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Liu Y, Zhang Q, Chen D, Shi W, Gao X, Liu Y, Hu B, Wang A, Li X, An X, Yang Y, Li X, Liu Z, Wang J. Positive regulation of ABA signaling by MdCPK4 interacting with and phosphorylating MdPYL2/12 in Arabidopsis. JOURNAL OF PLANT PHYSIOLOGY 2024; 293:154165. [PMID: 38237440 DOI: 10.1016/j.jplph.2023.154165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 12/01/2023] [Accepted: 12/18/2023] [Indexed: 02/23/2024]
Abstract
The phytohormone abscisic acid (ABA) regulates plant growth and development and stress resistance through the ABA receptor PYLs. To date, no interaction between CPK and PYL has been reported, even in Arabidopsis and rice. In this study, we found that MdCPK4 from Malus domestica (Md for short) interacts with two MdPYLs, MdPYL2/12, in the nucleus and the cytoplasm in vivo and phosphorylates the latter in vitro as well. Compared with the wild type (WT), the MdCPK4- or MdPYL2/12-overexpressing Arabidopsis lines showed more sensitivity to ABA, and therefore stronger drought resistance. The ABA-related genes (ABF1, ABF2, ABF4, RD29A and SnRK2.2) were significantly upregulated in the overexpressing (OE) lines after ABA treatment. These results indicate that MdCPK4 and MdPYL2/12 act as positive regulators in response to ABA-mediated drought resistance in apple. Our results reveal the relationship between MdCPK4 and MdPYL2/12 in ABA signaling, which will further enrich the molecular mechanism of drought resistance in plants.
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Affiliation(s)
- Yingying Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Qian Zhang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Dixu Chen
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Wensen Shi
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Xuemeng Gao
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Yu Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Bo Hu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Anhu Wang
- Xichang University, Xichang, 615013, Sichuan, China
| | - Xiaoyi Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Xinyuan An
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Yi Yang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Xufeng Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Zhibin Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Jianmei Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China.
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Liao X, Zhao Y, Li H, Hou W, Tang X, Zhou R. A simple and rapid method for isolating high-quality RNA from kenaf with high polysaccharide and polyphenol contents. Biotechniques 2023; 75:218-226. [PMID: 37880956 DOI: 10.2144/btn-2023-0077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023] Open
Abstract
The extraction of high-quality RNA from kenaf is essential for genetic and molecular biology research. However, the presence of high levels of polysaccharide and polyphenol compounds in kenaf poses challenges for RNA isolation. We proposed a simplified, time-saving and cost-effective method for isolating high quantities of RNA from various kenaf tissues. This method exhibited superior efficiency in RNA isolation compared with the conventional cetyltrimethylammonium bromide method and demonstrated greater adaptability to different samples than commercial kits. Furthermore, the high-quality RNA obtained from this method was successfully utilized for RT-PCR, real-time RT-PCR and northern blot analysis. Moreover, this proposed protocol also enables the acquisition of both high-quality and -quantity gDNA through RNase A treatment. In addition, the effectiveness of this approach in isolating high-quality RNA from other plant species has been experimentally confirmed.
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Affiliation(s)
- Xiaofang Liao
- Cash Crop Research Institute of Guangxi Academy of Agricultural Science, Nanning, 530007, China
- Key Laboratory of Plant Genetic & Breeding, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Yanhong Zhao
- Cash Crop Research Institute of Guangxi Academy of Agricultural Science, Nanning, 530007, China
| | - Hongwei Li
- Key Laboratory of Plant Genetic & Breeding, College of Agriculture, Guangxi University, Nanning, 530005, China
- Faculty of Mechanical & Energy Engineering, Shaoyang University, Shaoyang, 422099, China
| | - Wenhuan Hou
- Cash Crop Research Institute of Guangxi Academy of Agricultural Science, Nanning, 530007, China
| | - Xingfu Tang
- Cash Crop Research Institute of Guangxi Academy of Agricultural Science, Nanning, 530007, China
| | - Ruiyang Zhou
- Key Laboratory of Plant Genetic & Breeding, College of Agriculture, Guangxi University, Nanning, 530005, China
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3
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Md Ahaik FA, Mohd Taufik SH, Faiqah Johari NA, Zainal Abidin AA, Balia Yusof ZN. Optimization of nucleic acid extraction and amplification of a thiamine biosynthesis gene fragment from selected Malaysian seaweeds. Genes Genet Syst 2023; 97:247-256. [PMID: 36631109 DOI: 10.1266/ggs.22-00088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Obtaining high-quality nucleic acid extracted from seaweeds is notoriously difficult due to contamination with polysaccharides and polyphenolic compounds after cell disruption. Specific methods need to be employed for RNA isolation in different seaweed species, and therefore studies of the thiamine biosynthesis pathway have been limited. Two selected Malaysian species which are highly abundant and underutilized, namely Gracilaria sp. and Padina sp., representing the red and brown seaweeds, respectively, were collected to develop optimized total RNA extraction methods. Prior to that, DNA was extracted, and amplification of the 18S rRNA gene and the THIC gene (encoding the first enzyme in the pyrimidine branch of the thiamine biosynthesis pathway) from the DNA template was successful in Gracilaria sp. only. RNA was then extracted from both seaweeds using three different existing methods, with some modifications, using cetyltrimethylammonium bromide, guanidine thiocyanate and sodium dodecyl sulphate. Methods I and III proved to be efficient for Padina sp. and Gracilaria sp., respectively, for the extraction of highly purified RNA, with A260/A280 values of 2.0 and 1.8. However, amplification of the housekeeping gene glyceraldehyde-3-phosphate dehydrogenase and the THIC gene was successful in only Gracilaria sp. cDNA derived from extracted RNA. Further modifications are required to improve the exploitation of nucleic acids from brown seaweeds, which has been proven to be difficult. This work should pave the way for molecular studies of seaweeds generally and for the elucidation, specifically, of the thiamine biosynthesis pathway.
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Affiliation(s)
- Fatin Amira Md Ahaik
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia
| | - Siti Hajar Mohd Taufik
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia
| | - Nur Asna Faiqah Johari
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia
| | | | - Zetty Norhana Balia Yusof
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia.,Aquatic Animal Health and Therapeutics Laboratory (AquaHealth), Institute of Bioscience, Universiti Putra Malaysia.,Bioprocessing and Biomanufacturing Research Complex, Universiti Putra Malaysia
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CHEN XC, LU Y, LIU Y, ZHOU JW, ZHANG YF, GAO HY, LI D, GAO W. Identification of a cytochrome P450 from Tripterygium hypoglaucum (Levl.) Hutch that catalyzes polpunonic acid formation in celastrol biosynthesis. Chin J Nat Med 2022; 20:691-700. [DOI: 10.1016/s1875-5364(22)60205-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Indexed: 11/03/2022]
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5
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Molecular cloning and functional characterization of multiple ApOSCs from Andrographis paniculata. Chin J Nat Med 2021; 18:659-665. [PMID: 32928509 DOI: 10.1016/s1875-5364(20)60004-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Indexed: 11/22/2022]
Abstract
Triterpenoids have been described in Andrographis paniculata. Oleanolic acid exhibits high biological activity and is widely used in the clinic, and β-sitosterol not only has good biological activity but also plays an important physiological role in plants. However, analysis of the biosynthetic pathway of triterpenoids in Andrographis paniculata has not been reported. Here, we provide the first report of the isolation and identification of nine 2, 3-oxidosqualene cyclases (ApOSC3 to ApOSC11) from A. paniculata. The results showed that ApOSC4 represented a monofunctional synthase that could convert 2, 3-oxidosqualene to β-amyrin. ApOSC5 as a bifunctional 2, 3-oxidosqualene cyclases, could transfer 2, 3-oxidosqualene to β-amyrin and α-amyrin. ApOSC6 to ApOSC8 composed the multifunctional 2, 3-oxidosqualene cyclases that could convert 2, 3-oxidosqualene to β-amyrin, α-amyrin and one or two undetermined triterpenoids. This study provides a better understanding of the biosynthetic pathway of triterpenoids in A. paniculata, and the discovery of multifunctional 2, 3-oxidosqualene cyclases ApOSC5 to ApOSC8 of the facilitates knowledge of the compounds diversity in A. paniculata.
