yun-Yun Pan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Shenzhen, Guangdong, China.,Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, Guangdong, China
| | - Gui-Zhen Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Shenzhen, Guangdong, China.,Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, Guangdong, China
| | - Li Jun Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Shenzhen, Guangdong, China.,Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, Guangdong, China
| | - Xin-Yi Wu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Shenzhen, Guangdong, China.,Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, Guangdong, China
| | - Jie Huang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Shenzhen, Guangdong, China.,Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, Guangdong, China
| |
Collapse
|
21
|
Wang Q, Liang J, Liu H. In vitro effects of four polysaccharides containing β-D-Glup on intestinal function. INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2019. [DOI: 10.1080/10942912.2019.1628778] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Qin Wang
- College of Light Industry and Food, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Jiaxi Liang
- College of Light Industry and Food, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Huifan Liu
- College of Light Industry and Food, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| |
Collapse
|
22
|
Liu H, Fang C, Zhang T, Guo L, Ye Q. Molecular authentication and differentiation of Dendrobium species by rDNA ITS region sequence analysis. AMB Express 2019; 9:53. [PMID: 31004252 PMCID: PMC6474905 DOI: 10.1186/s13568-019-0767-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 03/23/2019] [Indexed: 11/16/2022] Open
Abstract
Owing to their significant medicinal and edible values, the natural Dendrobium species have underdone over-collection and habitat destruction, and cultivated species emerged for candidates. However, these Dendrobium plants are similar in shape to be easily confused, leading to extreme difficulties for identification based on their morphological and chemical features. In this study, the rDNA ITS region sequence analysis was developed for rapid and accurate identification of thirteen wild and cultivated Dendrobium species belonging to two sections Formosae and Chrysotoxae. By cloning and sequencing the rDNA ITS region genes from 13 Dendrobium species, the phylogenetic relationships among them were analyzed. Results showed that the variation of the ITS region, together with the lengths and Guanine and Cytosine contents of ITS, 5.8s rDNA, ITS1 and ITS2 sequences occurred in the tested Dendrobium species, and which from section Chrysotoxae was higher than that from section Formsae. Phylogenetic analysis based on neighbor-joining and maximum p-arsimony trees indicated that the Dendrobium species of sections Formosae and Chrysotoxae could be well divided into two groups. A majority of Dendrobium species exhibited distinctive ITS2 secondary structures, while for those with close genetic relationships were similar. Therefore, the ITS2 region sequence analysis is simple, quick, and highly reliable that can be used as an effective tool for molecular identification and classification, as well as the reconstruction of the phylogeny of wild and cultivated Dendrobium species belonging to different sections.
Collapse
|
23
|
Wu YG, Wang KW, Zhao ZR, Zhang P, Liu H, Zhou GJ, Cheng Y, Wu WJ, Cai YH, Wu BL, Chen FY. A novel polysaccharide from Dendrobium devonianum serves as a TLR4 agonist for activating macrophages. Int J Biol Macromol 2019; 133:564-574. [PMID: 31004640 DOI: 10.1016/j.ijbiomac.2019.04.125] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 03/26/2019] [Accepted: 04/16/2019] [Indexed: 12/15/2022]
Abstract
Dendrobium devonianum has been used as herbal medicines and nutraceutical products since ancient time in China. However, its chemical composition and pharmacological mechanisms are not fully known. In present studies, by chemical purification and characteristic identification, we discovered a novel polysaccharide from D. devonianum, which was designated as DvP-1 with molecular weights of 9.52 × 104 Da. DvP-1 is a homogeneous heteropolysaccharide consisting of D-mannose and d-glucose in the molar ration of 10.11: 1. The main glycosidic linkages were β-1, 4-Manp, which were substituted with acetyl groups at the O-2, O-3 and/or O-6 positions. DvP-1 was found to directly stimulate the activation of macrophages in vitro, as evidenced by inducing morphologic change, thereby promoting the production of cytokines TNF-α, IL-6 and NO, and enhancing the pinocytic activity of macrophages. By establishing a zebrafish model, we also found that DvP-1 could alleviate vinorelbine-induced decrease of macrophages in vivo. Further findings indicated that DvP-1 activated macrophages through several toll-like receptors (TLRs), but mainly through TLR4. DvP-1 served as a TLR4 agonist and induced ERK, JNK, p38, and IκB-α phosphorylation, suggesting the activation of MAPK and NFκB signaling pathways downstream of TLR4. These findings could help us further understand the immunomodulating effects of D. devonianum in Chinese medicines or health foods for immunocompromised persons. They also show the medicinal value of DvP-1 for the treatment of cancer and infectious diseases caused by TLR4 dysfunction.
