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Mandaliya VB, Bhatt P, Thaker VS. High quality RNA extraction protocol for polyphenolics-rich Cotton tissue. Anal Biochem 2024; 694:115604. [PMID: 38986795 DOI: 10.1016/j.ab.2024.115604] [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] [Received: 03/24/2024] [Revised: 06/22/2024] [Accepted: 07/07/2024] [Indexed: 07/12/2024]
Abstract
The extraction of high-quality RNA from cotton (Gossypium spp.) is challenging because of the presence of high polyphenolics, polysaccharides, quinones, and other secondary metabolites. A high-throughput RNA extraction protocol is a prerequisite. This Triton-X-100-based RNA extraction method utilizes Polyvinyl pyrrolidone polymer (PVPP) treatment which efficiently removes phenolics, and the application of Lithium chloride (LiCl) has been found that successfully precipitated the high-quality RNA from cotton tissue. Cytoplasmic male sterility (CMS) is a maternally inherited trait associated with specific mitochondrial genome rearrangements or mutations. The suitability of RNA extracted from Cotton CMS lines was assessed. cDNA was synthesized from RNA and assayed for mitochondrial genes (cox3, nad3, nad9) associated with male sterility. This paper discuss the advantages and limitation of this protocol over existing protocol for RNA extraction for polyphenolics-rich plant tissue.
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Affiliation(s)
- Viralkumar B Mandaliya
- Centre for Advanced Studies in Plant Biotechnology and Genetic Engineering (CPBGE), Department of Biosciences, Saurashtra University, Rajkot, 360 005, Gujarat, India; Department of Microbiology, Faculty of Science, Marwadi University, Rajkot, 360 003, Gujarat, India.
| | - Pritesh Bhatt
- Centre for Advanced Studies in Plant Biotechnology and Genetic Engineering (CPBGE), Department of Biosciences, Saurashtra University, Rajkot, 360 005, Gujarat, India; Virus Research and Diagnostic Laboratory (VRDL), All India Institute of Medical Sciences (AIIMS), Rajkot, Gujarat, India.
| | - Vrinda S Thaker
- Centre for Advanced Studies in Plant Biotechnology and Genetic Engineering (CPBGE), Department of Biosciences, Saurashtra University, Rajkot, 360 005, Gujarat, India.
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Vicentin L, Canales J, Calderini DF. The trade-off between grain weight and grain number in wheat is explained by the overlapping of the key phases determining these major yield components. FRONTIERS IN PLANT SCIENCE 2024; 15:1380429. [PMID: 38919825 PMCID: PMC11196766 DOI: 10.3389/fpls.2024.1380429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 05/20/2024] [Indexed: 06/27/2024]
Abstract
Enhancing grain yield is a primary goal in the cultivation of major staple crops, including wheat. Recent research has focused on identifying the physiological and molecular factors that influence grain weight, a critical determinant of crop yield. However, a bottleneck has arisen due to the trade-off between grain weight and grain number, whose underlying causes remain elusive. In a novel approach, a wheat expansin gene, TaExpA6, known for its expression in root tissues, was engineered to express in the grains of the spring wheat cultivar Fielder. This modification led to increases in both grain weight and yield without adversely affecting grain number. Conversely, a triple mutant line targeting the gene TaGW2, a known negative regulator of grain weight, resulted in increased grain weight but decreased grain number, potentially offsetting yield gains. This study aimed to evaluate the two aforementioned modified wheat genotypes (TaExpA6 and TaGW2) alongside their respective wild-type counterparts. Conducted in southern Chile, the study employed a Complete Randomized Block Design with four replications, under well-managed field conditions. The primary metrics assessed were grain yield, grain number, and average grain weight per spike, along with detailed measurements of grain weight and dimensions across the spike, ovary weight at pollination (Waddington's scale 10), and post-anthesis expression levels of TaExpA6 and TaGW2. Results indicated that both the TaExpA6 and the triple mutant lines achieved significantly higher average grain weights compared to their respective wild types. Notably, the TaExpA6 line did not exhibit a reduction in grain number, thereby enhancing grain yield per spike. By contrast, the triple mutant line showed a reduced grain number per spike, with no significant change in overall yield. TaExpA6 expression peaked at 10 days after anthesis (DAA), and its effect on grain weight over the WT became apparent after 15 DAA. In contrast, TaGW2 gene disruption in the triple mutant line increased ovary size at anthesis, leading to improved grain weight above the WT from the onset of grain filling. These findings suggest that the trade-off between grain weight and number could be attributed to the overlapping of the critical periods for the determination of these traits.