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Garcia T, Duitama J, Zullo SS, Gil J, Ariani A, Dohle S, Palkovic A, Skeen P, Bermudez-Santana CI, Debouck DG, Martínez-Castillo J, Gepts P, Chacón-Sánchez MI. Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean. Nat Commun 2021; 12:702. [PMID: 33514713 PMCID: PMC7846787 DOI: 10.1038/s41467-021-20921-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/22/2020] [Indexed: 01/30/2023] Open
Abstract
Lima bean (Phaseolus lunatus L.), one of the five domesticated Phaseolus bean crops, shows a wide range of ecological adaptations along its distribution range from Mexico to Argentina. These adaptations make it a promising crop for improving food security under predicted scenarios of climate change in Latin America and elsewhere. In this work, we combine long and short read sequencing technologies with a dense genetic map from a biparental population to obtain the chromosome-level genome assembly for Lima bean. Annotation of 28,326 gene models show high diversity among 1917 genes with conserved domains related to disease resistance. Structural comparison across 22,180 orthologs with common bean reveals high genome synteny and five large intrachromosomal rearrangements. Population genomic analyses show that wild Lima bean is organized into six clusters with mostly non-overlapping distributions and that Mesomerican landraces can be further subdivided into three subclusters. RNA-seq data reveal 4275 differentially expressed genes, which can be related to pod dehiscence and seed development. We expect the resources presented here to serve as a solid basis to achieve a comprehensive view of the degree of convergent evolution of Phaseolus species under domestication and provide tools and information for breeding for climate change resiliency.
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Affiliation(s)
- Tatiana Garcia
- grid.10689.360000 0001 0286 3748Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia ,grid.17088.360000 0001 2150 1785Present Address: Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI USA
| | - Jorge Duitama
- grid.7247.60000000419370714Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | - Stephanie Smolenski Zullo
- grid.27860.3b0000 0004 1936 9684Department of Plant Sciences/MS1, University of California, Davis, CA USA
| | - Juanita Gil
- grid.7247.60000000419370714Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia ,grid.411017.20000 0001 2151 0999Present Address: Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR USA
| | - Andrea Ariani
- grid.27860.3b0000 0004 1936 9684Department of Plant Sciences/MS1, University of California, Davis, CA USA ,Present Address: BASF BBCC - Innovation Center, Gent, Belgium
| | - Sarah Dohle
- grid.27860.3b0000 0004 1936 9684Department of Plant Sciences/MS1, University of California, Davis, CA USA
| | - Antonia Palkovic
- grid.27860.3b0000 0004 1936 9684Department of Plant Sciences/MS1, University of California, Davis, CA USA
| | - Paola Skeen
- grid.10689.360000 0001 0286 3748Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia ,Present Address: Nunhems USA, Vegetable Seeds BASF, Acampo, CA USA
| | - Clara Isabel Bermudez-Santana
- grid.10689.360000 0001 0286 3748Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Daniel G. Debouck
- grid.418348.20000 0001 0943 556XCentro Internacional de Agricultura Tropical, Cali, Colombia
| | - Jaime Martínez-Castillo
- grid.418270.80000 0004 0428 7635Centro de Investigación Científica de Yucatán, Yucatán, Mexico
| | - Paul Gepts
- grid.27860.3b0000 0004 1936 9684Department of Plant Sciences/MS1, University of California, Davis, CA USA
| | - Maria Isabel Chacón-Sánchez
- grid.10689.360000 0001 0286 3748Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia
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7
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Zhang G, Liu W, Feng Y, Li D, Li K, Sun Q, Zhai L, Wu T, Zhang X, Xu X, Wang Y, Han Z. Ethylene Response Factors MbERF4 and MbERF72 Suppress Iron Uptake in Woody Apple Plants by Modulating Rhizosphere pH. PLANT & CELL PHYSIOLOGY 2020; 61:699-711. [PMID: 31868909 DOI: 10.1093/pcp/pcz234] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 12/18/2019] [Indexed: 05/26/2023]
Abstract
Iron (Fe) deficiency limits the yield of fruit trees. When subjected to Fe deficiency, H+ secretion increases in the rhizosphere of dicotyledonous plants and pH decreases. This leads to the acidification of the soil and promotes Fe3+ to Fe2+ conversion, which plants can better uptake. This study investigated the relationship between two inhibitory transcription factors (ethylene response factors MbERF4 and MbERF72) and the H+-ATPase gene MbHA2. Two species of apple woody plants were studied: the Fe-inefficient Malus baccata and the Fe-efficient Malus xiaojinensis. Yeast one-hybrid and electrophoretic mobility shift assays showed that both MbERF4 and MbERF72 bind to the GCC cassette (AGCCGCC) of the MbHA2 promoter. Moreover, yeast two-hybrid and bimolecular fluorescence complementation assays showed that MbERF4 interacts with MbERF72. Furthermore, β-glucuronidase and luciferase reporter assays showed that the MbERF4- and MbERF72-induced repression of MbHA2 expression is synergistic. Virus-induced gene silencing of MbERF4 or MbERF72 increased MbHA2 expression, and thus lowered the rhizosphere pH in M. baccata. Consequently, the high expressions of MbERF4 and MbERF72 induced by Fe deficiency contributed to the Fe sensitivity of M. baccata. Moreover, the low expressions of MxERF4 and MxERF72 contributed to the Fe-deficiency tolerance of M. xiaojinensis via different binding conditions to the HA2 promoter. In summary, this study identified the relationship of two inhibitory transcription factors with the H+-ATPase gene and proposed a model in which ERF4 and ERF72 affect the rhizosphere pH in response to Fe deficiency.
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Affiliation(s)
- Guifen Zhang
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Wei Liu
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yi Feng
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Duyue Li
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Keting Li
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Qiran Sun
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Longmei Zhai
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing 100193, China
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Liu Y, Zhou J, Hu T, Lu Y, Gao L, Tu L, Gao J, Huang L, Gao W. Identification and functional characterization of squalene epoxidases and oxidosqualene cyclases from Tripterygium wilfordii. PLANT CELL REPORTS 2020; 39:409-418. [PMID: 31838574 DOI: 10.1007/s00299-019-02499-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 12/05/2019] [Indexed: 05/20/2023]
Abstract
We cloned two squalene epoxidases and five oxidosqualene cyclases, and identified their function using CRISPR/Cas9 tool and yeast heterologous expression. Triterpenes are the main active ingredients of Tripterygium wilfordii Hook.f., a traditional Chinese medicinal plant with many encouraging preclinical applications. However, the biosynthetic pathways of triterpenes in this plant are poorly understood. Here, we report on the isolation and identification of two squalene epoxidases (SQE6 and SQE7) and five oxidosqualene cyclases (OSC4-8) from T. wilfordii. Yeast complementation assays showed that TwSQE6 and TwSQE7 can functionally complement an erg1 yeast mutant that was constructed using the CRISPR/Cas9 system. The putative OSC genes were functionally characterized by heterologous expression in yeast. GC/MS analysis of the fermentation products of the transgenic yeast showed that both TwOSC4 and TwOSC6 are cycloartenol synthases, while TwOSC8 is a β-amyrin synthase. The discovery of these genes expands our knowledge of key enzymes in triterpenoid biosynthesis, and provides additional target genes for increasing the production of triterpenes in T. wilfordii tissue cultures by disrupting competing pathways, or in chassis cells by reconstituting the triterpenoid biosynthetic pathway.
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Affiliation(s)
- Yuan Liu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, People's Republic of China
| | - Jiawei Zhou
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, People's Republic of China
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, 100069, People's Republic of China
| | - Tianyuan Hu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, People's Republic of China
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, 100069, People's Republic of China
| | - Yun Lu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, People's Republic of China
| | - Linhui Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, People's Republic of China
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, People's Republic of China
| | - Lichan Tu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, People's Republic of China
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, 100069, People's Republic of China
| | - Jie Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, People's Republic of China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, People's Republic of China
| | - Wei Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, People's Republic of China.
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, 100069, People's Republic of China.
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, 10069, People's Republic of China.
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Guan L, Ma X, Zhou X, Tan B, Wang ZY. An optimized method to obtain high-quality RNA from cassava storage root. 3 Biotech 2019; 9:118. [PMID: 30854278 PMCID: PMC6399363 DOI: 10.1007/s13205-019-1608-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/01/2019] [Indexed: 12/23/2022] Open
Abstract
Extracting RNA with high quality and integrity is crucial for molecular biology studies in eukaryotes. However, RNA isolation from cassava storage root raises a great concern because it contains large amounts of polysaccharides and polyphenol compounds. In the current study, four RNA extraction methods were evaluated for extracting RNA from cassava storage root. We found that the modified TM method (MTM) is timesaving and low-cost extraction method with high quality and quantities of RNA. The effectiveness of the improved method was assessed for qPCR analysis of four selected genes from total RNA of storage root. The improved protocol generated 4.18-5.94 µg RNA/g fresh weight. An A260/280 ratios of RNA samples are ranged from 2.14 to 2.17. The RIN values are ranged from 7.2 to 8.0. Importantly, isolated total RNA by MTM was successfully used for library construction and transcriptome sequencing. Therefore, we provide an efficient and low-cost method, MTM, for extracting high quality and quantities of RNA from cassava storage root.