Collapse
Affiliation(s)
- Yue-Guo Wu
- Institute of Materia Medica, Zhejiang Academy of Medical Sciences, Hangzhou 310013, China
| | - Kui-Wu Wang
- Department of Applied Chemistry, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Zheng-Rong Zhao
- Institute of Materia Medica, Zhejiang Academy of Medical Sciences, Hangzhou 310013, China
| | - Ping Zhang
- Institute of Materia Medica, Zhejiang Academy of Medical Sciences, Hangzhou 310013, China
| | - Hua Liu
- Institute of Materia Medica, Zhejiang Academy of Medical Sciences, Hangzhou 310013, China.
| | - Gui-Jiao Zhou
- School of Basic Medical Sciences & Forensic Medicine, Hangzhou Medical College, Hangzhou 310053, China
| | - Yan Cheng
- School of Basic Medical Sciences & Forensic Medicine, Hangzhou Medical College, Hangzhou 310053, China
| | - Wen-Jie Wu
- School of Basic Medical Sciences & Forensic Medicine, Hangzhou Medical College, Hangzhou 310053, China
| | - Yi-Heng Cai
- School of Basic Medical Sciences & Forensic Medicine, Hangzhou Medical College, Hangzhou 310053, China
| | - Bei-Li Wu
- Institute of Materia Medica, Zhejiang Academy of Medical Sciences, Hangzhou 310013, China
| | - Feng-Yang Chen
- School of Basic Medical Sciences & Forensic Medicine, Hangzhou Medical College, Hangzhou 310053, China.
| |
Collapse
|
24
|
Zhao ZR, Xu SF, Zhang P, Liu H, Wu YG, Zhou GJ, Cai YH, Zhao JR, Chen FY. Comparison of Immunomodulating Activities of Dendrobium devonianum and Dendrobium officinale In vitro and In vivo. INT J PHARMACOL 2019. [DOI: 10.3923/ijp.2019.441.448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
25
|
Yuan Y, Liu X, Wang J, Zhang J. Morphological and microscopic identification of three major medicinal Dendrobium species in Ta-pieh Mountains area. Microsc Res Tech 2019; 82:483-493. [PMID: 30636024 DOI: 10.1002/jemt.23191] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/19/2018] [Accepted: 11/20/2018] [Indexed: 11/11/2022]
Abstract
Dendrobium is an important medicinal material in China. It has the effect of nourishing the stomach, nourishing yin and clearing heat. In China, there are many types of Dendrobium, and different Dendrobium species have different efficacy. The present study is aimed at distinguishing three major Dendrobium species from morphological and microscopic identification in Ta-pieh mountains area. In this article, the roots, stems and leaves of Dendrobium huoshanense, Dendrobium officinale, and Dendrobium moniliforme are used as materials to compare the differences of tissues of these three Dendrobium species by morphological indexes and microscopic identification of different Dendrobium. The stem morphology of these three Dendrobium species was significantly different except for stem internodes number and the middle part of the stem diameter by measuring the stems of Dendrobium. To ensure the safe use of Dendrobium, we built a fast and convenient method combining normal and fluorescence microscopy was applied in the present study to distinguish D. huoshanense, D. officinale, and D. moniliforme. The microscopic results show that different types of Dendrobium exhibit different states that can be distinguished under normal light normal and fluorescence microscopy. This comparative study of morphology and microscopy contributes to the development of identification and quality evaluation of Dendrobium.