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Affiliation(s)
- Lucas Vicentin
- Graduate School, Faculty of Agricultural Science, Universidad Austral de Chile, Valdivia, Chile
- Institute of Plant Production and Protection, Universidad Austral de Chile, Valdivia, Chile
| | - Javier Canales
- Institute of Biochemistry and Microbiology, Universidad Austral de Chile, Valdivia, Chile
- National Agency for Research and Development of Chile-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Daniel F. Calderini
- Institute of Plant Production and Protection, Universidad Austral de Chile, Valdivia, Chile
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Sasi S, Krishnan S, Kodackattumannil P, Shamisi AA, Aldarmaki M, Lekshmi G, Kottackal M, Amiri KMA. DNA-free high-quality RNA extraction from 39 difficult-to-extract plant species (representing seasonal tissues and tissue types) of 32 families, and its validation for downstream molecular applications. PLANT METHODS 2023; 19:84. [PMID: 37568159 PMCID: PMC10416385 DOI: 10.1186/s13007-023-01063-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023]
Abstract
BACKGROUND High-purity RNA serves as the basic requirement for downstream molecular analysis of plant species, especially the differential expression of genes to various biotic and abiotic stimuli. But, the extraction of high-quality RNA is usually difficult from plants rich in polysaccharides and polyphenols, and their presence usually interferes with the downstream applications. The aim of the study is to optimize the extraction of high-quality RNA from diverse plant species/tissues useful for downstream molecular applications. RESULTS Extraction of RNA using commercially available RNA extraction kits and routine hexadecyltrimethylammonium bromide (CTAB) methods did not yield good quality DNA-free RNA from Prosopis cineraria, Conocarpus erectus, and Phoenix dactylifera. A reliable protocol for the extraction of high-quality RNA from mature leaves of these difficult-to-extract trees was optimized after screening nine different methods. The DNase I-, and proteinase K treatment-free modified method, consisting of extraction with CTAB method followed by TRIzol, yielded high-quality DNA-free RNA with an A260/A280 and A260/A230 ratios > 2.0. Extraction of RNA from Conocarpus, the most difficult one, was successful by avoiding the heat incubation of ground tissue in a buffer at 65 oC. Pre-warming of the buffer for 5-10 min was sufficient to extract good-quality RNA. RNA integrity number of the extracted RNA samples ranged between 7 and 9.1, and the gel electrophoresis displayed intact bands of 28S and 18S RNA. A cDNA library constructed from the RNA of P. cineraria was used for the downstream applications. Real-time qPCR analysis using the cDNA from P. cineraria RNA confirmed the quality. The extraction of good quality RNA from samples of the desert-growing P. cineraria (> 20-years-old) collected in alternate months of the year 2021 (January to December covering winter, spring, autumn, and the very dry and hot summer) proved the efficacy of the protocol. The protocol's broad applicability was further validated by extracting good-quality RNA from 36 difficult-to-extract plant species, including tissues such as roots, flowers, floral organs, fruits, and seeds. CONCLUSIONS The modified DNase I and Proteinase K treatment-free protocol enables to extract DNA-free, high-quality, intact RNA from a total of 39 difficult-to-extract plant species belonging to 32 angiosperm families is useful to extract good-quality RNA from dicots and monocots irrespective of tissue types and growing seasons.