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Affiliation(s)
- Lulu Guan
- Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228 Hainan China
| | - Xiaowen Ma
- Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228 Hainan China
| | - Xiaoxia Zhou
- Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228 Hainan China
| | - Bowen Tan
- Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228 Hainan China
| | - Zhen-Yu Wang
- Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228 Hainan China
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Behnam B, Bohorquez-Chaux A, Castaneda-Mendez OF, Tsuji H, Ishitani M, Becerra Lopez-Lavalle LA. An optimized isolation protocol yields high-quality RNA from cassava tissues ( Manihot esculenta Crantz). FEBS Open Bio 2019; 9:814-825. [PMID: 30984554 PMCID: PMC6443859 DOI: 10.1002/2211-5463.12561] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 09/07/2018] [Accepted: 09/26/2018] [Indexed: 12/12/2022] Open
Abstract
We developed and modified a precise, rapid, and reproducible protocol isolating high-quality RNA from tissues of multiple varieties of cassava plants (Manihot esculenta Crantz). The resulting method is suitable for use in mini, midi, and maxi preparations and rapidly achieves high total RNA yields (170-600 μg·g-1) using low-cost chemicals and consumables and with minimal contamination from polysaccharides, polyphenols, proteins, and other secondary metabolites. In particular, A 260 : A 280 ratios were > 2.0 for RNA from various tissues, and all of the present RNA samples yielded ribosomal integrity number values of greater than six. The resulting high purity and quality of isolated RNA will facilitate downstream applications (quantitative reverse transcriptase-polymerase chain reaction or RNA sequencing) in cassava molecular breeding.
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Affiliation(s)
- Babak Behnam
- Kihara Institute for Biological Research Yokohama City University Yokohama Japan
| | | | | | - Hiroyuki Tsuji
- Kihara Institute for Biological Research Yokohama City University Yokohama Japan
| | - Manabu Ishitani
- International Center for Tropical Agriculture (CIAT) Valle del Cauca Colombia
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Zhou J, Zhang Y, Hu T, Su P, Zhang Y, Liu Y, Huang L, Gao W. Functional characterization of squalene epoxidase genes in the medicinal plant Tripterygium wilfordii. Int J Biol Macromol 2018; 120:203-212. [DOI: 10.1016/j.ijbiomac.2018.08.073] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 08/08/2018] [Accepted: 08/16/2018] [Indexed: 11/25/2022]
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12
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An ethylene response factor (MxERF4) functions as a repressor of Fe acquisition in Malus xiaojinensis. Sci Rep 2018; 8:1068. [PMID: 29348657 PMCID: PMC5773544 DOI: 10.1038/s41598-018-19518-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 12/01/2017] [Indexed: 12/19/2022] Open
Abstract
Iron (Fe) is an essential element for plants; however, its availability is limited as it forms insoluble complexes in the soil. Consequently, plants have developed mechanisms to adapt to low Fe conditions. We demonstrate that ethylene is involved in Fe deficiency-induced physiological responses in Malus xiaojinensis, and describe the identification of MxERF4 as a protein-protein interaction partner with the MxFIT transcription factor, which is involved in the iron deficiency response. Furthermore, we demonstrate that MxERF4 acts as an MxFIT interaction partner to suppresses the expression of the Fe transporter MxIRT1, by binding directly to its promoter, requiring the EAR motif of the MxERF4 protein. Suppression of MxERF4 expression in M. xiaojinensis, using virus induced gene silencing resulted in an increase in MxIRT1 expression. Taken together, the results suggest a repression mechanism, where ethylene initiates the Fe deficiency response, and the response is then dampened, which may require a transient inhibition of Fe acquisition via the action of MxERF4.
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Xiao Y, He X, Ojeda-Lassalle Y, Poovaiah C, Coleman HD. Expression of a hyperthermophilic endoglucanase in hybrid poplar modifies the plant cell wall and enhances digestibility. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:225. [PMID: 30147748 PMCID: PMC6094567 DOI: 10.1186/s13068-018-1224-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/06/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND Expression of glycosyl hydrolases in lignocellulosic biomass has been proposed as an alternative to improve efficiency of cellulosic ethanol production. In planta production of hyperthermophilic hydrolytic enzymes could prevent the detrimental effects often seen resulting from the expression of recombinant mesophilic enzymes to plant hosts. Utilizing lignocellulosic feedstocks to produce hyperthermophilic hydrolases provides additional benefits for ethanol production in the way of transgenic feedstocks serving as both enzyme providers and cellulosic substrates. RESULTS In this study, transgenic hybrid poplar (Populus alba × grandidentata) was generated to express a hyperthermophilic endoglucanase from Thermotoga neapolitana with an optimal temperature over 100 °C. Functional hyperthermoactive endoglucanase was successfully produced in the transgenic events, and altered phenotypic growth was observed in transgenic lines. Moreover, the line with the highest TnCelB expression in both leaf and developing xylem had reduced lignin content and cellulose crystallinity, resulting in a more digestible cell wall. The activation of TnCelB by a post-harvest heat treatment resulted in enhanced saccharification efficiencies of transgenic poplar lines with moderate TnCelB expression and without alteration of cellulose and lignin when not heat-treated. In planta high-level overexpression of a hyperthermophilic endoglucanase paired with heat treatment following harvest, resulted in biomass that was comparable with wild-type lines that underwent a traditional pretreatment for saccharification. CONCLUSIONS Overexpression of hyperthermophilic endoglucanase in feedstock had impacts on plant growth and cell wall composition, especially when the enzyme was highly expressed. Improved glucan saccharification efficiencies from transgenic lines before and after heat treatment could reduce both the economic and environmental costs associated with ethanol production from lignocellulosic biomass.
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Affiliation(s)
- Yao Xiao
- Biology Department, Syracuse University, Syracuse, NY 13244 USA
| | - Xuejun He
- Biology Department, Syracuse University, Syracuse, NY 13244 USA
| | | | - Charleson Poovaiah
- Biology Department, Syracuse University, Syracuse, NY 13244 USA
- Present Address: Scion, Te Papa Tipu Innovation Park, 49 Sala Street, Rotorua, 3010 New Zealand
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Zhang J, Huo YB, Liu Y, Feng JT, Ma ZQ, Zhu CS, Zhang X. Differential expressed analysis of Tripterygium wilfordii unigenes involved in terpenoid backbone biosynthesis. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2017; 19:823-832. [PMID: 27649810 DOI: 10.1080/10286020.2016.1232713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Tripterygium wilfordii Hook. f. is the traditional medicinal plants in China. Triptolide, wilforgine, and wilforine are the bioactive compounds in T. wilfordii. In this study, the contents of three metabolites and transcription levels of 21 genes involved in three metabolites biosynthesis in T. wilfordii were examined using high-performance liquid chromatography and reverse transcription PCR after application of methyl jasmonate (MeJA) on hairy roots in time course experiment (3-24 h). The results indicated that application of MeJA inhibited triptolide accumulation and promoted wilforgine and wilforine metabolites biosynthesis. In hairy roots, wilforgine content reached 693.36 μg/g at 6 h after adding MeJA, which was 2.23-fold higher than control. The accumulation of triptolide and wilforine in hairy roots increased the maximum at 9 h, which was 1.3- and 1.6-folds more than the control. Most of the triptolide secretes into the medium, but wilforgine and wilforine cannot secrete into the medium. The expression levels of unigenes which involved terpenoid backbone biosynthesis exist the correlation with marker metabolites (triptolide, wilforgine and wilforine) after induction by MeJA, and can be then used to infer flux bottlenecks in T. wilfordii secondary metabolites accumulation. These results showed that these genes may have potential applications in the metabolic engineering of T. wilfordii metabolites production.
