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Habán M, Korczyk-Szabó J, Čerteková S, Ražná K. Lavandula Species, Their Bioactive Phytochemicals, and Their Biosynthetic Regulation. Int J Mol Sci 2023; 24:ijms24108831. [PMID: 37240177 DOI: 10.3390/ijms24108831] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/12/2023] [Accepted: 05/14/2023] [Indexed: 05/28/2023] Open
Abstract
Lavandula species are one of the most useful aromatic and medicinal plants and have great economic potential. The phytopharmaceutical contribution of the secondary metabolites of the species is unquestionable. Most recent studies have been focusing on the elucidation of the genetic background of secondary metabolite production in lavender species. Therefore, knowledge of not only genetic but especially epigenetic mechanisms for the regulation of secondary metabolites is necessary for the modification of those biosynthesis processes and the understanding of genotypic differences in the content and compositional variability of these products. The review discusses the genetic diversity of Lavandula species in relation to the geographic area, occurrence, and morphogenetic factors. The role of microRNAs in secondary-metabolites biosynthesis is described.
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Affiliation(s)
- Miroslav Habán
- Institute of Agronomic Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
- Department of Pharmacognosy and Botany, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, 83232 Bratislava, Slovakia
| | - Joanna Korczyk-Szabó
- Institute of Agronomic Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
| | - Simona Čerteková
- Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
| | - Katarína Ražná
- Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
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2
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MicroRNAs in Medicinal Plants. Int J Mol Sci 2022; 23:ijms231810477. [PMID: 36142389 PMCID: PMC9500639 DOI: 10.3390/ijms231810477] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Medicinal plant microRNAs (miRNAs) are an endogenous class of small RNA central to the posttranscriptional regulation of gene expression. Biosynthetic research has shown that the mature miRNAs in medicinal plants can be produced from either the standard messenger RNA splicing mechanism or the pre-ribosomal RNA splicing process. The medicinal plant miRNA function is separated into two levels: (1) the cross-kingdom level, which is the regulation of disease-related genes in animal cells by oral intake, and (2) the intra-kingdom level, which is the participation of metabolism, development, and stress adaptation in homologous or heterologous plants. Increasing research continues to enrich the biosynthesis and function of medicinal plant miRNAs. In this review, peer-reviewed papers on medicinal plant miRNAs published on the Web of Science were discussed, covering a total of 78 species. The feasibility of the emerging role of medicinal plant miRNAs in regulating animal gene function was critically evaluated. Staged progress in intra-kingdom miRNA research has only been found in a few medicinal plants, which may be mainly inhibited by their long growth cycle, high demand for growth environment, immature genetic transformation, and difficult RNA extraction. The present review clarifies the research significance, opportunities, and challenges of medicinal plant miRNAs in drug development and agricultural production. The discussion of the latest results furthers the understanding of medicinal plant miRNAs and helps the rational design of the corresponding miRNA/target genes functional modules.
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Yang K, Han H, Li Y, Ye J, Xu F. Significance of miRNA in enhancement of flavonoid biosynthesis. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:217-226. [PMID: 34806280 DOI: 10.1111/plb.13361] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 10/15/2021] [Indexed: 05/20/2023]
Abstract
Flavonoid metabolism shows very strong plasticity in plant development and coping with the changing environment. Flavonoid biosynthesis is regulated by many metabolic pathways, including transcriptional regulation, post-transcriptional control, post-translational regulationand epigenetic regulation. miRNA is a form of endogenous noncoding single-strand small molecule RNA that primarily regulates the expression of target genes horizontally after transcription through splicing and translational suppression. It also plays an important role in regulating plant growth and development, secondary metabolism and biotic and abiotic stress. miRNA can regulate the formation of flavonoids by acting on structural genes or indirectly by using an MBW transcription complex comprising MYB-bHLH-WD40. This study summarizes the biosynthesis and mechanisms of miRNA, and provides a summary of the mechanisms of miRNAs involved in production of flavonoids, in order to elucidate the biosynthesis pathway and complex regulatory network of plant flavonoids. We aim to provide new insights into improving the content of flavonoid active ingredients in plants.
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Affiliation(s)
- K Yang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - H Han
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - Y Li
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - J Ye
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - F Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
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Hossain R, Quispe C, Saikat ASM, Jain D, Habib A, Janmeda P, Islam MT, Radha, Daştan SD, Kumar M, Butnariu M, Cho WC, Sharifi-Rad J, Kipchakbayeva A, Calina D. Biosynthesis of Secondary Metabolites Based on the Regulation of MicroRNAs. BIOMED RESEARCH INTERNATIONAL 2022; 2022:9349897. [PMID: 35281611 PMCID: PMC8916866 DOI: 10.1155/2022/9349897] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 02/07/2022] [Indexed: 12/12/2022]
Abstract
MicroRNA (miRNA), a noncoding ribonucleic acid, is considered to be important for the progression of gene expression in plants and animals by rupture or translational repression of targeted mRNAs. Many types of miRNA regulate plant metabolism, growth, and response to biotic and abiotic factors. miRNA characterization helps to expose its function in regulating the process of post-transcriptional genetic regulation. There are a lot of factors associated with miRNA function, but the function of miRNA in the organic synthesis of by-products by natural products is not yet fully elucidated. The current review is aimed at observing and characterizing miRNAs and identifying those involved in the functioning of the biosynthesis of secondary metabolites in plants, with their use in controlled manipulation.
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Affiliation(s)
- Rajib Hossain
- 1Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Cristina Quispe
- 2Facultad de Ciencias de la Salud, Universidad Arturo Prat, Avda. Arturo Prat 2120, Iquique 1110939, Chile
| | - Abu Saim Mohammad Saikat
- 3Department of Biochemistry and Molecular Biology, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Divya Jain
- 4Department of Bioscience and Biotechnology, Banasthali Vidyapith, Rajasthan, India
| | - Arslan Habib
- 5Lab of Infectious and Molecular Immunology, School of Life Sciences, Fudan University, Shanghai, China
| | - Pracheta Janmeda
- 4Department of Bioscience and Biotechnology, Banasthali Vidyapith, Rajasthan, India
| | - Muhammad Torequl Islam
- 1Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Radha
- 6School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan 173229, India
| | - Sevgi Durna Daştan
- 7Department of Biology, Faculty of Science, Sivas Cumhuriyet University, Sivas 58140, Turkey
- 8Beekeeping Development Application and Research Center, Sivas Cumhuriyet University, Sivas 58140, Turkey
| | - Manoj Kumar
- 9Chemical and Biochemical Processing Division, ICAR-Central Institute for Research on Cotton Technology, Mumbai 400019, India
| | - Monica Butnariu
- 10Banat's University of Agricultural Sciences and Veterinary Medicine “King Michael I of Romania” from Timisoara, Timisoara, Romania
| | - William C. Cho
- 11Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | | | - Aliya Kipchakbayeva
- 13Faculty of Chemistry and Chemical Technology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Daniela Calina
- 14Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, Craiova 200349, Romania
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Zhu WJ, Liu Y, Cao YN, Peng LX, Yan ZY, Zhao G. Insights into Health-Promoting Effects of Plant MicroRNAs: A Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:14372-14386. [PMID: 34813309 DOI: 10.1021/acs.jafc.1c04737] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Plant-derived microRNAs (miRNAs) play a significant role in human health and are "dark nutrients", as opposed to traditional plant nutrients, as well as important components of food diversification. Studies have revealed that multiple plant-derived miRNA pathways affect human health. First, plant miRNAs regulate plant growth and development and accumulation of metabolites, which alters the food quality and thus indirectly interferes with the health of the host. Moreover, when absorbed in vivo, some miRNAs may target the host cell mRNAs to affect protein expression. In addition, plant miRNAs target and reshape the human gut microbiota (GM), which interferes with the physiology and metabolism of the host. Therefore, miRNAs play a significant role in the cross-kingdom communication of plants, GM, and the host and in maintaining a balance of the three. Future contributions of plant miRNAs can bring new perspectives and opportunities to better understand food nutrition and health care research, which will facilitate the right exploitation of plant resources.