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Affiliation(s)
- Shina Sasi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Saranya Krishnan
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Preshobha Kodackattumannil
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Aysha Al Shamisi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Maitha Aldarmaki
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Geetha Lekshmi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Martin Kottackal
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates.
| | - Khaled M A Amiri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates.
- Department of Biology, College of Science, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates.
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Nath O, Fletcher SJ, Hayward A, Shaw LM, Agarwal R, Furtado A, Henry RJ, Mitter N. A Comprehensive High-Quality DNA and RNA Extraction Protocol for a Range of Cultivars and Tissue Types of the Woody Crop Avocado. PLANTS 2022; 11:plants11030242. [PMID: 35161230 PMCID: PMC8838124 DOI: 10.3390/plants11030242] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 01/11/2023]
Abstract
High-quality DNA and RNA forms the basis of genomic and genetic investigations. The extraction of DNA and RNA from woody trees, like avocado (Persea americana Mill.), is challenging due to compounds which interact with nucleic acids and influence separation. Previously reported methods of DNA and RNA extraction from avocado have issues of low yield, quality and applicability across different cultivars and tissue types. In the current study, methods have been optimised for high-quality DNA extraction from 40 avocado cultivars and RNA extraction from multiple tissue types, including roots, stem, leaves, flowers and fruits. The method is based on the modification of the cetyltrimethylammonium bromide buffer, centred around the specific optimisation of chemicals, such as sodium dodecyl sulphate, polyvinylpyrrolidone, sodium sulphite, polyethylene glycol and β-mercaptoethanol. The DNA extraction method yielded high-molecular weight DNA from the leaf tissue of 40 avocado cultivars belonging to Mexican, Guatemalan and West Indian avocado horticultural groups. The method was further optimised for RNA extraction from different avocado plant parts, enabling extraction using amounts as low as ~10 mg of starting material. The DNA and RNA extracted was successfully used for long- and short-read sequencing and gene expression analysis. The methods developed may also be applicable to other recalcitrant plant species.
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Cárdenas Espinosa MJ, Schmidgall T, Wagner G, Kappelmeyer U, Schreiber S, Heipieper HJ, Eberlein C. An optimized method for RNA extraction from the polyurethane oligomer degrading strain Pseudomonas capeferrum TDA1 growing on aromatic substrates such as phenol and 2,4-diaminotoluene. PLoS One 2021; 16:e0260002. [PMID: 34780548 PMCID: PMC8592408 DOI: 10.1371/journal.pone.0260002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/30/2021] [Indexed: 11/18/2022] Open
Abstract
Bacterial degradation of xenobiotic compounds is an intense field of research already for decades. Lately, this research is complemented by downstream applications including Next Generation Sequencing (NGS), RT-PCR, qPCR, and RNA-seq. For most of these molecular applications, high-quality RNA is a fundamental necessity. However, during the degradation of aromatic substrates, phenolic or polyphenolic compounds such as polycatechols are formed and interact irreversibly with nucleic acids, making RNA extraction from these sources a major challenge. Therefore, we established a method for total RNA extraction from the aromatic degrading Pseudomonas capeferrum TDA1 based on RNAzol® RT, glycogen and a final cleaning step. It yields a high-quality RNA from cells grown on TDA1 and on phenol compared to standard assays conducted in the study. To our knowledge, this is the first report tackling the problem of polyphenolic compound interference with total RNA isolation in bacteria. It might be considered as a guideline to improve total RNA extraction from other bacterial species.