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Affiliation(s)
- Jing Zhang
- a Research & Development Center of Biorational Pesticides, Northwest A & F University , Yangling 712100 , China
- b Research Center of Biopesticide Technology & Engineering Center Shaanxi Province , Yangling 712100 , China
| | - Yan-Bo Huo
- a Research & Development Center of Biorational Pesticides, Northwest A & F University , Yangling 712100 , China
| | - Yan Liu
- a Research & Development Center of Biorational Pesticides, Northwest A & F University , Yangling 712100 , China
| | - Jun-Tao Feng
- a Research & Development Center of Biorational Pesticides, Northwest A & F University , Yangling 712100 , China
- b Research Center of Biopesticide Technology & Engineering Center Shaanxi Province , Yangling 712100 , China
| | - Zhi-Qing Ma
- a Research & Development Center of Biorational Pesticides, Northwest A & F University , Yangling 712100 , China
- b Research Center of Biopesticide Technology & Engineering Center Shaanxi Province , Yangling 712100 , China
| | - Chuan-Shu Zhu
- a Research & Development Center of Biorational Pesticides, Northwest A & F University , Yangling 712100 , China
- b Research Center of Biopesticide Technology & Engineering Center Shaanxi Province , Yangling 712100 , China
| | - Xing Zhang
- a Research & Development Center of Biorational Pesticides, Northwest A & F University , Yangling 712100 , China
- b Research Center of Biopesticide Technology & Engineering Center Shaanxi Province , Yangling 712100 , China
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15
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Yang F, Wang G, Xu W, Hong N. A rapid silica spin column-based method of RNA extraction from fruit trees for RT-PCR detection of viruses. J Virol Methods 2017; 247:61-67. [PMID: 28583858 DOI: 10.1016/j.jviromet.2017.05.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 02/07/2017] [Accepted: 05/31/2017] [Indexed: 12/01/2022]
Abstract
Efficient recovery of high quality RNA is very important for successful RT-PCR detection of plant RNA viruses. High levels of polyphenols and polysaccharides in plant tissues can irreversibly bind to and/or co-precipitate with RNA, which influences RNA isolation. In this study, a silica spin column-based RNA isolation method was developed by using commercially available silica columns combined with the application of a tissue lysis solution, and binding and washing buffers with high concentration guanidinium thiocyanate (GuSCN, 50% w/v), which helps remove plant proteins, polysaccharides and polyphenolic compounds. The method was successfully used to extract high quality RNA from citrus (Citrus aurantifolia), grapevine (Vitis vinifera), peach (Prunus persica), pear (Pyrus spp.), taro (Colocosia esculenta) and tobacco (Nicotiana benthamiana) samples. The method was comparable to conventional CTAB method in RNA isolation efficiency, but it was more sample-adaptable and cost-effective than commercial kits. High quality RNA isolated using silica spin column-based method was successfully used for the RT-PCR and/or multiplex RT-PCR amplification of woody fruit tree viruses and a viroid. The study provided a useful tool for the detection and characterization of plant viruses.
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Affiliation(s)
- Fan Yang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Guoping Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; National Indoor Conservation Center of Virus-free Germplasm of Fruit Crops, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Wenxing Xu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Ni Hong
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; National Indoor Conservation Center of Virus-free Germplasm of Fruit Crops, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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Xiao H, Kim WS, Meng B. A highly effective and versatile technology for the isolation of RNAs from grapevines and other woody perennials for use in virus diagnostics. Virol J 2015; 12:171. [PMID: 26482551 PMCID: PMC4615883 DOI: 10.1186/s12985-015-0376-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/05/2015] [Indexed: 10/31/2022] Open
Abstract
BACKGROUND Isolation of pure RNA from woody perennials, especially fruit crops such as grapevine rich in complex secondary metabolites, has remained very challenging. Lack of effective RNA isolation technology has resulted in difficulties in viral diagnosis and discovery as well as studies on many biological processes of these highly important woody plants. It is imperative to develop and refine methodologies with which large amounts of pure nucleic acids can be readily isolated from woody perennials. METHODS We compared five commonly used RNA isolation kits in isolating total RNA from twelve species of woody perennials. We made modifications to select RNA isolation systems to simplify and improve their efficiency in RNA isolation. The yield and quality of isolated RNAs were assessed via gel electrophoresis and spectrophotometric measurement. We also performed RT-PCR and RT-qPCR to detect several major viruses from grapevines. RESULTS Two of the kits were shown to be the best in both the yield and quality of the isolated RNA from all twelve woody species. Using disposable extraction bags for tissue homogenization not only improved the yield without affecting quality, but also made the RNA isolation technology simpler, less costly, and suitable for adoption by many potential users with facility limitations. This system was successfully applied to a wide range of woody plants, including fruit crops, ornamentals and timber trees. Inclusion of polyvinylpyrrolidone in the extraction buffer drastically improved the performance of the system in isolating total RNA from old grapevine leaves collected later in the season. This modification made our system highly effective in isolating quality RNA from grapevine leaves throughout the entire growing season. We further demonstrated that the resulting nucleic acid preparations are suitable for detection of several major grapevine viruses with RNA or DNA genomes using PCR, RT-PCR and qPCR as well as for assays on plant microRNAs. CONCLUSIONS This improved RNA isolation system would have wide applications in viral diagnostics and discovery, studies on gene expression and regulation, transcriptomics, and small RNA biology in grapevines. We believe this system will also be useful in diverse applications pertaining to research on many other woody perennials and recalcitrant plant species.
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Affiliation(s)
- Huogen Xiao
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
| | - Won-Sik Kim
- Norgen BioTek, Thorald, ON, L2V 4Y6, Canada.
| | - Baozhong Meng
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
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Feng J, Wang J, Fan P, Jia W, Nie L, Jiang P, Chen X, Lv S, Wan L, Chang S, Li S, Li Y. High-throughput deep sequencing reveals that microRNAs play important roles in salt tolerance of euhalophyte Salicornia europaea. BMC PLANT BIOLOGY 2015; 15:63. [PMID: 25848810 PMCID: PMC4349674 DOI: 10.1186/s12870-015-0451-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 02/06/2015] [Indexed: 05/07/2023]
Abstract
BACKGROUND microRNAs (miRNAs) are implicated in plant development processes and play pivotal roles in plant adaptation to environmental stresses. Salicornia europaea, a salt mash euhalophyte, is a suitable model plant to study salt adaptation mechanisms. S. europaea is also a vegetable, forage, and oilseed that can be used for saline land reclamation and biofuel precursor production on marginal lands. Despite its importance, no miRNA has been identified from S. europaea thus far. RESULTS Deep sequencing was performed to investigate small RNA transcriptome of S. europaea. Two hundred and ten conserved miRNAs comprising 51 families and 31 novel miRNAs (including seven miRNA star sequences) belonging to 30 families were identified. About half (13 out of 31) of the novel miRNAs were only detected in salt-treated samples. The expression of 43 conserved and 13 novel miRNAs significantly changed in response to salinity. In addition, 53 conserved and 13 novel miRNAs were differentially expressed between the shoots and roots. Furthermore, 306 and 195 S. europaea unigenes were predicted to be targets of 41 conserved and 29 novel miRNA families, respectively. These targets encoded a wide range of proteins, and genes involved in transcription regulation constituted the largest category. Four of these genes encoding laccase, F-box family protein, SAC3/GANP family protein, and NADPH cytochrome P-450 reductase were validated using 5'-RACE. CONCLUSIONS Our results indicate that specific miRNAs are tightly regulated by salinity in the shoots and/or roots of S. europaea, which may play important roles in salt tolerance of this euhalophyte. The S. europaea salt-responsive miRNAs and miRNAs that target transcription factors, nucleotide binding site-leucine-rich repeat proteins and enzymes involved in lignin biosynthesis as well as carbon and nitrogen metabolism may be applied in genetic engineering of crops with high stress tolerance, and genetic modification of biofuel crops with high biomass and regulatable lignin biosynthesis.
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Affiliation(s)
- Juanjuan Feng
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Jinhui Wang
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Pengxiang Fan
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
- />Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson road, East Lansing, MI 48824 USA
| | - Weitao Jia
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Lingling Nie
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Ping Jiang
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Xianyang Chen
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Sulian Lv
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Lichuan Wan
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
| | - Sandra Chang
- />Beijing Engineering Research Center for Biofuels, Tsinghua University, Beijing, 100084 China
- />Institute of Nuclear and New Energy Technology, Tsinghua University, Beijing, 100084 China
| | - Shizhong Li
- />Beijing Engineering Research Center for Biofuels, Tsinghua University, Beijing, 100084 China
- />Institute of Nuclear and New Energy Technology, Tsinghua University, Beijing, 100084 China
| | - Yinxin Li
- />Institute of Botany, Key Laboratory of Plant Molecular Physiology, Chinese Academy of Sciences, Beijing, 100093 China
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Pappi PG, Chaintoutis SC, Dovas CI, Efthimiou KE, Katis NI. Development of one-tube real-time qRT-PCR and evaluation of RNA extraction methods for the detection of Eggplant mottled dwarf virus in different species. J Virol Methods 2015; 212:59-65. [DOI: 10.1016/j.jviromet.2014.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 10/30/2014] [Accepted: 11/04/2014] [Indexed: 12/31/2022]
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Ouyang K, Li J, Huang H, Que Q, Li P, Chen X. A simple method for RNA isolation from various tissues of the tree Neolamarckia cadamba. BIOTECHNOL BIOTEC EQ 2014; 28:1008-1013. [PMID: 26019587 PMCID: PMC4434054 DOI: 10.1080/13102818.2014.981086] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 07/28/2014] [Indexed: 10/31/2022] Open
Abstract
Plant tissues contain abundant polysaccharides, phenolic compounds and other metabolites, which makes it difficult to isolate high-quality RNA from them. In addition, Neolamarckia cadamba contains large quantities of other components, particularly RNA-binding alkaloids, which makes the isolation even more challenging. Here, we describe a concise and efficient RNA isolation method that combines the cetyltrimethyl ammonium bromide (CTAB) and Plant RNA Kit (Omega) protocols. Gel electrophoresis showed that RNA extracted from all tissues, using this protocol, was of good integrity and without DNA contamination. Furthermore, the isolated RNA was of high purity, with an A260/A280 ratio of 2.1 and an A260/A230 ratio of >2.0. The isolated RNA was also suitable for downstream applications, such as reverse transcription-polymerase chain reaction (RT-PCR) and quantitative RT-PCR (RT-qPCR). The RNA isolation method was also efficient for recalcitrant plant tissues.