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Affiliation(s)
- Wen-Jing Zhu
- Key Laboratory of Coarse Cereal Processing of Ministry of Agriculture and Rural Affairs; Sichuan Province Engineering Technology Research Center of Coarse Cereal Industrialization, Chengdu University, Chengdu 610106, People's Republic of China
| | - Yu Liu
- Key Laboratory of Coarse Cereal Processing of Ministry of Agriculture and Rural Affairs; Sichuan Province Engineering Technology Research Center of Coarse Cereal Industrialization, Chengdu University, Chengdu 610106, People's Republic of China
| | - Ya-Nan Cao
- Key Laboratory of Coarse Cereal Processing of Ministry of Agriculture and Rural Affairs; Sichuan Province Engineering Technology Research Center of Coarse Cereal Industrialization, Chengdu University, Chengdu 610106, People's Republic of China
| | - Lian-Xin Peng
- Key Laboratory of Coarse Cereal Processing of Ministry of Agriculture and Rural Affairs; Sichuan Province Engineering Technology Research Center of Coarse Cereal Industrialization, Chengdu University, Chengdu 610106, People's Republic of China
| | - Zhu-Yun Yan
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China
| | - Gang Zhao
- Key Laboratory of Coarse Cereal Processing of Ministry of Agriculture and Rural Affairs; Sichuan Province Engineering Technology Research Center of Coarse Cereal Industrialization, Chengdu University, Chengdu 610106, People's Republic of China
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6
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Identification and profiling of conserved microRNAs in different developmental stages of crown imperial (Fritillaria imperialis L.) using high-throughput sequencing. Mol Biol Rep 2021; 49:1121-1132. [PMID: 34779986 DOI: 10.1007/s11033-021-06938-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/05/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Novel strategies for improvement of ornamental plants and their properties relay on miRNA control of differential plant gene expression modulation. Still, in response to the same abiotic stresses, some conserved miRNA families show different expression patterns in different plant species. In parallel, the use of deep sequencing technologies reveals new levels of complexity of regulatory networks in plants through identification of new miRNAs. METHODS AND RESULTS Fritillaria imperialis plants were collected from their natural habitats in Koohrang, Chaharmahal va Bakhtiari, Iran. Several tissues including stamen, pistil, petal, sepal, leaf, stem, bulb and fruit were collected during three developmental stages (stem elongation, flower development and seed head stages). Using RNAseq and qRT-PCR approach, this research revealed 21 conserved miRNAs, matching 15 miRNA families, in Fritilaria imperialis. CONCLUSIONS The expression of seven conserved miRNAs (Fim-miR156b, Fim-miR159, Fim-miR166a-5p, Fim-miR169d-5p, Fim-miR171c, Fim-miR393 and Fim-miR396e-3p) was further investigated in different tissues and three developmental stages, suggesting different roles for these miRNAs during growth and development of crown imperial. Gained knowledge from this research can open the door to find efficient ways to secure crown imperial survival, preservation and utilization and if proven useful may be applied in other plant species as well.
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Li C, Wang M, Qiu X, Zhou H, Lu S. Noncoding RNAs in Medicinal Plants and their Regulatory Roles in Bioactive Compound Production. Curr Pharm Biotechnol 2021; 22:341-359. [PMID: 32469697 DOI: 10.2174/1389201021666200529101942] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/14/2020] [Accepted: 03/30/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Noncoding RNAs (ncRNAs), such as microRNAs (miRNAs), small interfering RNAs (siRNAs) and long noncoding RNAs (lncRNAs), play significant regulatory roles in plant development and secondary metabolism and are involved in plant response to biotic and abiotic stresses. They have been intensively studied in model systems and crops for approximately two decades and massive amount of information have been obtained. However, for medicinal plants, ncRNAs, particularly their regulatory roles in bioactive compound biosynthesis, are just emerging as a hot research field. OBJECTIVE This review aims to summarize current knowledge on herbal ncRNAs and their regulatory roles in bioactive compound production. RESULTS So far, scientists have identified thousands of miRNA candidates from over 50 medicinal plant species and 11794 lncRNAs from Salvia miltiorrhiza, Panax ginseng, and Digitalis purpurea. Among them, more than 30 miRNAs and five lncRNAs have been predicted to regulate bioactive compound production. CONCLUSION The regulation may achieve through various regulatory modules and pathways, such as the miR397-LAC module, the miR12112-PPO module, the miR156-SPL module, the miR828-MYB module, the miR858-MYB module, and other siRNA and lncRNA regulatory pathways. Further functional analysis of herbal ncRNAs will provide useful information for quality and quantity improvement of medicinal plants.
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Affiliation(s)
- Caili Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Meizhen Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Xiaoxiao Qiu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Hong Zhou
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Shanfa Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
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8
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Sabzehzari M, Naghavi MR. Phyto-miRNAs-based regulation of metabolites biosynthesis in medicinal plants. Gene 2019; 682:13-24. [PMID: 30267812 DOI: 10.1016/j.gene.2018.09.049] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/20/2018] [Accepted: 09/25/2018] [Indexed: 12/20/2022]
Abstract
Medicinal plants, are known to produce a wide range of plant secondary metabolites (PSMs) applied as insecticides, drugs, dyes and toxins in agriculture, medicine, industry and bio-warfare plus bio-terrorism, respectively. However, production of PSMs is usually in small quantities, so we need to find novel ways to increase both quantity and quality of them. Fortunately, biotechnology suggests several options through which secondary metabolism in plants can be engineered in innovative ways to: 1) over-produce the useful metabolites, 2) down-produce the toxic metabolites, 3) produce the new metabolites. Among the ways, RNA interference (RNAi) technology which involves gene-specific regulation by small non-coding RNAs (sncRNAs) have been recently emerged as a promising tool for plant biotechnologist, not only to decipher the function of plant genes, but also for development of the plants with improved and novel traits through manipulation of both desirable and undesirable genes. Among sncRNAs, miRNAs have been recorded various regulatory roles in plants such as development, signal transduction, response to environmental stresses, metabolism. Certainly, the use of miRNAs in metabolic engineering requires identification of miRNAs involved in metabolites biosynthesis, understanding of the biosynthetic pathways, as well as the identification of key points of the pathways in which the miRNAs have their own effect. Thus, we firstly consider these three issues on metabolic engineering of medicinal plants. Our review shows, application of miRNAs can open a novel perspective to metabolic engineering of medicinal plants.
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Affiliation(s)
- M Sabzehzari
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Iran
| | - M R Naghavi
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Iran.