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Affiliation(s)
| | - Tabea Schmidgall
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Georg Wagner
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Uwe Kappelmeyer
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Stephan Schreiber
- Department Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Hermann J. Heipieper
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Christian Eberlein
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
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The First De Novo Transcriptome Assembly and Transcriptomic Dynamics of the Mangrove Tree Rhizophora stylosa Griff. (Rhizophoraceae). Int J Mol Sci 2021; 22:ijms222111964. [PMID: 34769393 PMCID: PMC8584393 DOI: 10.3390/ijms222111964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 10/30/2021] [Accepted: 11/02/2021] [Indexed: 12/13/2022] Open
Abstract
Mangroves are salt-tolerant plant species that grow in coastal saline water and are adapted to harsh environmental conditions. In this study, we de novo assembled and functionally annotated the transcriptome of Rhizophora stylosa, the widely distributed mangrove from the largest mangrove family (Rhizophoraceae). The final transcriptome consists of 200,491 unigenes with an average length, and N50 of 912.7 and 1334 base pair, respectively. We then compared the genome-wide expression profiles between the two morphologically distinct natural populations of this species growing under different levels of salinity depending on their distance from the ocean. Among the 200,491 unigenes, 40,253 were identified as differentially expressed between the two populations, while 15,741 and 24,512 were up- and down-regulated, respectively. Functional annotation assigned thousands of upregulated genes in saline environment to the categories related to abiotic stresses such as response to salt-, osmotic-, and oxidative-stress. Validation of those genes may contribute to a better understanding of adaptation in mangroves species. This study reported, for the first time, the transcriptome of R. stylosa, and the dynamic of it in response to salt stress and provided a valuable resource for elucidation of the molecular mechanism underlying the salt stress response in mangroves and other plants that live under stress.
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De Novo Transcriptome Assembly, Functional Annotation, and Transcriptome Dynamics Analyses Reveal Stress Tolerance Genes in Mangrove Tree ( Bruguiera gymnorhiza). Int J Mol Sci 2021; 22:ijms22189874. [PMID: 34576037 PMCID: PMC8467813 DOI: 10.3390/ijms22189874] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/09/2021] [Accepted: 09/11/2021] [Indexed: 12/13/2022] Open
Abstract
Their high adaptability to difficult coastal conditions makes mangrove trees a valuable resource and an interesting model system for understanding the molecular mechanisms underlying stress tolerance and adaptation of plants to the stressful environmental conditions. In this study, we used RNA sequencing (RNA-Seq) for de novo assembling and characterizing the Bruguiera gymnorhiza (L.) Lamk leaf transcriptome. B. gymnorhiza is one of the most widely distributed mangrove species from the biggest family of mangroves; Rhizophoraceae. The de novo assembly was followed by functional annotations and identification of individual transcripts and gene families that are involved in abiotic stress response. We then compared the genome-wide expression profiles between two populations of B. gymnorhiza, growing under different levels of stress, in their natural habitats. One population living in high salinity environment, in the shore of the Pacific Ocean- Japan, and the other population living about one kilometre farther from the ocean, and next to the estuary of a river; in less saline and more brackish condition. Many genes involved in response to salt and osmotic stress, showed elevated expression levels in trees growing next to the ocean in high salinity condition. Validation of these genes may contribute to future salt-resistance research in mangroves and other woody plants. Furthermore, the sequences and transcriptome data provided in this study are valuable scientific resources for future comparative transcriptome research in plants growing under stressful conditions.
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Chacuttayapong W, Enoki H, Nabetani Y, Matsui M, Oguchi T, Motohashi R. Transformation of Jatropha curcas L. for production of larger seeds and increased amount of biodiesel. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2021; 38:247-256. [PMID: 34393603 PMCID: PMC8329273 DOI: 10.5511/plantbiotechnology.21.0422b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/22/2021] [Indexed: 06/13/2023]
Abstract
The development of green energy is important to mitigate global warming. Jatropha (Jatropha curcas L.) is a promising candidate for the production of alternative biofuel, which could reduce the burden on the Earth's resources. Jatropha seeds contain a large quantity of lipids that can be used to produce biofuel, and the rest of the plant has many other uses. Currently, techniques for plant genetic transformation are extensively employed to study, create, and improve the specific characteristics of the target plant. Successful transformation involves the alteration of plants and their genetic materials. The aim of this study was to generate Jatropha plants that can support biofuel production by increasing their seed size using genes found via the rice FOX-hunting system. The present study improved previous protocols, enabling the production of transgenic Jatropha in two steps: the first step involved using auxins and dark incubation to promote root formation in excised shoots and the second step involved delaying the timing of antibiotic selection in the cultivation medium. Transgenic plants were subjected to PCR analysis; the transferred gene expression was confirmed via RT-PCR and the ploidy level was investigated. The results suggest that the genes associated with larger seed size in Arabidopsis thaliana, which were found using the rice FOX-hunting system, produce larger seeds in Jatropha.