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Affiliation(s)
- Kunxi Ouyang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University , Guangzhou , Guangdong , P.R. China
| | - Juncheng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University , Guangzhou , Guangdong , P.R. China
| | - Hao Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University , Guangzhou , Guangdong , P.R. China ; Guangxi Botanical Garden of Medicinal Plants , Nanning , Guangxi , P.R. China
| | - Qingmin Que
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University , Guangzhou , Guangdong , P.R. China
| | - Pei Li
- Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants, Ministry of Education, National Engineering Laboratory for Forest Tree Breeding, Beijing Forestry University , Beijing , P.R. China
| | - Xiaoyang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University , Guangzhou , Guangdong , P.R. China
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20
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Peng J, Xia Z, Chen L, Shi M, Pu J, Guo J, Fan Z. Rapid and efficient isolation of high-quality small RNAs from recalcitrant plant species rich in polyphenols and polysaccharides. PLoS One 2014; 9:e95687. [PMID: 24787387 PMCID: PMC4006784 DOI: 10.1371/journal.pone.0095687] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 03/29/2014] [Indexed: 11/30/2022] Open
Abstract
Small RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), are important regulators of plant development and gene expression. The acquisition of high-quality small RNAs is the first step in the study of its expression and function analysis, yet the extraction method of small RNAs in recalcitrant plant tissues with various secondary metabolites is not well established, especially for tropical and subtropical plant species rich in polysaccharides and polyphenols. Here, we developed a simple and efficient method for high quality small RNAs extraction from recalcitrant plant species. Prior to RNA isolation, a precursory step with a CTAB-PVPP buffer system could efficiently remove compounds and secondary metabolites interfering with RNAs from homogenized lysates. Then, total RNAs were extracted by Trizol reagents followed by a differential precipitation of high-molecular-weight (HMW) RNAs using polyethylene glycol (PEG) 8000. Finally, small RNAs could be easily recovered from supernatant by ethanol precipitation without extra elimination steps. The isolated small RNAs from papaya showed high quality through a clear background on gel and a distinct northern blotting signal with miR159a probe, compared with other published protocols. Additionally, the small RNAs extracted from papaya were successfully used for validation of both predicted miRNAs and the putative conserved tasiARFs. Furthermore, the extraction method described here was also tested with several other subtropical and tropical plant tissues. The purity of the isolated small RNAs was sufficient for such applications as end-point stem-loop RT-PCR and northern blotting analysis, respectively. The simple and feasible extraction method reported here is expected to have excellent potential for isolation of small RNAs from recalcitrant plant tissues rich in polyphenols and polysaccharides.
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Affiliation(s)
- Jun Peng
- State Key Laboratory of Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, China
- Ministry of Agriculture Key Laboratory of Integrated Pest Management on Tropical Crops, Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Zihao Xia
- State Key Laboratory of Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, China
| | - Ling Chen
- State Key Laboratory of Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, China
| | - Minjing Shi
- Ministry of Agriculture Key Laboratory for Rubber Biology, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, China
| | - Jinji Pu
- Ministry of Agriculture Key Laboratory of Integrated Pest Management on Tropical Crops, Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Jianrong Guo
- Ministry of Agriculture Key Laboratory of Integrated Pest Management on Tropical Crops, Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Zaifeng Fan
- State Key Laboratory of Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, China
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Fan P, Nie L, Jiang P, Feng J, Lv S, Chen X, Bao H, Guo J, Tai F, Wang J, Jia W, Li Y. Transcriptome analysis of Salicornia europaea under saline conditions revealed the adaptive primary metabolic pathways as early events to facilitate salt adaptation. PLoS One 2013; 8:e80595. [PMID: 24265831 PMCID: PMC3827210 DOI: 10.1371/journal.pone.0080595] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 10/04/2013] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Halophytes such as Salicornia europaea have evolved to exhibit unique mechanisms controlled by complex networks and regulated by numerous genes and interactions to adapt to habitats with high salinity. However, these mechanisms remain unknown. METHODS To investigate the mechanism by which halophytes tolerate salt based on changes in the whole transcriptome, we performed transcriptome sequencing and functional annotation by database search. Using the unigene database, we conducted digital gene expression analysis of S. europaea at various time points after these materials were treated with NaCl. We also quantified ion uptakes. Gene functional enrichment analysis was performed to determine the important pathways involved in this process. RESULTS A total of 57,151 unigenes with lengths of >300 bp were assembled, in which 57.5% of these unigenes were functionally annotated. Differentially expressed genes indicated that cell wall metabolism and lignin biosynthetic pathways were significantly enriched in S. europaea to promote the development of the xylem under saline conditions. This result is consistent with the increase in sodium uptake as ions pass through the xylem. Given that PSII efficiency remained unaltered, salt treatment activated the expression of electron transfer-related genes encoded by the chloroplast chromosome. Chlorophyll biosynthesis was also inhibited, indicating the energy-efficient state of the electron transfer system of S. europaea. CONCLUSIONS The key function of adjusting important primary metabolic pathways in salt adaption was identified by analyzing the changes in the transcriptome of S. europaea. These pathways could involve unique salt tolerance mechanisms in halophytes. This study also provided information as the basis of future investigations on salt response genes in S. europaea. Ample gene resources were also provided to improve the genes responsible for the salt tolerance ability of crops.
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Affiliation(s)
- Pengxiang Fan
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
| | - Lingling Nie
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
| | - Ping Jiang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
| | - Juanjuan Feng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
| | - Sulian Lv
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
| | - Xianyang Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
| | - Hexigeduleng Bao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
| | - Jie Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
| | - Fang Tai
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
| | - Jinhui Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
| | - Weitao Jia
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
| | - Yinxin Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
- * E-mail:
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Henderson DC, Hammond J. CKC: isolation of nucleic acids from a diversity of plants using CTAB and silica columns. Mol Biotechnol 2013; 53:109-17. [PMID: 22271458 DOI: 10.1007/s12033-012-9494-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
To assay for viruses in plant samples, we required a method for nucleic acid isolation that is rapid, simple, and applicable to the widest possible variety of plants. A protocol for isolation of total nucleic acid (TNA) was developed by combining common CTAB methods with silica spin columns. We report data on TNA purity and RNA quality from over 30 plant genera representing 25 families. Measurements showed that RNA is of high quality, and one-step RT-PCR was successfully performed on all samples. The protocol can be completed in less than 2 h.
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Affiliation(s)
- David C Henderson
- USDA-ARS, United States National Arboretum, Floral and Nursery Plants Research Unit, B-010A, Beltsville, MD 20705, USA.