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9
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Sabzehzari M, Naghavi M. Phyto-miRNA: A molecule with beneficial abilities for plant biotechnology. Gene 2019; 683:28-34. [DOI: 10.1016/j.gene.2018.09.054] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 09/27/2018] [Indexed: 12/13/2022]
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10
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Kerima OZ, Niranjana P, Vinay Kumar B, Ramachandrappa R, Puttappa S, Lalitha Y, Jalali SK, Ballal CR, Thulasiram HV. De novo transcriptome analysis of the egg parasitoid Trichogramma chilonis Ishii (Hymenoptera: Trichogrammatidae): A biological control agent. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Vaccaro MC, Alfieri M, Malafronte N, De Tommasi N, Leone A. Increasing the synthesis of bioactive abietane diterpenes in Salvia sclarea hairy roots by elicited transcriptional reprogramming. PLANT CELL REPORTS 2017; 36:375-386. [PMID: 27853836 DOI: 10.1007/s00299-016-2076-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 11/08/2016] [Indexed: 05/18/2023]
Abstract
Transcriptional activation of genes belonging to the plastidial MEP-derived isoprenoid pathway by elicitation with methyl jasmonate and coronatine enhanced the content of bioactive abietane diterpenes in Salvia sclarea hairy roots. We have shown that aethiopinone, an abietane diterpene synthesized in Salvia sclarea roots is cytotoxic and induces apoptosis in human melanoma cells. To develop a production platform for this compound and other abietane diterpenes, hairy root technology was combined with the elicitation of methyl jasmonate (MeJA) or the phytotoxin coronatine (Cor). Both MeJA and Cor induced a significant accumulation of aethiopinone, but prolonged exposure to MeJA irremediably caused inhibition of hairy root growth, which was unaffected by Cor treatment. Considering together the fold increase in aethiopinone content and the final hairy root biomass, the best combination was a Cor treatment for 28 days, which allowed to obtain up to 105.34 ± 2.30 mg L-1 of this compound to be obtained, corresponding to a 24-fold increase above the basal content in untreated hairy roots. MeJA or Cor elicitation also enhanced the synthesis of other bioactive abietane-quinone diterpenes. The elicitor-dependent steering effect was due to a coordinated transcriptional activation of several biosynthetic genes belonging to the plastidial MEP-derived isoprenoid pathway. High correlations between aethiopinone content and MeJA or Cor-elicited level of gene transcripts were found for DXS2 (r 2 = 0.99), DXR (r 2 = 0.99), and GGPPS (r 2 = 0.98), encoding enzymes acting upstream of GGPP, the common precursor of diterpenes and other plastidial-derived terpenes, as well as CPPS (r 2 = 0.99), encoding the enzyme involved in the first cyclization steps leading to copalyl-diphosphate, the precursor of abietane-like diterpenes. These results point to these genes as possible targets of metabolic engineering approaches to establish a more efficient production platform for such promising anti-proliferative plant-derived compounds.
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Affiliation(s)
- M C Vaccaro
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 134D, 80084, Fisciano, Italy
| | - M Alfieri
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 134D, 80084, Fisciano, Italy
| | - N Malafronte
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 134D, 80084, Fisciano, Italy
| | - N De Tommasi
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 134D, 80084, Fisciano, Italy
| | - A Leone
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 134D, 80084, Fisciano, Italy.
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12
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Gottardini E, Cristofori A, Pellegrini E, La Porta N, Nali C, Baldi P, Sablok G. Suppression Substractive Hybridization and NGS Reveal Differential Transcriptome Expression Profiles in Wayfaring Tree (Viburnum lantana L.) Treated with Ozone. FRONTIERS IN PLANT SCIENCE 2016; 7:713. [PMID: 27313581 PMCID: PMC4887494 DOI: 10.3389/fpls.2016.00713] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 05/09/2016] [Indexed: 05/29/2023]
Abstract
Tropospheric ozone (O3) is a global air pollutant that causes high economic damages by decreasing plant productivity. It enters the leaves through the stomata, generates reactive oxygen species, which subsequent decrease in photosynthesis, plant growth, and biomass accumulation. In order to identify genes that are important for conferring O3 tolerance or sensitivity to plants, a suppression subtractive hybridization analysis was performed on the very sensitive woody shrub, Viburnum lantana, exposed to chronic O3 treatment (60 ppb, 5 h d(-1) for 45 consecutive days). Transcript profiling and relative expression assessment were carried out in asymptomatic leaves, after 15 days of O3 exposure. At the end of the experiment symptoms were observed on all treated leaves and plants, with an injured leaf area per plant accounting for 16.7% of the total surface. Cloned genes were sequenced by 454-pyrosequencing and transcript profiling and relative expression assessment were carried out on sequenced reads. A total of 38,800 and 12,495 high quality reads obtained in control and O3-treated libraries, respectively (average length of 319 ± 156.7 and 255 ± 107.4 bp). The Ensembl transcriptome yielded a total of 1241 unigenes with a total sequence length of 389,126 bp and an average length size of 389 bp (guanine-cytosine content = 49.9%). mRNA abundance was measured by reads per kilobase per million and 41 and 37 ensembl unigenes showed up- and down-regulation respectively. Unigenes functionally associated to photosynthesis and carbon utilization were repressed, demonstrating the deleterious effect of O3 exposure. Unigenes functionally associated to heat-shock proteins and glutathione were concurrently induced, suggesting the role of thylakoid-localized proteins and antioxidant-detoxification pathways as an effective strategy for responding to O3. Gene Ontology analysis documented a differential expression of co-regulated transcripts for several functional categories, including specific transcription factors (MYB and WRKY). This study demonstrates that a complex sequence of events takes place in the cells at intracellular and membrane level following O3 exposure and elucidates the effects of this oxidative stress on the transcriptional machinery of the non-model plant species V. lantana, with the final aim to provide the molecular supportive knowledge for the use of this plant as O3-bioindicator.
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Affiliation(s)
- Elena Gottardini
- Fondazione Edmund Mach, Sustainable Agro-Ecosystems and Bioresources Department, Research and Innovation CentreTrento, Italy
| | - Antonella Cristofori
- Fondazione Edmund Mach, Sustainable Agro-Ecosystems and Bioresources Department, Research and Innovation CentreTrento, Italy
| | - Elisa Pellegrini
- Department of Agriculture, Food and Environment, University of PisaPisa, Italy
| | - Nicola La Porta
- Fondazione Edmund Mach, Sustainable Agro-Ecosystems and Bioresources Department, Research and Innovation CentreTrento, Italy
- MOUNTFOR Project Centre, European Forest InstituteTrento, Italy
- Consiglio Nazionale delle Ricerche, Istituto per la Valorizzazione del Legno e delle Specie ArboreeFlorence, Italy
| | - Cristina Nali
- Department of Agriculture, Food and Environment, University of PisaPisa, Italy
| | - Paolo Baldi
- Fondazione Edmund Mach, Genomics and Biology of Fruit Crops Department, Research and Innovation CentreTrento, Italy
| | - Gaurav Sablok
- Fondazione Edmund Mach, Sustainable Agro-Ecosystems and Bioresources Department, Research and Innovation CentreTrento, Italy
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology SydneySydney, NSW, Australia
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13
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New insights of medicinal plant therapeutic activity-The miRNA transfer. Biomed Pharmacother 2015; 74:228-32. [PMID: 26349990 DOI: 10.1016/j.biopha.2015.08.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 08/04/2015] [Indexed: 01/21/2023] Open
Abstract
MicroRNA (miRNA) has become the spotlight of the biomedical research around the world and is considered to be a major post-transcriptional gene regulator. This small, endogenous RNA (21-25 nucleotides long) plays an important role by targeting specific mRNAs in plants, animals and humans. Herbal medicine has been used for thousands of years, however little is known about its molecular mechanism of action. Since the discovery of plant miRNA in human tissue and sera after ingestion, the connection between the two kingdoms is presented under a new perspective. Forward pharmacology, such as miRNA therapeutics could be the next best step toward identifying novel therapeutic options involving medicinal plants. Besides reporting the latest findings regarding the cross-kingdom transfer of miRNA and its therapeutic application, this review can inform further investigations that could lead to a modern definition of herbal medicine.