Collapse
Affiliation(s)
- Yingdan Yuan
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.,Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, China
| | - Xin Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.,Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, China
| | - Jinping Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.,Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, China
| | - Jinchi Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.,Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, China
| |
Collapse
|
26
|
Accurate authentication of Dendrobium officinale and its closely related species by comparative analysis of complete plastomes. Acta Pharm Sin B 2018; 8:969-980. [PMID: 30505665 PMCID: PMC6251949 DOI: 10.1016/j.apsb.2018.05.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/18/2018] [Accepted: 05/21/2018] [Indexed: 01/26/2023] Open
Abstract
Owing to its great medicinal and ornamental values, Dendrobium officinale is frequently adulterated with other Dendrobium species on the market. Unfortunately, the utilization of the common DNA markers ITS, ITS2, and matK+rbcL is unable to distinguish D. officinale from 5 closely related species of it (D. tosaense, D. shixingense, D. flexicaule, D. scoriarum and D. aduncum). Here, we compared 63 Dendrobium plastomes comprising 40 newly sequenced plastomes of the 6 species and 23 previously published plastomes. The plastomes of D. officinale and its closely related species were shown to have conserved genome structure and gene content. Comparative analyses revealed that small single copy region contained higher variation than large single copy and inverted repeat regions, which was mainly attributed to the loss/retention of ndh genes. Furthermore, the intraspecific sequence variability among different Dendrobium species was shown to be diversified, which necessitates a cautious evaluation of genetic markers specific for different Dendrobium species. By evaluating the maximum likelihood trees inferred from different datasets, we found that the complete plastome sequence dataset had the highest discriminatory power for D. officinale and its closely related species, indicating that complete plastome sequences can be used to accurately authenticate Dendrobium species.
Collapse
Key Words
- Authentication
- BS, bootstrap value
- CE, capillary electrophoresis
- Complete plastome sequence
- Dendrobium officinale
- Genetic marker
- HPLC, high-pressure liquid chromatography
- IR, inverted repeat region
- Indels, insertions/deletions
- LSC, large single copy region
- ML, maximum likelihood
- NGS, next-generation sequencing
- Plastomic comparison
- SNPs, single nucleotide polymorphisms
- SSC, small single copy region
- SV, sequence variability.
Collapse
|
27
|
Zheng SG, Hu YD, Zhao RX, Yan S, Zhang XQ, Zhao TM, Chun Z. Genome-wide researches and applications on Dendrobium. PLANTA 2018; 248:769-784. [PMID: 30066218 DOI: 10.1007/s00425-018-2960-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/21/2018] [Indexed: 05/10/2023]
Abstract
This review summarizes current knowledge of chromosome characterization, genetic mapping, genomic sequencing, quality formation, floral transition, propagation, and identification in Dendrobium. The widely distributed Dendrobium has been studied for a long history, due to its important economic values in both medicine and ornamental. In recent years, some species of Dendrobium and other orchids had been reported on genomic sequences, using the next-generation sequencing technology. And the chloroplast genomes of many Dendrobium species were also revealed. The chromosomes of most Dendrobium species belong to mini-chromosomes, and showed 2n = 38. Only a few of genetic studies were reported in Dendrobium. After revealing of genomic sequences, the techniques of transcriptomics, proteomics and metabolomics could be employed on Dendrobium easily. Some other molecular biological techniques, such as gene cloning, gene editing, genetic transformation and molecular marker developing, had also been applied on the basic research of Dendrobium, successively. As medicinal plants, insights into the biosynthesis of some medicinal components were the most important. As ornamental plants, regulation of flower related characteristics was the most important. More, knowledge of growth and development, environmental interaction, evolutionary analysis, breeding of new cultivars, propagation, and identification of species and herbs were also required for commercial usage. All of these studies were improved using genomic sequences and related technologies. To answer some key scientific issues in Dendrobium, quality formation, flowering, self-incompatibility and seed germination would be the focus of future research. And genome related technologies and studies would be helpful.