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23
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Wang X, Chang L, Wang B, Wang D, Li P, Wang L, Yi X, Huang Q, Peng M, Guo A. Comparative proteomics of Thellungiella halophila leaves from plants subjected to salinity reveals the importance of chloroplastic starch and soluble sugars in halophyte salt tolerance. Mol Cell Proteomics 2013; 12:2174-95. [PMID: 23660471 DOI: 10.1074/mcp.m112.022475] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Thellungiella halophila, a close relative of Arabidopsis, is a model halophyte used to study plant salt tolerance. The proteomic/physiological/transcriptomic analyses of Thellungiella plant leaves subjected to different salinity levels, reported herein, indicate an extraordinary ability of Thellungiella to adapt to large concentrations of exogenous saline by compartmentalizing Na(+) into cell vacuoles and accumulating proline and soluble sugars as organic osmolytes. Salinity stress stimulated the accumulation of starch in chloroplasts, which resulted in a greatly increased content of starch and total sugars in leaves. Comparative proteomics of Thellungiella leaves identified 209 salt-responsive proteins. Among these, the sequences of 108 proteins were strongly homologous to Arabidopsis protein sequences, and 30 had previously been identified as Thellungiella proteins. Functional classification of these proteins into 16 categories indicated that the majority are involved in carbohydrate metabolism, followed by those involved in energy production and conversion, and then those involved in the transport of inorganic ions. Pathway analysis revealed that most of the proteins are involved in starch and sucrose metabolism, carbon fixation, photosynthesis, and glycolysis. Of these processes, the most affected were starch and sucrose metabolism, which might be pivotal for salt tolerance. The gene expression patterns of the 209 salt-responsive proteins revealed through hierarchical clustering of microarray data and the expression patterns of 29 Thellungiella genes evaluated via quantitative RT-PCR were similar to those deduced via proteomic analysis, which underscored the possibility that starch and sucrose metabolism might play pivotal roles in determining the salt tolerance ability of Thellungiella. Our observations enabled us to propose a schematic representation of the systematic salt-tolerance phenotype in Thellungiella and suggested that the increased accumulation of starch, soluble sugars, and proline, as well as subcellular compartmentalization of sodium, might collectively denote important mechanisms for halophyte salt tolerance.
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Affiliation(s)
- Xuchu Wang
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China.
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Rajakani R, Narnoliya L, Sangwan NS, Sangwan RS, Gupta V. Activated charcoal-mediated RNA extraction method for Azadirachta indica and plants highly rich in polyphenolics, polysaccharides and other complex secondary compounds. BMC Res Notes 2013; 6:125. [PMID: 23537338 PMCID: PMC3626780 DOI: 10.1186/1756-0500-6-125] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 03/20/2013] [Indexed: 11/26/2022] Open
Abstract
Background High quality RNA is a primary requisite for numerous molecular biological applications but is difficult to isolate from several plants rich in polysaccharides, polyphenolics and other secondary metabolites. These compounds either bind with nucleic acids or often co-precipitate at the final step and many times cannot be removed by conventional methods and kits. Addition of vinyl-pyrollidone polymers in extraction buffer efficiently removes polyphenolics to some extent, but, it failed in case of Azadirachta indica and several other medicinal and aromatic plants. Findings Here we report the use of adsorption property of activated charcoal (0.03%–0.1%) in RNA isolation procedures to remove complex secondary metabolites and polyphenolics to yield good quality RNA from Azadirachta indica. We tested and validated our modified RNA isolation method across 21 different plants including Andrographis paniculata, Aloe vera, Rosa damascena, Pelargonium graveolens, Phyllanthus amarus etc. from 13 other different families, many of which are considered as tough system for isolating RNA. The A260/280 ratio of the extracted RNA ranged between 1.8-2.0 and distinct 28S and 18S ribosomal RNA bands were observed in denaturing agarose gel electrophoresis. Analysis using Agilent 2100 Bioanalyzer revealed intact total RNA yield with very good RNA Integrity Number. Conclusions The RNA isolated by our modified method was found to be of high quality and amenable for sensitive downstream molecular applications like subtractive library construction and RT-PCR. This modified RNA isolation procedure would aid and accelerate the biotechnological studies in complex medicinal and aromatic plants which are extremely rich in secondary metabolic compounds.
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Affiliation(s)
- Raja Rajakani
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India
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Kumar A, Singh K. Isolation of high quality RNA from Phyllanthus emblica and its evaluation by downstream applications. Mol Biotechnol 2013; 52:269-75. [PMID: 22209897 DOI: 10.1007/s12033-011-9492-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Next generation sequencing is a high-throughput technique widely used for transcriptome profiling. Isolation of high quality RNA is a prerequisite for such large scale transcriptome analysis. Phyllanthus emblica is an important medicinal plant having high amount of metabolites like vitamin C, flavonoids, polyphenolic compounds, tannins, which are responsible for its wondered medicinal properties. High concentration of secondary metabolites like polysaccharides and polyphenols proved to be an obstacle in isolating RNA of good quality. Any compromise with quality of RNA affects the downstream applications and requires extra cleaning steps that further reduce RNA quantity. We have developed a protocol for isolation of high quality RNA from P. embilca. RNA was successfully assessed for downstream applications like reverse transcription polymerase chain reaction, rapid amplification of cDNA ends, mRNA library preparation, and sequencing using HiSeq(™) 2000 sequencing technology. The protocol is simple and can be completed in 4-5 h.
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Affiliation(s)
- Avneesh Kumar
- Department of Biotechnology, Panjab University, Chandigarh 160014, India
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Ren HJ, Liu RD, Wang ZQ, Cui J. Construction and use of a Trichinella spiralis phage display library to identify the interactions between parasite and host enterocytes. Parasitol Res 2013; 112:1857-63. [DOI: 10.1007/s00436-013-3339-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 02/01/2013] [Indexed: 12/14/2022]
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Cimino D, De Pittà C, Orso F, Zampini M, Casara S, Penna E, Quaglino E, Forni M, Damasco C, Pinatel E, Ponzone R, Romualdi C, Brisken C, De Bortoli M, Biglia N, Provero P, Lanfranchi G, Taverna D. miR148b is a major coordinator of breast cancer progression in a relapse‐associated microRNA signature by targeting ITGA5, ROCK1, PIK3CA, NRAS, and CSF1. FASEB J 2012; 27:1223-35. [DOI: 10.1096/fj.12-214692] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Daniela Cimino
- Molecular Biotechnology Center (MBC)University of TorinoTurinItaly
- Department of Oncological SciencesUniversity of TorinoTurinItaly
- Center for Molecular Systems BiologyUniversity of TorinoTurinItaly
| | - Cristiano De Pittà
- Department of Biology and Centro Ricerche Interdepartimentale Biotecnologie Innovative (CRIBI) Biotechnology CenterUniversity of PadovaPaduaItaly
| | - Francesca Orso
- Molecular Biotechnology Center (MBC)University of TorinoTurinItaly
- Department of Oncological SciencesUniversity of TorinoTurinItaly
- Center for Molecular Systems BiologyUniversity of TorinoTurinItaly
| | - Matteo Zampini
- Department of Biology and Centro Ricerche Interdepartimentale Biotecnologie Innovative (CRIBI) Biotechnology CenterUniversity of PadovaPaduaItaly
| | - Silvia Casara
- Department of Biology and Centro Ricerche Interdepartimentale Biotecnologie Innovative (CRIBI) Biotechnology CenterUniversity of PadovaPaduaItaly
| | - Elisa Penna
- Molecular Biotechnology Center (MBC)University of TorinoTurinItaly
- Department of Oncological SciencesUniversity of TorinoTurinItaly
| | - Elena Quaglino
- Molecular Biotechnology Center (MBC)University of TorinoTurinItaly
- Department of Clinical and Biological SciencesUniversity of TorinoTurinItaly
| | - Marco Forni
- Molecular Biotechnology Center (MBC)University of TorinoTurinItaly
| | - Christian Damasco
- Molecular Biotechnology Center (MBC)University of TorinoTurinItaly
- Department of Genetics, Biology, and BiochemistryUniversity of TorinoTurinItaly
| | - Eva Pinatel
- Molecular Biotechnology Center (MBC)University of TorinoTurinItaly
- Department of Genetics, Biology, and BiochemistryUniversity of TorinoTurinItaly
| | | | - Chiara Romualdi
- Department of Biology and Centro Ricerche Interdepartimentale Biotecnologie Innovative (CRIBI) Biotechnology CenterUniversity of PadovaPaduaItaly
| | - Cathrin Brisken
- National Centers of Competence in Research (NCCR) Molecular OncologyInstitut Suisse de Recherche Expérimentale sur le Cancer (ISREC)School of Life SciencesÉcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Michele De Bortoli
- Department of Oncological SciencesUniversity of TorinoTurinItaly
- Center for Molecular Systems BiologyUniversity of TorinoTurinItaly
| | - Nicoletta Biglia
- Department of Gynecology and ObstetricsUniversity of TorinoTurinItaly
| | - Paolo Provero
- Molecular Biotechnology Center (MBC)University of TorinoTurinItaly
- Department of Genetics, Biology, and BiochemistryUniversity of TorinoTurinItaly
| | - Gerolamo Lanfranchi
- Department of Biology and Centro Ricerche Interdepartimentale Biotecnologie Innovative (CRIBI) Biotechnology CenterUniversity of PadovaPaduaItaly
| | - Daniela Taverna
- Molecular Biotechnology Center (MBC)University of TorinoTurinItaly
- Department of Oncological SciencesUniversity of TorinoTurinItaly
- Center for Molecular Systems BiologyUniversity of TorinoTurinItaly
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Huang K, Mellor KE, Paul SN, Lawson MJ, Mackey AJ, Timko MP. Global changes in gene expression during compatible and incompatible interactions of cowpea (Vigna unguiculata L.) with the root parasitic angiosperm Striga gesnerioides. BMC Genomics 2012; 13:402. [PMID: 22900582 PMCID: PMC3505475 DOI: 10.1186/1471-2164-13-402] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 08/03/2012] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Cowpea, Vigna unguiculata L. Walp., is one of the most important food and forage legumes in the semi-arid tropics. While most domesticated forms of cowpea are susceptible to the root parasitic weed Striga gesnerioides, several cultivars have been identified that show race-specific resistance. Cowpea cultivar B301 contains the RSG3-301 gene for resistance to S. gesnerioides race SG3, but is susceptible to race SG4z. When challenged by SG3, roots of cultivar B301 develop a strong resistance response characterized by a hypersensitive reaction and cell death at the site of parasite attachment. In contrast, no visible response occurs in B301 roots parasitized by SG4z. RESULTS Gene expression in the roots of the cowpea cultivar B301 during compatible (susceptible) and incompatible (resistant) interactions with S. gesnerioides races SG4z and SG3, respectively, were investigated at the early (6 days post-inoculation (dpi)) and late (13 dpi) stages of the resistance response using a Nimblegen custom design cowpea microarray. A total of 111 genes were differentially expressed in B301 roots at 6 dpi; this number increased to 2102 genes at 13 dpi. At 13 dpi, a total of 1944 genes were differentially expressed during compatible (susceptible) interactions of B301 with SG4z. Genes and pathways involved in signal transduction, programmed cell death and apoptosis, and defense response to biotic and abiotic stress were differentially expressed in the early resistance response; at the later time point, enrichment was primarily for defense-related gene expression, and genes encoding components of lignifications and secondary wall formation. In compatible interactions (B301-SG4z), multiple defense pathways were repressed, including those involved in lignin biosynthesis and secondary cell wall modifications, while cellular transport processes for nitrogen and sulfur were increased. CONCLUSION Distinct changes in global gene expression profiles occur in host roots following successful and unsuccessful attempted parasitism by Striga. Induction of specific defense related genes and pathways defines components of a unique resistance mechanism. Some genes and pathways up-regulated in the host resistance response to SG3 are repressed in the susceptible interactions, suggesting that the parasite is targeting specific components of the host's defense. These results add to our understanding of plant-parasite interactions and the evolution of resistance to parasitic weeds.