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New opportunities for the regulation of secondary metabolism in plants: focus on microRNAs. Biotechnol Lett 2015; 37:1719-27. [PMID: 26003096 DOI: 10.1007/s10529-015-1863-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 05/14/2015] [Indexed: 12/22/2022]
Abstract
Plant cell cultures are of particular interest in industrial applications as a source of biologically active substances. It is difficult, however, to achieve stable production of secondary metabolites for many plant cell cultures using classical techniques. Novel approaches should be developed for removal of the inhibitor blocks that prevent pathway activation and shift the regulatory balance to the activation of entire biosynthetic pathways. MicroRNAs (miRNAs) are small RNAs that play important regulatory roles in various biological processes. Only recently miRNAs have been demonstrated as active in secondary metabolism regulation. In this work, we summarize recent data on the emerging approaches based on regulation of secondary metabolism by miRNAs.
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Vashisht I, Mishra P, Pal T, Chanumolu S, Singh TR, Chauhan RS. Mining NGS transcriptomes for miRNAs and dissecting their role in regulating growth, development, and secondary metabolites production in different organs of a medicinal herb, Picrorhiza kurroa. PLANTA 2015; 241:1255-68. [PMID: 25663583 DOI: 10.1007/s00425-015-2255-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 01/26/2015] [Indexed: 05/21/2023]
Abstract
This study is the first endeavor on mining of miRNAs and analyzing their involvement in development and secondary metabolism of an endangered medicinal herb Picrorhiza kurroa (P. kurroa ). miRNAs are ubiquitous non-coding RNA species that target complementary sequences of mRNA and result in either translational repression or target degradation in eukaryotes. The role of miRNAs has not been investigated in P. kurroa which is a medicinal herb of industrial value due to the presence of secondary metabolites, picroside-I and picroside-II. Computational identification of miRNAs was done in 6 transcriptomes of P. kurroa generated from root, shoot, and stolon organs varying for growth, development, and culture conditions. All available plant miRNA entries were retrieved from miRBase and used as backend datasets to computationally identify conserved miRNAs in transcriptome data sets. Total 18 conserved miRNAs were detected in P. kurroa followed by target prediction and functional annotation which suggested their possible role in controlling various biological processes. Validation of miRNA and expression analysis by qRT-PCR and 5' RACE revealed that miRNA-4995 has a regulatory role in terpenoid biosynthesis ultimately affecting the production of picroside-I. miR-5532 and miR-5368 had negligible expression in field-grown samples as compared to in vitro-cultured samples suggesting their role in regulating P. kurroa growth in culture conditions. The study has thus identified novel functions for existing miRNAs which can be further validated for their potential regulatory role.
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Affiliation(s)
- Ira Vashisht
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173234, Himachal Pradesh, India
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R. V. S, Kumari P, Rupwate SD, Rajasekharan R, Srinivasan M. Exploring triacylglycerol biosynthetic pathway in developing seeds of Chia (Salvia hispanica L.): a transcriptomic approach. PLoS One 2015; 10:e0123580. [PMID: 25875809 PMCID: PMC4395390 DOI: 10.1371/journal.pone.0123580] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 03/04/2015] [Indexed: 11/18/2022] Open
Abstract
Chia (Salvia hispanica L.), a member of the mint family (Lamiaceae), is a rediscovered crop with great importance in health and nutrition and is also the highest known terrestrial plant source of heart-healthy omega-3 fatty acid, alpha linolenic acid (ALA). At present, there is no public genomic information or database available for this crop, hindering research on its genetic improvement through genomics-assisted breeding programs. The first comprehensive analysis of the global transcriptome profile of developing Salvia hispanica L. seeds, with special reference to lipid biosynthesis is presented in this study. RNA from five different stages of seed development was extracted and sequenced separately using the Illumina GAIIx platform. De novo assembly of processed reads in the pooled transcriptome using Trinity yielded 76,014 transcripts. The total transcript length was 66,944,462 bases (66.9 Mb), with an average length of approximately 880 bases. In the molecular functions category of Gene Ontology (GO) terms, ATP binding and nucleotide binding were found to be the most abundant and in the biological processes category, the metabolic process and the regulation of transcription-DNA-dependent and oxidation-reduction process were abundant. From the EuKaryotic Orthologous Groups of proteins (KOG) classification, the major category was “Metabolism” (31.97%), of which the most prominent class was ‘carbohydrate metabolism and transport’ (5.81% of total KOG classifications) followed by ‘secondary metabolite biosynthesis transport and catabolism’ (5.34%) and ‘lipid metabolism’ (4.57%). A majority of the candidate genes involved in lipid biosynthesis and oil accumulation were identified. Furthermore, 5596 simple sequence repeats (SSRs) were identified. The transcriptome data was further validated through confirmative PCR and qRT-PCR for select lipid genes. Our study provides insight into the complex transcriptome and will contribute to further genome-wide research and understanding of chia. The identified novel UniGenes will facilitate gene discovery and creation of genomic resource for this crop.
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Affiliation(s)
- Sreedhar R. V.