Collapse
Affiliation(s)
- Shi-Gang Zheng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Ya-Dong Hu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Ruo-Xi Zhao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Shou Yan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100041, China
| | - Xue-Qin Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100041, China
| | - Ting-Mei Zhao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100041, China
| | - Ze Chun
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
| |
Collapse
|
28
|
Wang LR, Wang SQ, Niu JF, Wang SP, Wang ZZ. The complete chloroplast genome sequence of an endangered species, Dendrobium pendulum Roxb. (Orchidaceae). CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-017-0830-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
29
|
Chattopadhyay P, Banerjee G, Banerjee N. Distinguishing Orchid Species by DNA Barcoding: Increasing the Resolution of Population Studies in Plant Biology. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2018; 21:711-720. [PMID: 29257732 DOI: 10.1089/omi.2017.0131] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Increasing the resolution of population studies in plant biology is one of the leading frontiers for omics sciences. One of the most pervasive challenges in molecular phylogenetics is the incongruence between phylogenies obtained using different data sets such as individual genes [like ribulose bisphosphate carboxylase large chain (rbcL) and maturase K (matK)] and intergenic spacers (IGS) [like nuclear ribosomal internal transcribed spacer 1 (nrITS 1) and 2 (nrITS 2), and chloroplast IGS between transfer RNA for leucine and phenylalanine (cp trnL-trnF IGS)]. To solve this challenge, we have screened the four well-established candidate gene sequences (i.e., rbcL, matK, trnL-trnF IGS, and 18S-ITS1-5.8S-ITS2-28S nrDNA) of 65 Indian orchid species. We also have included 31 different species of Dendrobium to identify the suitable locus for resolving the phylogeny-related problem below the taxonomic rank of genus. The Consortium for the Barcode of Life has recommended the locus rbcL and matK for barcoding of all land plants, including orchids. However, in this study, matK and rbcL (species resolving capacity 52% and 48%, respectively) were found to work above the taxonomic limit of genus, and thus cannot be considered a suitable tool to resolve closely related species of Dendrobium, whereas, we found that the locus 18S-ITS1-5.8S-ITS2-28S nrDNA is the best choice with the highest species resolving ability (95.23%) and the highest mean Kimura 2-parameter distance (254 for intergeneric and 144 for intrageneric) for phylogeny construction, and thus have been taken as the most promising single-locus barcode for orchids.
Collapse
Affiliation(s)
- Pritam Chattopadhyay
- 1 Department of Botany, Visva-Bharati , Santiniketan, India .,2 Department of Biotechnology, Gauhati University , Guwahati, India
| | - Goutam Banerjee
- 3 Department of Biochemistry, University of Calcutta , Kolkata, India
| | | |
Collapse
|
30
|
Niu Z, Pan J, Xue Q, Zhu S, Liu W, Ding X. Plastome-wide comparison reveals new SNV resources for the authentication of Dendrobium huoshanense and its corresponding medicinal slice (Huoshan Fengdou). Acta Pharm Sin B 2018; 8:466-477. [PMID: 29881686 PMCID: PMC5989833 DOI: 10.1016/j.apsb.2017.12.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/24/2017] [Accepted: 11/08/2017] [Indexed: 11/06/2022] Open
Abstract
Dendrobium species and their corresponding medicinal slices have been extensively used as traditional Chinese medicine (TCM) in many Asian countries. However, it is extremely difficult to identify Dendrobium species based on their morphological and chemical features. In this study, the plastomes of D. huoshanense were used as a model system to investigate the hypothesis that plastomic mutational hotspot regions could provide a useful single nucleotide variants (SNVs) resource for authentication studies. We surveyed the plastomes of 17 Dendrobium species, including the newly sequenced plastome of D. huoshanense. A total of 19 SNVs that could be used for the authentication of D. huoshanense were detected. On the basis of this comprehensive comparison, we identified the four most informative hotspot regions in the Dendrobium plastome that encompass ccsA to ndhF, matK to 3'trnG, rpoB to psbD, and trnT to rbcL. Furthermore, to established a simple and accurate method for the authentication of D. huoshanense and its medicinal slices, a total of 127 samples from 20 Dendrobium species including their corresponding medicinal slices (Fengdous) were used in this study. Our results suggest that D. huoshanense and its medicinal slices can be rapidly and unequivocally identified using this method that combines real-time PCR with the amplification refractory mutation system (ARMS).