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Affiliation(s)
- Wiluk Chacuttayapong
- Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Shizuoka 422-8529, Japan
| | - Harumi Enoki
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Shizuoka 422-8529, Japan
| | - Yusei Nabetani
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Shizuoka 422-8529, Japan
| | - Minami Matsui
- Synthetic Genomics Research group, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Taichi Oguchi
- Tsukuba Plant‐Innovation Research Center, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8572, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8572, Japan
| | - Reiko Motohashi
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Shizuoka 422-8529, Japan
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Shizuoka 422-8529, Japan
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9
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Calderini DF, Castillo FM, Arenas‐M A, Molero G, Reynolds MP, Craze M, Bowden S, Milner MJ, Wallington EJ, Dowle A, Gomez LD, McQueen‐Mason SJ. Overcoming the trade-off between grain weight and number in wheat by the ectopic expression of expansin in developing seeds leads to increased yield potential. THE NEW PHYTOLOGIST 2021; 230:629-640. [PMID: 33124693 PMCID: PMC8048851 DOI: 10.1111/nph.17048] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/21/2020] [Indexed: 05/19/2023]
Abstract
Wheat is the most widely grown crop globally, providing 20% of all human calories and protein. Achieving step changes in genetic yield potential is crucial to ensure food security, but efforts are thwarted by an apparent trade-off between grain size and number. Expansins are proteins that play important roles in plant growth by enhancing stress relaxation in the cell wall, which constrains cell expansion. Here, we describe how targeted overexpression of an α-expansin in early developing wheat seeds leads to a significant increase in grain size without a negative effect on grain number, resulting in a yield boost under field conditions. The best-performing transgenic line yielded 12.3% higher average grain weight than the control, and this translated to an increase in grain yield of 11.3% in field experiments using an agronomically appropriate plant density. This targeted transgenic approach provides an opportunity to overcome a common bottleneck to yield improvement across many crops.
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Affiliation(s)
- Daniel F. Calderini
- Institute of Plant Production and ProtectionUniversidad Austral de ChileCampus Isla TejaValdivia5090000Chile
| | - Francisca M. Castillo
- Institute of Plant Production and ProtectionUniversidad Austral de ChileCampus Isla TejaValdivia5090000Chile
- Institute of Biochemistry and MicrobiologyFaculty of SciencesUniversidad Austral de ChileValdivia5090000Chile
| | - Anita Arenas‐M
- Institute of Plant Production and ProtectionUniversidad Austral de ChileCampus Isla TejaValdivia5090000Chile
- Institute of Biochemistry and MicrobiologyFaculty of SciencesUniversidad Austral de ChileValdivia5090000Chile
| | - Gemma Molero
- International Maize and Wheat Improvement Center (CIMMYT)El BatánTexcocoCP 56237Mexico
| | - Matthew P. Reynolds
- International Maize and Wheat Improvement Center (CIMMYT)El BatánTexcocoCP 56237Mexico
| | | | | | | | | | - Adam Dowle
- CNAPBiology DepartmentUniversity of YorkWentworth Way, HeslingtonYorkYO10 5YWUK
| | - Leonardo D. Gomez
- CNAPBiology DepartmentUniversity of YorkWentworth Way, HeslingtonYorkYO10 5YWUK
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Cervera A, de la Peña M. Cloning and Detection of Genomic Retrozymes and Their circRNA Intermediates. Methods Mol Biol 2021; 2167:27-44. [PMID: 32712913 DOI: 10.1007/978-1-0716-0716-9_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Retrozymes are a novel family of non-autonomous retrotransposable elements that contain hammerhead ribozyme motifs. These retroelements are found widespread in eukaryotic genomes, with active copies present in many species, which rely on other autonomous transposons for mobilization. Contrary to other retrotransposons, transcription of retrozymes in vivo leads to the formation and accumulation of circular RNAs, which can be readily detected by RNA blotting. In this chapter, we describe the procedures needed to carry out the cloning of genomic retrozymes, and to detect by northern blot their circular RNA retrotransposition intermediates.