- CSIR-Lipidomic Centre (CSIR-LIPIC), CSIR-Central Food Technological Research Institute (CSIR-CFTRI) Resource Centre, Allalasandra, GKVK Post, Bangalore—560 065, Karnataka, India
| | - Priya Kumari
- CSIR-Lipidomic Centre (CSIR-LIPIC), CSIR-Central Food Technological Research Institute (CSIR-CFTRI) Resource Centre, Allalasandra, GKVK Post, Bangalore—560 065, Karnataka, India
- Academy of Scientific and Innovative Research, CSIR, New Delhi—110 025, India
| | - Sunny D. Rupwate
- CSIR-Lipidomic Centre (CSIR-LIPIC), CSIR-Central Food Technological Research Institute (CSIR-CFTRI), Mysore—570 020, Karnataka, India
| | - Ram Rajasekharan
- CSIR-Lipidomic Centre (CSIR-LIPIC), CSIR-Central Food Technological Research Institute (CSIR-CFTRI), Mysore—570 020, Karnataka, India
| | - Malathi Srinivasan
- CSIR-Lipidomic Centre (CSIR-LIPIC), CSIR-Central Food Technological Research Institute (CSIR-CFTRI) Resource Centre, Allalasandra, GKVK Post, Bangalore—560 065, Karnataka, India
- Academy of Scientific and Innovative Research, CSIR, New Delhi—110 025, India
- * E-mail:
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Hao DC, Chen SL, Osbourn A, Kontogianni VG, Liu LW, Jordán MJ. Temporal transcriptome changes induced by methyl jasmonate in Salvia sclarea. Gene 2014; 558:41-53. [PMID: 25536164 DOI: 10.1016/j.gene.2014.12.043] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 12/18/2014] [Accepted: 12/19/2014] [Indexed: 10/24/2022]
Abstract
Salvia sclarea is a traditional medicinal and aromatic plant that grows in Europe and produces various economically important compounds, including phenylpropanoid derivatives and terpenoids. Methyl jasmonate (MeJA) is commonly used to elicit plant stress responses. However, how MeJA enhances production of secondary metabolites in S. sclarea is not well understood. We performed a genome-wide analysis of temporal gene expression in S. sclarea leaves and roots. The transcriptome profiles 0, 10 and 26 h after MeJA treatment were analyzed by Illumina RNA-Seq. A total of 16,142 isogenes (average length 866bp; N50 1035bp) were obtained by de novo assembly of 35,757,567 raw sequencing reads. When these sequencing reads were mapped onto the assembled Unigenes, 3236, 2792 and 798 Unigenes were found to be expressed differentially between 0 and 10h, 0 and 26 h, and 10 and 26h, respectively. These included many secondary metabolite biosynthesis, stress and defense-related genes. A qRT-PCR analysis confirmed the expression profiles of selected differentially expressed genes (DEGs) revealed by RNA-Seq data, and also extended our analysis of differential gene expression to 73 h. Our investigations revealed temporal differences in the responses of S. sclarea to MeJA treatment. MeJA treatment induced the expression of a large number of genes involved in phenylpropanoid biosynthesis, especially between 0 and 10h, and 0 and 26 h. Additionally, many genes encoding transcription factors, cytochrome P450s, glycosyltransferases, methyltransferases and transporters were shown to respond to MeJA elicitation. DEGs related to structural molecule activity and cell death showed a significant temporal variation. A chromatographic analysis of metabolites at 26h, 73h and six days after MeJA treatment indicated that these transcriptomic changes precede MeJA-induced changes in secondary metabolite content. This study sheds light on the molecular mechanisms of MeJA elicitation and is helpful in understanding how exogenous MeJA treatment mediates extensive plant transcriptome reprogramming/remodeling. Our results can be utilized to characterize genes related to secondary metabolism and their regulation, and in breeding S. sclarea for desirable chemotypes.
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Affiliation(s)
- Da Cheng Hao
- Biotechnology Institute, School of Environment, Dalian Jiaotong University, Dalian 116028, China.
| | - Shi Lin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Anne Osbourn
- Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, UK.
| | | | - Li Wei Liu
- Department of Mathematics, School of Science, Dalian Jiaotong University, Dalian 116028, China
| | - Maria J Jordán
- Instituto Murciano de Investigación y Desarrollo Agrario y Alimentario (IMIDA), Departamento de Recursos Naturales y Desarrollo Rural, C./Mayor s/n, 30150 La Alberca, Murcia, Spain
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18
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Singh N, Sharma A. In-silico identification of miRNAs and their regulating target functions in Ocimum basilicum. Gene 2014; 552:277-82. [DOI: 10.1016/j.gene.2014.09.040] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 08/29/2014] [Accepted: 09/18/2014] [Indexed: 12/15/2022]
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Firmino AAP, Fonseca FCDA, de Macedo LLP, Coelho RR, Antonino de Souza Jr JD, Togawa RC, Silva-Junior OB, Pappas-Jr GJ, da Silva MCM, Engler G, Grossi-de-Sa MF. Transcriptome analysis in cotton boll weevil (Anthonomus grandis) and RNA interference in insect pests. PLoS One 2013; 8:e85079. [PMID: 24386449 PMCID: PMC3874031 DOI: 10.1371/journal.pone.0085079] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 11/22/2013] [Indexed: 12/16/2022] Open
Abstract
Cotton plants are subjected to the attack of several insect pests. In Brazil, the cotton boll weevil, Anthonomus grandis, is the most important cotton pest. The use of insecticidal proteins and gene silencing by interference RNA (RNAi) as techniques for insect control are promising strategies, which has been applied in the last few years. For this insect, there are not much available molecular information on databases. Using 454-pyrosequencing methodology, the transcriptome of all developmental stages of the insect pest, A. grandis, was analyzed. The A. grandis transcriptome analysis resulted in more than 500.000 reads and a data set of high quality 20,841 contigs. After sequence assembly and annotation, around 10,600 contigs had at least one BLAST hit against NCBI non-redundant protein database and 65.7% was similar to Tribolium castaneum sequences. A comparison of A. grandis, Drosophila melanogaster and Bombyx mori protein families’ data showed higher similarity to dipteran than to lepidopteran sequences. Several contigs of genes encoding proteins involved in RNAi mechanism were found. PAZ Domains sequences extracted from the transcriptome showed high similarity and conservation for the most important functional and structural motifs when compared to PAZ Domains from 5 species. Two SID-like contigs were phylogenetically analyzed and grouped with T. castaneum SID-like proteins. No RdRP gene was found. A contig matching chitin synthase 1 was mined from the transcriptome. dsRNA microinjection of a chitin synthase gene to A. grandis female adults resulted in normal oviposition of unviable eggs and malformed alive larvae that were unable to develop in artificial diet. This is the first study that characterizes the transcriptome of the coleopteran, A. grandis. A new and representative transcriptome database for this insect pest is now available. All data support the state of the art of RNAi mechanism in insects.
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Affiliation(s)
- Alexandre Augusto Pereira Firmino
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
- Graduate Program in Cellular and Molecular Biology, Center of Biotechnology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- * E-mail: (AAPF); (MFGS)
| | - Fernando Campos de Assis Fonseca
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
- Graduate Program in Biology Molecular, Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - Leonardo Lima Pepino de Macedo
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Roberta Ramos Coelho
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
- Graduate Program in Biology Molecular, Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - José Dijair Antonino de Souza Jr
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
- Graduate Program in Biology Molecular, Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | | | | | | | | | - Gilbert Engler
- Plateau Microscopique, Institut National de la Recherche Agronomique, Sophia-Antipolis, France
| | - Maria Fatima Grossi-de-Sa
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
- * E-mail: (AAPF); (MFGS)
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Rock CD. Trans-acting small interfering RNA4: key to nutraceutical synthesis in grape development? TRENDS IN PLANT SCIENCE 2013; 18:601-10. [PMID: 23993483 PMCID: PMC3818397 DOI: 10.1016/j.tplants.2013.07.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 07/12/2013] [Accepted: 07/31/2013] [Indexed: 05/19/2023]
Abstract
The facility and versatility of microRNAs (miRNAs) to evolve and change likely underlies how they have become dominant constituents of eukaryotic genomes. In this opinion article I propose that trans-acting small interfering RNA gene 4 (TAS4) evolution may be important for biosynthesis of polyphenolics, arbuscular symbiosis, and bacterial pathogen etiologies. Expression-based and phylogenetic evidence shows that TAS4 targets two novel grape (Vitis vinifera L.) MYB transcription factors (VvMYBA6, VvMYBA7) that spawn phased small interfering RNAs (siRNAs) which probably function in nutraceutical bioflavonoid biosynthesis and fruit development. Characterization of the molecular mechanisms of TAS4 control of plant development and integration into biotic and abiotic stress- and nutrient-signaling regulatory networks has applicability to molecular breeding and the development of strategies for engineering healthier foods.