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Affiliation(s)
- Kan Huang
- Department of Biology, University of Virginia, Gilmer Hall 044, Charlottesville, VA, 22904, USA
| | - Karolina E Mellor
- Department of Biology, University of Virginia, Gilmer Hall 044, Charlottesville, VA, 22904, USA
| | - Shom N Paul
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Mark J Lawson
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Aaron J Mackey
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Michael P Timko
- Department of Biology, University of Virginia, Gilmer Hall 044, Charlottesville, VA, 22904, USA
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Mellor KE, Hoffman AM, Timko MP. Use of ex vitro composite plants to study the interaction of cowpea (Vigna unguiculata L.) with the root parasitic angiosperm Striga gesnerioides. PLANT METHODS 2012; 8:22. [PMID: 22741546 PMCID: PMC3441300 DOI: 10.1186/1746-4811-8-22] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 06/21/2012] [Indexed: 05/29/2023]
Abstract
BACKGROUND Cowpea (Vigna unguiculata L.) is an important grain and forage legume grown throughout sub-Saharan Africa primarily by subsistence farmers on poor, drought prone soils. Genetic improvement of the crop is being actively pursued and numerous functional genomics studies are underway aimed at characterizing gene controlling key agronomic characteristics for disease and pest resistances. Unfortunately, similar to other legumes, efficient plant transformation technology is a rate-limiting step in analysis of gene function in cowpea. RESULTS Here we describe an optimized protocol for the rapid generation of transformed hairy roots on ex vitro composite plants of cowpea using Agrobacterium rhizogenes. We further demonstrate the applicability of cowpea composite plants to study gene expression involved in the resistance response of the plant roots to attack by the root parasitic weed, Striga gesnerioides. The utility of the new system and critical parameters of the method are described and discussed herein. CONCLUSIONS Cowpea composite plants offer a rapid alternative to methods requiring stable transformation and whole plant regeneration for studying gene expression in resistance or susceptibility responses to parasitic weeds. Their use can likely be readily adapted to look at the effects of both ectopic gene overexpression as well as gene knockdown of root associated defense responses and to the study of a broader range of root associated physiological and aphysiological processes including root growth and differentiation as well as interactions with other root pests, parasites, and symbionts.
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Affiliation(s)
- Karolina E Mellor
- Department of Biology, University of Virginia, Gilmer Hall 044, Charlottesville, VA 22903, USA
| | - Ava M Hoffman
- Department of Biology, University of Virginia, Gilmer Hall 044, Charlottesville, VA 22903, USA
| | - Michael P Timko
- Department of Biology, University of Virginia, Gilmer Hall 044, Charlottesville, VA 22903, USA
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Samanta P, Sadhukhan S, Das S, Joshi A, Sen SK, Basu A. Isolation of RNA from field-grown jute (Corchorus capsularis) plant in different developmental stages for effective downstream molecular analysis. Mol Biotechnol 2012; 49:109-15. [PMID: 21327574 DOI: 10.1007/s12033-011-9376-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Jute (Corchorus capsularis), as a natural fibre producing plant species, ranks next to cotton only. Today, biotechnological approach has been considered as most accepted means for any genetic improvement of plant species. However, genetic control of the fibre development in jute has not yet been explored sufficiently for desired genetic improvement. One of the major impediments in exploring the genetic architecture in this crop at molecular level is the availability of good quality RNA from field-grown plant tissues mostly due to the presence of high amount of mucilage and phenolics. Development of a suitable RNA isolation method is becoming essential for deciphering developmental stage-specific gene expression pattern related to fibre formation in this crop species. A combination of modified hot borate buffer followed by isopycnic centrifugation (termed as HBIC) was adopted and found to be the best isolation method yielding sufficient quantity (~350-500 μg/gm fresh tissue) and good quality (A(260/280) ratio 1.88 to 1.91) RNA depending on the developmental stage of stem tissue from field-grown jute plant. The poly A(+) RNA purified from total RNA isolated by the present method was found amenable to efficient RT-PCR and cDNA library construction. The present development of RNA isolation was found to be appropriate for gene expression analysis related to fibre formation in this economically important jute plant in near future.
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Affiliation(s)
- Pradipta Samanta
- Advanced Laboratory for Plant Genetic Engineering, Indian Institute of Technology, Kharagpur 721302, India
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Fan P, Feng J, Jiang P, Chen X, Bao H, Nie L, Jiang D, Lv S, Kuang T, Li Y. Coordination of carbon fixation and nitrogen metabolism in
Salicornia europaea
under salinity: Comparative proteomic analysis on chloroplast proteins. Proteomics 2011; 11:4346-67. [DOI: 10.1002/pmic.201100054] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 08/16/2011] [Accepted: 08/18/2011] [Indexed: 12/30/2022]
Affiliation(s)
- Pengxiang Fan
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P. R. China
| | - Juanjuan Feng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P. R. China
| | - Ping Jiang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P. R. China
| | - Xianyang Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P. R. China
| | - Hexigeduleng Bao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P. R. China
| | - Lingling Nie
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P. R. China
| | - Dan Jiang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P. R. China
| | - Sulian Lv
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P. R. China
| | - Tingyun Kuang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P. R. China
| | - Yinxin Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P. R. China
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Biteau F, Nisse E, Hehn A, Miguel S, Hannewald P, Bourgaud F. A Rapid and Efficient Method for Isolating High Quality DNA from Leaves of Carnivorous Plants from the Drosera Genus. Mol Biotechnol 2011; 51:247-53. [DOI: 10.1007/s12033-011-9462-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Wang X, Xiao H, Chen G, Zhao X, Huang C, Chen C, Wang F. Isolation of high-quality RNA from Reaumuria soongorica, a desert plant rich in secondary metabolites. Mol Biotechnol 2011; 48:165-72. [PMID: 21136208 DOI: 10.1007/s12033-010-9357-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
RNA isolation is a prerequisite for the study of the molecular mechanisms of stress tolerance in the desert plant Reaumuria soongorica, an extreme xeric semi-shrub. However, R. soongorica that contains high levels of secondary metabolites that co-precipitate with RNA, making RNA isolation difficult. Here the authors propose a new protocol suitable for isolating high-quality RNA from the leaves of R. soongorica. Based on a CTAB method described by Liu et al., the protocol has been improved as follows: the samples were ground with PVPP to effectively inhibit the oxidation of phenolics, contaminating DNA was removed with DNase I, and NaAc was used along with ethanol for precipitation to enhance the RNA yield and shorten the precipitation time. Gel electrophoresis and spectrophotometric analysis indicated that this isolation method provides RNA with no DNA contamination. Moreover, the yield (183.79 ± 40.36 μg/g) and quality were superior to those using the method of Liu et al., which yields RNA with significant DNA contamination at 126.30 ± 29.43 μg/g. Gene amplification showed that the RNA obtained using this protocol is suitable for use in downstream molecular procedures. This method was found to work equally well for isolating RNA from other desert plants. Thus, it is likely to be widely applicable.