Collapse
Affiliation(s)
| | | | | | | | | | - Xiaoyu Ding
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| |
Collapse
|
31
|
Lu J, Liu Y, Xu J, Mei Z, Shi Y, Liu P, He J, Wang X, Meng Y, Feng S, Shen C, Wang H. High-Density Genetic Map Construction and Stem Total Polysaccharide Content-Related QTL Exploration for Chinese Endemic Dendrobium (Orchidaceae). FRONTIERS IN PLANT SCIENCE 2018; 9:398. [PMID: 29636767 PMCID: PMC5880926 DOI: 10.3389/fpls.2018.00398] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/12/2018] [Indexed: 05/19/2023]
Abstract
Plants of the Dendrobium genus are orchids with not only ornamental value but also high medicinal value. To understand the genetic basis of variations in active ingredients of the stem total polysaccharide contents (STPCs) among different Dendrobium species, it is of paramount importance to understand the mechanism of STPC formation and identify genes affecting its process at the whole genome level. Here, we report the first high-density single-nucleotide polymorphism (SNP) integrated genetic map with a good genome coverage of Dendrobium. The specific-locus amplified fragment sequencing (SLAF-seq) technology led to identification of 7,013,400 SNPs from 1,503,626 high-quality SLAF markers from two parents (Dendrobium moniliforme ♀ × Dendrobium officinale ♂) and their interspecific F1 hybrid population. The final genetic map contained 8, 573 SLAF markers, covering 19 linkage groups (LGs). This genetic map spanned a length of 2,737.49 cM, where the average distance between markers is 0.32 cM. In total, 5 quantitative trait loci (QTL) related to STPC were identified, 3 of which have candidate genes within the confidence intervals of these stable QTLs based on the D. officinale genome sequence. This study will build a foundation up for the mapping of other medicinal-related traits and provide an important reference for the molecular breeding of these Chinese herb.
Collapse
Affiliation(s)
- Jiangjie Lu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- *Correspondence: Jiangjie Lu
| | - Yuyang Liu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Jing Xu
- Center of Rare Plant Medicine Research of Zhejiang Province, Wuyi, China
- Zhejiang ShouXianGu Pharmaceutical Co. Ltd., Wuyi, China
| | - Ziwei Mei
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yujun Shi
- School of Foreign Languages, Zhejiang Gongshang University, Hangzhou, China
| | - Pengli Liu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Jianbo He
- Soybean Research Institute, Nanjing Agricultural University, Nanjing, China
| | - Xiaotong Wang
- Center of Rare Plant Medicine Research of Zhejiang Province, Wuyi, China
- Zhejiang ShouXianGu Pharmaceutical Co. Ltd., Wuyi, China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Shangguo Feng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Chenjia Shen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Huizhong Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
- Huizhong Wang
| |
Collapse
|
32
|
Dendrobium officinale Kimura et Migo: A Review on Its Ethnopharmacology, Phytochemistry, Pharmacology, and Industrialization. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2017; 2017:7436259. [PMID: 28386292 PMCID: PMC5366227 DOI: 10.1155/2017/7436259] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 10/23/2016] [Indexed: 12/04/2022]
Abstract
Ethnopharmacological Relevance. Dendrobii Officinalis Caulis, the stems of Dendrobium officinale Kimura et Migo, as a tonic herb in Chinese materia medica and health food in folk, has been utilized for the treatment of yin-deficiency diseases for decades. Methods. Information for analysis of Dendrobium officinale Kimura et Migo was obtained from libraries and Internet scientific databases such as PubMed, Web of Science, Google Scholar, ScienceDirect, Wiley InterScience, Ingenta, Embase, CNKI, and PubChem. Results. Over the past decades, about 190 compounds have been isolated from Dendrobium officinale Kimura et Migo. Its wide modern pharmacological actions in hepatoprotective effect, anticancer effect, hypoglycemic effect, antifatigue effect, gastric ulcer protective effect, and so on were reported. This may mainly attribute to the major and bioactive components: polysaccharides. However, other small molecule components require further study. Conclusions. Due to the lack of systematic data of Dendrobium officinale, it is important to explore its ingredient-function relationships with modern pharmacology. Recently, studies on the chemical constituents of Dendrobium officinale concentrated in crude polysaccharides and its structure-activity relationships remain scant. Further research is required to determine the Dendrobium officinale toxicological action and pharmacological mechanisms of other pure ingredients and crude extracts. In addition, investigation is needed for better quality control and novel drug or product development.