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Affiliation(s)
- Amelia Cervera
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València (CSIS-UPV), Valencia, Spain
| | - Marcos de la Peña
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València (CSIS-UPV), Valencia, Spain.
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11
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A rapid RNA extraction method from oil palm tissues suitable for reverse transcription quantitative real-time PCR (RT-qPCR). 3 Biotech 2020; 10:530. [PMID: 33214977 DOI: 10.1007/s13205-020-02514-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 10/27/2020] [Indexed: 10/23/2022] Open
Abstract
Cetyltrimethylammonium bromide (CTAB) is the preferred detergent in RNA extraction of oil palm tissues. However, the CTAB-based protocol is time-consuming. In this study, a combination of the CTAB-based method and silica-based purification reduced the extraction time from two days to five hours. Quality of total RNA from 27 different tissues of oil palm was shown to have an RNA integrity number (RIN) value of more than seven. The extracted RNA was evaluated by RT-qPCR using three reference oil palm genes (GRAS, CYP2, and SLU7) and three putative mesocarp-specific transcripts annotated as WRKY DNA-binding protein 70 (WRKY-70), metallothionein (MT) and pentatricopeptide repeat (PPR) genes. Tissue-specific expression profiling across complete developmental stages of mesocarp and vegetative tissues was determined in this study. Overall, the RNA extraction protocol described here is rapid, simple and yields good quality RNAs from oil palm tissues.
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Ting NC, Sherbina K, Khoo JS, Kamaruddin K, Chan PL, Chan KL, Halim MAA, Sritharan K, Yaakub Z, Mayes S, Massawe F, Chang PL, Nuzhdin SV, Sambanthamurthi R, Singh R. Expression of fatty acid and triacylglycerol synthesis genes in interspecific hybrids of oil palm. Sci Rep 2020; 10:16296. [PMID: 33004875 PMCID: PMC7529811 DOI: 10.1038/s41598-020-73170-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 08/10/2020] [Indexed: 11/09/2022] Open
Abstract
Evaluation of transcriptome data in combination with QTL information has been applied in many crops to study the expression of genes responsible for specific phenotypes. In oil palm, the mesocarp oil extracted from E. oleifera × E. guineensis interspecific hybrids is known to have lower palmitic acid (C16:0) content compared to pure African palms. The present study demonstrates the effectiveness of transcriptome data in revealing the expression profiles of genes in the fatty acid (FA) and triacylglycerol (TAG) biosynthesis processes in interspecific hybrids. The transcriptome assembly yielded 43,920 putative genes of which a large proportion were homologous to known genes in the public databases. Most of the genes encoding key enzymes involved in the FA and TAG synthesis pathways were identified. Of these, 27, including two candidate genes located within the QTL associated with C16:0 content, showed differential expression between developmental stages, populations and/or palms with contrasting C16:0 content. Further evaluation using quantitative real-time PCR revealed that differentially expressed patterns are generally consistent with those observed in the transcriptome data. Our results also suggest that different isoforms are likely to be responsible for some of the variation observed in FA composition of interspecific hybrids.