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Affiliation(s)
- Xiaohua Wang
- Key Laboratory of Ecohydrology and of Inland River Basin, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
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Tong Z, Qu S, Zhang J, Wang F, Tao J, Gao Z, Zhang Z. A Modified Protocol for RNA Extraction from Different Peach Tissues Suitable for Gene Isolation and Real-Time PCR Analysis. Mol Biotechnol 2011; 50:229-36. [DOI: 10.1007/s12033-011-9433-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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de la Cruz-Leyva M, Zamudio-Maya M, Corona-Cruz A, González-de la Cruz J, Rojas-Herrera R. A method for isolating RNA from metabolically active bacterial flora associated with octopus. Lett Appl Microbiol 2011; 53:8-13. [DOI: 10.1111/j.1472-765x.2011.03057.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Ghawana S, Paul A, Kumar H, Kumar A, Singh H, Bhardwaj PK, Rani A, Singh RS, Raizada J, Singh K, Kumar S. An RNA isolation system for plant tissues rich in secondary metabolites. BMC Res Notes 2011; 4:85. [PMID: 21443767 PMCID: PMC3079660 DOI: 10.1186/1756-0500-4-85] [Citation(s) in RCA: 150] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2011] [Accepted: 03/28/2011] [Indexed: 11/30/2022] Open
Abstract
Background Secondary metabolites are reported to interfere with the isolation of RNA particularly with the recipes that use guanidinium-based salt. Such interference was observed in isolation of RNA with medicinal plants rheum (Rheum australe) and arnebia (Arnebia euchroma). A rapid and less cumbersome system for isolation of RNA was essential to facilitate any study related to gene expression. Findings An RNA isolation system free of guanidinium salt was developed that successfully isolated RNA from rheum and arnebia. The method took about 45 min and was successfully evaluated on twenty one tissues with varied secondary metabolites. The A260/280 ratio ranged between 1.8 - 2.0 with distinct 28 S and 18 S rRNA bands visible on a formaldehyde-agarose gel. Conclusions The present manuscript describes a rapid protocol for isolation of RNA, which works well with all the tissues examined so far. The remarkable feature was the success in isolation of RNA with those tissues, wherein the most commonly used methods failed. Isolated RNA was amenable to downstream applications such as reverse transcription-polymerase chain reaction (RT-PCR), differential display (DD), suppression subtractive hybridization (SSH) library construction, and northern hybridization.
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Affiliation(s)
- Sanjay Ghawana
- Biotechnology Division, Institute of Himalayan Bioresource Technology (CSIR), Palampur-176 061, Himachal Pradesh, India.
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High-Quality RNA Preparation from Rhodosporidium toruloides and cDNA Library Construction Therewith. Mol Biotechnol 2010; 47:144-51. [DOI: 10.1007/s12033-010-9322-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Rodríguez-García CM, Peraza-Echeverría L, Islas-Flores IR, Canto-Canché BB, Grijalva-Arango R. Isolation of retro-transcribed RNA from in vitro Mycosphaerella fijiensis-infected banana leaves. GENETICS AND MOLECULAR RESEARCH 2010; 9:1460-8. [PMID: 20677135 DOI: 10.4238/vol9-3gmr865] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
High polyphenol and polysaccharide levels in plant tissues such as banana fruit and leaves constitute a significant challenge to the extraction of sufficient amounts of high-quality RNA required for cDNA library synthesis and molecular analysis. To determine their comparative effectiveness at eliminating polyphenols, polysaccharides and proteins, three protocols for RNA extraction from in vitro banana plantlet leaves were tested: Concert(TM) Plant RNA isolation kit, a small-scale protocol based on Valderrama-Cháirez, and a modified version of the Valderrama-Cháirez protocol. RNA quantity and purity were evaluated by UV-spectrophotometry using DEPC-treated water and Tris-HCl, pH 7.5. Purity was greater using Tris-HCl. The Concert(TM) Plant protocol produced the poorest quality RNA. Reverse transcription into cDNAs from RNA isolated from in vitro banana plantlet leaves infected with Mycosphaerella fijiensis using the modified Valderrama-Cháirez protocol, followed by PCR using primers designed against gamma-actin from banana and M. fijiensis, yielded products of the anticipated size. In addition, this protocol reduced the processing time, lowered costs, used less expensive equipment, and could be used for other plants that have the same problems with high polyphenol and polysaccharide levels.
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Affiliation(s)
- C M Rodríguez-García
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Colonia Chuburná de Hidalgo, Mérida, Yucatán, México
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Das A, Spackman E, Pantin-Jackwood MJ, Suarez DL. Removal of real-time reverse transcription polymerase chain reaction (RT-PCR) inhibitors associated with cloacal swab samples and tissues for improved diagnosis of Avian influenza virus by RT-PCR. J Vet Diagn Invest 2010; 21:771-8. [PMID: 19901277 DOI: 10.1177/104063870902100603] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Real-time reverse transcription polymerase chain reaction (real-time RT-PCR) is routinely used for the rapid detection of Avian influenza virus (AIV) in clinical samples, but inhibitory substances present in some clinical specimens can reduce or block PCR amplification. Most commercial RNA extraction kits have limited capacity to remove inhibitors from clinical samples, but using a modified commercial protocol (Ambion MagMAX, Applied Biosystems, Foster City, CA) with an added high-salt wash of 2 M NaCl and 2 mM ethylenediamine tetra-acetic acid was shown to improve the ability of the kit to remove inhibitors from cloacal swabs and some tissues. Real-time RT-PCR was carried out in the presence of an internal positive control to detect inhibitors present in the purified RNA. Cloacal swabs from wild birds were analyzed by real-time RT-PCR comparing RNA extracted with the standard (MagMAX-S) and modified (MagMAX-M) protocols. Using the standard protocol on 2,668 samples, 18.4% of the samples had evidence of inhibitor(s) in the samples, but the modified protocol removed inhibitors from all but 21 (4.8%) of the problem samples. The modified protocol was also tested for RNA extraction from tissues using a TRIzol-MagMAX-M hybrid protocol. Tissues from chickens and ducks experimentally infected with high-pathogenicity Asian H5N1 AIV were analyzed by real-time RT-PCR, and the limit of detection of the virus was improved by 0.5-3.0 threshold cycle units with the RNA extracted by the MagMAX-M protocol. The MagMAX-M protocol reported in the present study can be useful in extracting high-quality RNA for accurate detection of AIV from cloacal swabs and tissues by real-time RT-PCR.
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Affiliation(s)
- Amaresh Das
- Southeast Poultry Research Laboratory, Agricultural Research Service, USDA, Athens, GA 30605, USA
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Wang X, Fan P, Song H, Chen X, Li X, Li Y. Comparative Proteomic Analysis of Differentially Expressed Proteins in Shoots of Salicornia europaea under Different Salinity. J Proteome Res 2009; 8:3331-45. [DOI: 10.1021/pr801083a] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xuchu Wang
- Research Center for Molecular and Developmental Biology, Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, P.R. China
| | - Pengxiang Fan
- Research Center for Molecular and Developmental Biology, Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, P.R. China
| | - Hongmiao Song
- Research Center for Molecular and Developmental Biology, Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, P.R. China
| | - Xianyang Chen
- Research Center for Molecular and Developmental Biology, Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, P.R. China
| | - Xiaofang Li
- Research Center for Molecular and Developmental Biology, Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, P.R. China
| | - Yinxin Li
- Research Center for Molecular and Developmental Biology, Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, P.R. China
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Li R, Mock R, Huang Q, Abad J, Hartung J, Kinard G. A reliable and inexpensive method of nucleic acid extraction for the PCR-based detection of diverse plant pathogens. J Virol Methods 2008; 154:48-55. [DOI: 10.1016/j.jviromet.2008.09.008] [Citation(s) in RCA: 170] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2008] [Revised: 09/09/2008] [Accepted: 09/11/2008] [Indexed: 11/25/2022]
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