Collapse
|
33
|
Li C, Qiu J, Ding L, Huang M, Huang S, Yang G, Yin J. Anthocyanin biosynthesis regulation of DhMYB2 and DhbHLH1 in Dendrobium hybrids petals. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 112:335-345. [PMID: 28131062 DOI: 10.1016/j.plaphy.2017.01.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 12/30/2016] [Accepted: 01/21/2017] [Indexed: 05/22/2023]
Abstract
Dendrobium hybrids orchid are popular throughout the world. They have various floral color and pigmentation patterns that are mainly caused by anthocyanins. It is well established that anthocyanin biosynthesis is regulated by the interplay between MYB and bHLH transcription factors (TF) in most plants. In this study, we identified one R2R3-MYB gene, DhMYB2, and one bHLH gene, DhbHLH1, from a Dendrobium hybrid. Their expression profiles were related to anthocyanin pigmentation in Dendrobium petals. Transient over-expression of these two TF genes showed that both DhMYB2 and DhbHLH1 resulted in anthocyanin production in white petals. The interaction between the two TFs was observed in vitro. In different Dendrobium hybrids petals with various pigmentations, DhMYB2 and DhbHLH1 were co-expressed with DhDFR and DhANS, which are regarded as potential regulatory targets of the two TFs. In flowers with distinct purple lips but white or yellow petals/sepals, the expression of DhbHLH1 was only related to anthocyanin accumulation in the lips. Taken together, DhMYB2 interacted with DhbHLH1 to regulate anthocyanin production in Dendrobium hybrid petals. DhbHLH1 was also responsible for the distinct anthocyanin pigmentation in lip tissues. The functional characterization of DhMYB2 and DhbHLH1 will improve understanding of anthocyanin biosynthesis modulation in Dendrobium orchids.
Collapse
Affiliation(s)
- Chonghui Li
- Tropical Crops Genetic Resources Institute, The Chinese Academy of Tropical Agricultural Sciences (CATAS)/Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Danzhou 571737, China; The Engineering Technology Research Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, Hainan Province, Danzhou 571737, China
| | - Jian Qiu
- Rubber Research Institute, CATAS/Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Danzhou 571737, China
| | - Ling Ding
- Tropical Crops Genetic Resources Institute, The Chinese Academy of Tropical Agricultural Sciences (CATAS)/Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Danzhou 571737, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Mingzhong Huang
- Tropical Crops Genetic Resources Institute, The Chinese Academy of Tropical Agricultural Sciences (CATAS)/Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Danzhou 571737, China; The Engineering Technology Research Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, Hainan Province, Danzhou 571737, China
| | - Surong Huang
- Tropical Crops Genetic Resources Institute, The Chinese Academy of Tropical Agricultural Sciences (CATAS)/Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Danzhou 571737, China; The Engineering Technology Research Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, Hainan Province, Danzhou 571737, China
| | - Guangsui Yang
- Tropical Crops Genetic Resources Institute, The Chinese Academy of Tropical Agricultural Sciences (CATAS)/Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Danzhou 571737, China; The Engineering Technology Research Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, Hainan Province, Danzhou 571737, China.
| | - Junmei Yin
- Tropical Crops Genetic Resources Institute, The Chinese Academy of Tropical Agricultural Sciences (CATAS)/Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Danzhou 571737, China; The Engineering Technology Research Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, Hainan Province, Danzhou 571737, China.
| |
Collapse
|
34
|
The medicinal and pharmaceutical importance of Dendrobium species. Appl Microbiol Biotechnol 2017; 101:2227-2239. [PMID: 28197691 DOI: 10.1007/s00253-017-8169-9] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 01/30/2017] [Accepted: 02/02/2017] [Indexed: 10/20/2022]
Abstract
Plants of the Dendrobium genus, one of the largest in the Orchidaceae, manifest a diversity of medicinal effects encompassing antiangiogenic, immunomodulating, antidiabetic, cataractogenesis-inhibiting, neuroprotective, hepatoprotective, anti-inflammatory, antiplatelet aggregation, antifungal, antibacterial, antiherpetic, antimalarial, aquaporin-5 stimulating, and hemagglutininating activities and also exert beneficial actions on colonic health and alleviate symptoms of hyperthyroidism. The active principles include a wide range of proteinaceous and non-proteinaceous molecules. This mini-review discusses the latest advances in what is known about the medicinal and pharmaceutical properties of members of the Dendrobium genus and explores how biotechnology can serve as a conduit to mass propagate valuable germplasm for sustainable exploration for the pharmaceutical industry.
Collapse
|