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Affiliation(s)
- Christopher D Rock
- Department of Biological Sciences, Texas Tech University (TTU), Lubbock, TX 79409-3131, USA.
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Legrand S, Marque G, Blassiau C, Bluteau A, Canoy AS, Fontaine V, Jaminon O, Bahrman N, Mautord J, Morin J, Petit A, Baranger A, Rivière N, Wilmer J, Delbreil B, Lejeune-Hénaut I. Combining gene expression and genetic analyses to identify candidate genes involved in cold responses in pea. JOURNAL OF PLANT PHYSIOLOGY 2013; 170:1148-57. [PMID: 23632303 DOI: 10.1016/j.jplph.2013.03.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 03/19/2013] [Accepted: 03/20/2013] [Indexed: 06/02/2023]
Abstract
Cold stress affects plant growth and development. In order to better understand the responses to cold (chilling or freezing tolerance), we used two contrasted pea lines. Following a chilling period, the Champagne line becomes tolerant to frost whereas the Terese line remains sensitive. Four suppression subtractive hybridisation libraries were obtained using mRNAs isolated from pea genotypes Champagne and Terese. Using quantitative polymerase chain reaction (qPCR) performed on 159 genes, 43 and 54 genes were identified as differentially expressed at the initial time point and during the time course study, respectively. Molecular markers were developed from the differentially expressed genes and were genotyped on a population of 164 RILs derived from a cross between Champagne and Terese. We identified 5 candidate genes colocalizing with 3 different frost damage quantitative trait loci (QTL) intervals and a protein quantity locus (PQL) rich region previously reported. This investigation revealed the role of constitutive differences between both genotypes in the cold responses, in particular with genes related to glycine degradation pathway that could confer to Champagne a better frost tolerance. We showed that freezing tolerance involves a decrease of expression of genes related to photosynthesis and the expression of a gene involved in the production of cysteine and methionine that could act as cryoprotectant molecules. Although it remains to be confirmed, this study could also reveal the involvement of the jasmonate pathway in the cold responses, since we observed that two genes related to this pathway were mapped in a frost damage QTL interval and in a PQL rich region interval, respectively.
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Affiliation(s)
- Sylvain Legrand
- Université Lille 1, UMR SADV 1281, Stress Abiotiques et Différenciation des Végétaux cultivés, Université Lille Nord de France, Lille 1, SN2, F-59650 Villeneuve d'Ascq, France.
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Karaca M, Ince AG, Aydin A, Ay ST. Cross-genera transferable e-microsatellite markers for 12 genera of the Lamiaceae family. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2013; 93:1869-1879. [PMID: 23238626 DOI: 10.1002/jsfa.5982] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Revised: 10/10/2012] [Accepted: 11/09/2012] [Indexed: 06/01/2023]
Abstract
BACKGROUND The Lamiaceae family contains many high-valued medicinal, aromatic and ornamental plant species. Several members of the genera in this family are under heavy pressure of collection for commercial use. DNA markers such as microsatellites could be used to identify commercially important genotypes and to select high-yielding ones for development of new varieties. RESULTS A total of 12,432 expressed sequence tags (ESTs) from Salvia fruticosa, S. miltiorrhiza, S. sclarea and Stenogyne rugosa were analyzed. A total of 6216 ESTs were found to be unique according the redundancy test used. Results of this study indicated that the use of redundant ESTs in comparison to non-redundant ESTs was advantageous in terms of higher cross-genera transferability of the markers. A total of 75 EST-microsatellite primer pairs were tested using two different polymerase chain reaction amplification profiles and 52 were found to be cross-genera transferable. Cross-genera transferability of the e-microsatellite primer pairs varied from one species to 12 species tested. It was noted that cross-genera transferability of e-microsatellite primer pairs decreased as the evolutionary distance between the sources and target species increased. CONCLUSION This study indicated that EST resources from Salvia spp. and Stenogyne rugosa could be successfully used to identify cross-genera transferable e-microsatellite markers for uncharacterized genomes of the genera in the Lamiaceae family. These e-microsatellite markers could allow one to perform comparative analyses of population structure and genomic studies, and facilitate comparative linkage mapping in the genera studied. E-microsatellite primer pairs reported in this manuscript are equivalent to a total of 135 e-microsatellite primer pairs since many e-microsatellite primer pairs show cross-genera transferability.
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Affiliation(s)
- Mehmet Karaca
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, 07059, Turkey.
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Ong SS, Wickneswari R. Characterization of microRNAs expressed during secondary wall biosynthesis in Acacia mangium. PLoS One 2012; 7:e49662. [PMID: 23251324 PMCID: PMC3507875 DOI: 10.1371/journal.pone.0049662] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2012] [Accepted: 10/16/2012] [Indexed: 11/23/2022] Open
Abstract
MicroRNAs (miRNAs) play critical regulatory roles by acting as sequence specific guide during secondary wall formation in woody and non-woody species. Although thousands of plant miRNAs have been sequenced, there is no comprehensive view of miRNA mediated gene regulatory network to provide profound biological insights into the regulation of xylem development. Herein, we report the involvement of six highly conserved amg-miRNA families (amg-miR166, amg-miR172, amg-miR168, amg-miR159, amg-miR394, and amg-miR156) as the potential regulatory sequences of secondary cell wall biosynthesis. Within this highly conserved amg-miRNA family, only amg-miR166 exhibited strong differences in expression between phloem and xylem tissue. The functional characterization of amg-miR166 targets in various tissues revealed three groups of HD-ZIP III: ATHB8, ATHB15, and REVOLUTA which play pivotal roles in xylem development. Although these three groups vary in their functions, -psRNA target analysis indicated that miRNA target sequences of the nine different members of HD-ZIP III are always conserved. We found that precursor structures of amg-miR166 undergo exhaustive sequence variation even within members of the same family. Gene expression analysis showed three key lignin pathway genes: C4H, CAD, and CCoAOMT were upregulated in compression wood where a cascade of miRNAs was downregulated. This study offers a comprehensive analysis on the involvement of highly conserved miRNAs implicated in the secondary wall formation of woody plants.
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Affiliation(s)
- Seong Siang Ong
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
- * E-mail: (SSO); (RW)
| | - Ratnam Wickneswari
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
- * E-mail: (SSO); (RW)
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Caissard JC, Olivier T, Delbecque C, Palle S, Garry PP, Audran A, Valot N, Moja S, Nicolé F, Magnard JL, Legrand S, Baudino S, Jullien F. Extracellular localization of the diterpene sclareol in clary sage (Salvia sclarea L., Lamiaceae). PLoS One 2012; 7:e48253. [PMID: 23133579 PMCID: PMC3484996 DOI: 10.1371/journal.pone.0048253] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 09/21/2012] [Indexed: 11/19/2022] Open
Abstract
Sclareol is a high-value natural product obtained by solid/liquid extraction of clary sage (Salvia sclarea L.) inflorescences. Because processes of excretion and accumulation of this labdane diterpene are unknown, the aim of this work was to gain knowledge on its sites of accumulation in planta. Samples were collected in natura or during different steps of the industrial process of extraction (steam distillation and solid/liquid extraction). Samples were then analysed with a combination of complementary analytical techniques (gas chromatography coupled to a mass spectrometer, polarized light microscopy, environmental scanning electron microscopy, two-photon fluorescence microscopy, second harmonic generation microscopy). According to the literature, it is hypothesized that sclareol is localized in oil pockets of secretory trichomes. This study demonstrates that this is not the case and that sclareol accumulates in a crystalline epicuticular form, mostly on calyces.