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Affiliation(s)
- Ngoot-Chin Ting
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia.,Biotechnology Research Centre, School of Biosciences, University of Nottingham Malaysia Campus, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Katrina Sherbina
- Quantitative and Computational Biology Section, University of Southern California, 1050 Childs Way, Los Angeles, CA, USA
| | - Jia-Shiun Khoo
- Codon Genomics Sdn. Bhd. Malaysia, No. 26, Jalan Dutamas 7, Taman Dutamas, Balakong, 43200, Seri Kembangan, Selangor, Malaysia
| | - Katialisa Kamaruddin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
| | - Pek-Lan Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
| | - Kuang-Lim Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
| | - Mohd Amin Ab Halim
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
| | - Kandha Sritharan
- United Plantations Bhd, Jendarata Estate, 36009, Teluk Intan, Perak, Malaysia
| | - Zulkifli Yaakub
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
| | - Sean Mayes
- Plant and Crop Sciences, Sutton Bonington Campus, Sutton Bonington, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Festo Massawe
- Biotechnology Research Centre, School of Biosciences, University of Nottingham Malaysia Campus, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Peter L Chang
- Molecular and Computational Biology Section, University of Southern California, 1050 Childs Way, Los Angeles, CA, USA
| | - Sergey V Nuzhdin
- Molecular and Computational Biology Section, University of Southern California, 1050 Childs Way, Los Angeles, CA, USA
| | - Ravigadevi Sambanthamurthi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
| | - Rajinder Singh
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia.
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13
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De Wever J, Tulkens D, Verwaeren J, Everaert H, Rottiers H, Dewettinck K, Lefever S, Messens K. A Combined RNA Preservation and Extraction Protocol for Gene Expression Studies in Cacao Beans. FRONTIERS IN PLANT SCIENCE 2020; 11:992. [PMID: 32695136 PMCID: PMC7338848 DOI: 10.3389/fpls.2020.00992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 06/17/2020] [Indexed: 05/23/2023]
Abstract
Despite the high economic importance of cacao beans, few RNA-based studies have been conducted on this plant material and hence no optimal RNA-extraction has been reported. Moreover, extraction of high-quality RNA from recalcitrant cacao bean tissue has shown many difficulties and requires optimization. Furthermore, cacao beans are mostly found at remote and under-resourced locations, which pressures the outsourcing of such analysis and thereby demands RNA-stable preservation and transportation of cacao beans. This study aims to select an appropriate RNA extraction and preservation/transportation method for cacao beans. For this purpose, three sample homogenization and five extraction protocols on cacao beans were compared. In addition, 13 preservation conditions-differing in tissue crushing degree, preservation method, duration, and temperature-were compared and evaluated. A comparative analysis revealed that CTAB-based homogenization and extraction outcompeted all tested commercial protocols in RNA yield and integrity, respectively. Preservation at -80°C affected RNA quality the least, whereas freeze-drying was most suitable for transportation at room temperature for maximum 1 week. The cacao bean RNA obtained from the selected methods were compatible for downstream applications. The results of this study will facilitate on-field sampling and transportation of genetically sensitive cacao material prior to cacao bean transcriptomic studies. In addition, valuable insights on sample homogenization, extraction, preservation, and transportation have been provided, which is of interest to every plant geneticist.