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Affiliation(s)
- Jean-Claude Caissard
- Laboratoire de Biotechnologies Végétales Appliquées aux Plantes Aromatiques et Médicinales, Université Jean Monnet, Université de Lyon, Saint-Etienne, France.
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Hao DC, Chen SL, Xiao PG, Liu M. Application of High-Throughput Sequencing in Medicinal Plant Transcriptome Studies. Drug Dev Res 2012. [DOI: 10.1002/ddr.21041] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Da-Cheng Hao
- Biotechnology Institute/School of Environment; Dalian Jiaotong University; Dalian; 116028; China
| | - Shi-Lin Chen
- Institute of Medicinal Plant Development; Chinese Academy of Medical sciences/Peking Union Medical College; Beijing; 100193; China
| | - Pei-Gen Xiao
- Institute of Medicinal Plant Development; Chinese Academy of Medical sciences/Peking Union Medical College; Beijing; 100193; China
| | - Ming Liu
- Biotechnology Institute/School of Environment; Dalian Jiaotong University; Dalian; 116028; China
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Shikata M, Yamaguchi H, Sasaki K, Ohtsubo N. Overexpression of Arabidopsis miR157b induces bushy architecture and delayed phase transition in Torenia fournieri. PLANTA 2012; 236:1027-1035. [PMID: 22552637 DOI: 10.1007/s00425-012-1649-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 04/04/2012] [Indexed: 05/31/2023]
Abstract
miR156/157 is a small RNA molecule that is highly conserved among various plant species. Overexpression of miR156/157 has been reported to induce bushy architecture and delayed phase transition in several plant species. To investigate the effect of miR157 overexpression in a horticultural plant, and to explore the applicability of miRNA to molecular breeding, we introduced Arabidopsis MIR157b (AtMIR157b) into torenia (Torenia fournieri). The resulting 35S:AtMIR157b plants showed a high degree of branching along with small leaves, which resembled miR156/157-overexpressing plants of other species. We also isolated torenia SBP-box genes with target miR156/157 sequences and confirmed that their expression was selectively downregulated in 35S:AtMIR157b plants. The reduced accumulation of mRNA was probably due to sequence specificity. Moreover, expression of torenia homologs of the SBP-box protein-regulated genes TfLFY and TfMIR172 was also reduced by AtmiR157 overexpression. These findings suggest that the molecular mechanisms of miR156/157 regulation are conserved between Arabidopsis and torenia. The bushy architecture and small leaves of 35S:AtMIR157b torenia plants could be applied in molecular breeding of various horticultural plants as well as for increasing biomass and crop production.
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Affiliation(s)
- Masahito Shikata
- National Institute of Floricultural Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8519, Japan.
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27
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Caniard A, Zerbe P, Legrand S, Cohade A, Valot N, Magnard JL, Bohlmann J, Legendre L. Discovery and functional characterization of two diterpene synthases for sclareol biosynthesis in Salvia sclarea (L.) and their relevance for perfume manufacture. BMC PLANT BIOLOGY 2012; 12:119. [PMID: 22834731 PMCID: PMC3520730 DOI: 10.1186/1471-2229-12-119] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 06/26/2012] [Indexed: 05/06/2023]
Abstract
BACKGROUND Sclareol is a diterpene natural product of high value for the fragrance industry. Its labdane carbon skeleton and its two hydroxyl groups also make it a valued starting material for semisynthesis of numerous commercial substances, including production of Ambrox® and related ambergris substitutes used in the formulation of high end perfumes. Most of the commercially-produced sclareol is derived from cultivated clary sage (Salvia sclarea) and extraction of the plant material. In clary sage, sclareol mainly accumulates in essential oil-producing trichomes that densely cover flower calices. Manool also is a minor diterpene of this species and the main diterpene of related Salvia species. RESULTS Based on previous general knowledge of diterpene biosynthesis in angiosperms, and based on mining of our recently published transcriptome database obtained by deep 454-sequencing of cDNA from clary sage calices, we cloned and functionally characterized two new diterpene synthase (diTPS) enzymes for the complete biosynthesis of sclareol in clary sage. A class II diTPS (SsLPPS) produced labda-13-en-8-ol diphosphate as major product from geranylgeranyl diphosphate (GGPP) with some minor quantities of its non-hydroxylated analogue, (9 S, 10 S)-copalyl diphosphate. A class I diTPS (SsSS) then transformed these intermediates into sclareol and manool, respectively. The production of sclareol was reconstructed in vitro by combining the two recombinant diTPS enzymes with the GGPP starting substrate and in vivo by co-expression of the two proteins in yeast (Saccharomyces cerevisiae). Tobacco-based transient expression assays of green fluorescent protein-fusion constructs revealed that both enzymes possess an N-terminal signal sequence that actively targets SsLPPS and SsSS to the chloroplast, a major site of GGPP and diterpene production in plants. CONCLUSIONS SsLPPS and SsSS are two monofunctional diTPSs which, together, produce the diterpenoid specialized metabolite sclareol in a two-step process. They represent two of the first characterized hydroxylating diTPSs in angiosperms and generate the dihydroxylated labdane sclareol without requirement for additional enzymatic oxidation by activities such as cytochrome P450 monoxygenases. Yeast-based production of sclareol by co-expresssion of SsLPPS and SsSS was efficient enough to warrant the development and use of such technology for the biotechnological production of scareol and other oxygenated diterpenes.
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Affiliation(s)
- Anne Caniard
- Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- Université de Lyon, Saint-Etienne, F-42023, France
- Université de Saint-Etienne, Jean Monnet, Saint-Etienne, F-42000, France
- Laboratoire BVpam, EA3061, 23 rue du Dr Paul Michelon, Saint-Etienne, F-42000, France
| | - Philipp Zerbe
- Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Sylvain Legrand
- Université Lille Nord de France, Lille, F-59000, France
- Université Lille1, Villeneuve d’Ascq, F-59655, France
- Stress Abiotiques et Différenciation des Végétaux Cultivés (SADV), UMR INRA 1281, Bâtiment SN2, Villeneuve d'Ascq, F-59655, France
| | - Allison Cohade
- Université de Lyon, Saint-Etienne, F-42023, France
- Université de Saint-Etienne, Jean Monnet, Saint-Etienne, F-42000, France
- Laboratoire BVpam, EA3061, 23 rue du Dr Paul Michelon, Saint-Etienne, F-42000, France
| | - Nadine Valot
- Université de Lyon, Saint-Etienne, F-42023, France
- Université de Saint-Etienne, Jean Monnet, Saint-Etienne, F-42000, France
- Laboratoire BVpam, EA3061, 23 rue du Dr Paul Michelon, Saint-Etienne, F-42000, France
| | - Jean-Louis Magnard
- Université de Lyon, Saint-Etienne, F-42023, France
- Université de Saint-Etienne, Jean Monnet, Saint-Etienne, F-42000, France
- Laboratoire BVpam, EA3061, 23 rue du Dr Paul Michelon, Saint-Etienne, F-42000, France
| | - Jörg Bohlmann
- Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Laurent Legendre
- Université de Lyon, Lyon, F-69622, France
- Université Lyon 1, Villeurbanne, France
- CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France
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Sharma V, Sarkar IN. Bioinformatics opportunities for identification and study of medicinal plants. Brief Bioinform 2012; 14:238-50. [PMID: 22589384 DOI: 10.1093/bib/bbs021] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Plants have been used as a source of medicine since historic times and several commercially important drugs are of plant-based origin. The traditional approach towards discovery of plant-based drugs often times involves significant amount of time and expenditure. These labor-intensive approaches have struggled to keep pace with the rapid development of high-throughput technologies. In the era of high volume, high-throughput data generation across the biosciences, bioinformatics plays a crucial role. This has generally been the case in the context of drug designing and discovery. However, there has been limited attention to date to the potential application of bioinformatics approaches that can leverage plant-based knowledge. Here, we review bioinformatics studies that have contributed to medicinal plants research. In particular, we highlight areas in medicinal plant research where the application of bioinformatics methodologies may result in quicker and potentially cost-effective leads toward finding plant-based remedies.
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Affiliation(s)
- Vivekanand Sharma
- Department of Microbiology and Molecular Genetics, University of Vermont, 89 Beaumont Avenue, Given Courtyard N309, Burlington, VT 05405, USA
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Laville R, Castel C, Filippi JJ, Delbecque C, Audran A, Garry PP, Legendre L, Fernandez X. Amphilectane diterpenes from Salvia sclarea: biosynthetic considerations. JOURNAL OF NATURAL PRODUCTS 2012; 75:121-6. [PMID: 22264035 DOI: 10.1021/np2004177] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Salviatrienes A and B, two new diterpenes belonging to the amphilectane/elisabethane family, have been isolated from an extract of clary sage (Salvia sclarea). These molecules are the first representatives of this family to be described from the plant kingdom. This study has led to consideration of the possible enzymatic machinery and biosynthesis pathways within S. sclarea.
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Affiliation(s)
- Rémi Laville
- LCMBA, UMR 6001 CNRS, Institut de Chimie de Nice, Faculté des Sciences, Université de Nice-Sophia Antipolis, Parc Valrose, 06108 Nice Cedex 2, France
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Manickavelu A, Kawaura K, Oishi K, Shin-I T, Kohara Y, Yahiaoui N, Keller B, Abe R, Suzuki A, Nagayama T, Yano K, Ogihara Y. Comprehensive functional analyses of expressed sequence tags in common wheat (Triticum aestivum). DNA Res 2012; 19:165-77. [PMID: 22334568 PMCID: PMC3325080 DOI: 10.1093/dnares/dss001] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
About 1 million expressed sequence tag (EST) sequences comprising 125.3 Mb nucleotides were accreted from 51 cDNA libraries constructed from a variety of tissues and organs under a range of conditions, including abiotic stresses and pathogen challenges in common wheat (Triticum aestivum). Expressed sequence tags were assembled with stringent parameters after processing with inbuild scripts, resulting in 37,138 contigs and 215,199 singlets. In the assembled sequences, 10.6% presented no matches with existing sequences in public databases. Functional characterization of wheat unigenes by gene ontology annotation, mining transcription factors, full-length cDNA, and miRNA targeting sites were carried out. A bioinformatics strategy was developed to discover single-nucleotide polymorphisms (SNPs) within our large EST resource and reported the SNPs between and within (homoeologous) cultivars. Digital gene expression was performed to find the tissue-specific gene expression, and correspondence analysis was executed to identify common and specific gene expression by selecting four biotic stress-related libraries. The assembly and associated information cater a framework for future investigation in functional genomics.
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Affiliation(s)
- Alagu Manickavelu
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
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Studholme DJ. Deep sequencing of small RNAs in plants: applied bioinformatics. Brief Funct Genomics 2011; 11:71-85. [PMID: 22184332 DOI: 10.1093/bfgp/elr039] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Small RNAs, including microRNA and short-interfering RNAs, play important roles in plants. In recent years, developments in sequencing technology have enabled the large-scale discovery of sRNAs in various cells, tissues and developmental stages and in response to various stresses. This review describes the bioinformatics challenges to analysing these large datasets of short-RNA sequences and some of the solutions to those challenges.
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Yu HP, Hsiao YL, Pan HY, Huang CH, Hou SY. Micro-RNA quantification using DNA polymerase and pyrophosphate quantification. Anal Biochem 2011; 419:228-33. [DOI: 10.1016/j.ab.2011.08.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Revised: 08/17/2011] [Accepted: 08/19/2011] [Indexed: 12/31/2022]
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Wong MML, Cannon CH, Wickneswari R. Identification of lignin genes and regulatory sequences involved in secondary cell wall formation in Acacia auriculiformis and Acacia mangium via de novo transcriptome sequencing. BMC Genomics 2011; 12:342. [PMID: 21729267 PMCID: PMC3161972 DOI: 10.1186/1471-2164-12-342] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2011] [Accepted: 07/05/2011] [Indexed: 01/11/2023] Open
Abstract
Background Acacia auriculiformis × Acacia mangium hybrids are commercially important trees for the timber and pulp industry in Southeast Asia. Increasing pulp yield while reducing pulping costs are major objectives of tree breeding programs. The general monolignol biosynthesis and secondary cell wall formation pathways are well-characterized but genes in these pathways are poorly characterized in Acacia hybrids. RNA-seq on short-read platforms is a rapid approach for obtaining comprehensive transcriptomic data and to discover informative sequence variants. Results We sequenced transcriptomes of A. auriculiformis and A. mangium from non-normalized cDNA libraries synthesized from pooled young stem and inner bark tissues using paired-end libraries and a single lane of an Illumina GAII machine. De novo assembly produced a total of 42,217 and 35,759 contigs with an average length of 496 bp and 498 bp for A. auriculiformis and A. mangium respectively. The assemblies of A. auriculiformis and A. mangium had a total length of 21,022,649 bp and 17,838,260 bp, respectively, with the largest contig 15,262 bp long. We detected all ten monolignol biosynthetic genes using Blastx and further analysis revealed 18 lignin isoforms for each species. We also identified five contigs homologous to R2R3-MYB proteins in other plant species that are involved in transcriptional regulation of secondary cell wall formation and lignin deposition. We searched the contigs against public microRNA database and predicted the stem-loop structures of six highly conserved microRNA families (miR319, miR396, miR160, miR172, miR162 and miR168) and one legume-specific family (miR2086). Three microRNA target genes were predicted to be involved in wood formation and flavonoid biosynthesis. By using the assemblies as a reference, we discovered 16,648 and 9,335 high quality putative Single Nucleotide Polymorphisms (SNPs) in the transcriptomes of A. auriculiformis and A. mangium, respectively, thus yielding useful markers for population genetics studies and marker-assisted selection. Conclusion We have produced the first comprehensive transcriptome-wide analysis in A. auriculiformis and A. mangium using de novo assembly techniques. Our high quality and comprehensive assemblies allowed the identification of many genes in the lignin biosynthesis and secondary cell wall formation in Acacia hybrids. Our results demonstrated that Next Generation Sequencing is a cost-effective method for gene discovery, identification of regulatory sequences, and informative markers in a non-model plant.
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Affiliation(s)
- Melissa M L Wong
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi 43600, Selangor, Malaysia
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Zhang C, Xing D. Single-Molecule DNA Amplification and Analysis Using Microfluidics. Chem Rev 2010; 110:4910-47. [DOI: 10.1021/cr900081z] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Chunsun Zhang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Da Xing
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
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