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Affiliation(s)
- Jocelyn De Wever
- Research Unit Molecular Biotechnology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
| | - Dieter Tulkens
- Research Unit Molecular Biotechnology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
| | - Jan Verwaeren
- Research Unit Knowledge-based Systems (KERMIT), Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Helena Everaert
- Research Unit Molecular Biotechnology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Food Structure & Function Research Group (FSF), Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Hayley Rottiers
- Research Unit Molecular Biotechnology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Food Structure & Function Research Group (FSF), Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Koen Dewettinck
- Food Structure & Function Research Group (FSF), Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Steve Lefever
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Bioinformatics Institute Ghent (BIG), Ghent University, Ghent, Belgium
| | - Kathy Messens
- Research Unit Molecular Biotechnology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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14
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Govender N, Senan S, Mohamed-Hussein ZA, Isa MNM, Yaakob Z, Ratnam W. RNA-seq data of the Jatropha curcas L. shoot system. Data Brief 2018; 21:71-74. [PMID: 30338276 PMCID: PMC6187019 DOI: 10.1016/j.dib.2018.09.081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 06/21/2018] [Accepted: 09/26/2018] [Indexed: 11/19/2022] Open
Abstract
Jatropha curcas L. or the physic nut is a monoecious shrub belonging to the Euphorbiaceae family. The plant is an ideal feedstock for biodiesel production; oil-rich seed (37–42%), has a broad range of growth habitat such as arid, semi-arid and tropical and a relatively feasible process for conversion of crude oil into biodiesel. The major constraint affecting the success of large-scale J. curcas plantation is seed yield inconsistency. Numerous research projects conducted on J. curcas with integrated genetic, genomic and transcriptomic approaches have been applied on the leaf, apical meristem, flower, root and fruit tissues. However, to date, no genomics data of J. curcas shoot system are publicly available, despite its importance in understanding flowering, fruiting and seed set qualities targeted for yield improvement. Here, we present eighteen sets of shoot and inflorescence transcriptomes generated from J. curcas plants with contrasting yields. Raw reads of the RNA-seq data are found in NCBI׳s Sequence Read Archive (SRA) database with the accession number SRP090662 (https://www.ncbi.nlm.nih.gov/sra/?term=SRP090662). This transcriptomic data could be integrated with the present genomic resources for in depth understanding of J. curcas reproductive system.
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Affiliation(s)
- Nisha Govender
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, 43600 Bangi, Selangor, Malaysia
- Center for Bioinformatics Research, Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM, 43600 Bangi, Selangor, Malaysia
- Corresponding author at: School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, 43600 Bangi, Selangor, Malaysia.
| | - Siju Senan
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, 43600 Bangi, Selangor, Malaysia
| | - Zeti-Azura Mohamed-Hussein
- Center for Bioinformatics Research, Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM, 43600 Bangi, Selangor, Malaysia
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, 43600 Bangi, Selangor, Malaysia
| | - Mohd Noor Mat Isa
- Malaysia Genome Institute, National Institutes of Biotechnology Malaysia, Ministry of Science, Technology and Innovation, Jalan Bangi, 43000 Kajang, Selangor, Malaysia
| | - Zahira Yaakob
- Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, UKM, 43600 Bangi, Selangor, Malaysia
| | - Wickneswari Ratnam
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, 43600 Bangi, Selangor, Malaysia
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15
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Govender N, Senan S, Sage EE, Mohamed-Hussein ZA, Mackeen MM, Wickneswari R. An integration of phenotypic and transcriptomic data analysis reveals yield-related hub genes in Jatropha curcas inflorescence. PLoS One 2018; 13:e0203441. [PMID: 30240391 PMCID: PMC6150480 DOI: 10.1371/journal.pone.0203441] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 08/21/2018] [Indexed: 02/07/2023] Open
Abstract
Jatropha curcas is an oil-rich seed crop with huge potentials for bioenergy production. The inflorescence carries a number of processes that are likely to affect the overall yield potentials; floral development, male-to-female flower ratio, floral abscission and fruit set. In this study, a weighted gene co-expression network analysis which integrates the transcriptome, physical and simple sugar data of J. curcas inflorescence was performed and nine modules were identified by means of hierarchical clustering. Among them, four modules (green4, antiquewhite2, brown2 and lightskyblue4) showed significant correlation to yield factors at p≤0.01. The four modules are categorized into two clusters; cluster 1 of green4 and antiquewhite2 modules correspond to number of flowers/inflorescence, total seed weight/plant, number of seeds/plant, and number of fruits/plant, whereas cluster 2 of brown2 and lightskyblue4 modules correspond to glucose and fructose. Descriptive characterizations of cluster 1 show putative involvement in gibberellin signaling and responses, whereas cluster 2 may have been involved in sugar signaling, signal transductions and regulation of flowerings. Our findings present a list of hub genes for J. curcas yield improvement and reproductive biology enhancement strategies.
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Affiliation(s)
- Nisha Govender
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
| | - Siju Senan
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
| | - Edison Eukun Sage
- School of Chemical Sciences and Food Technology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
| | - Zeti-Azura Mohamed-Hussein
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
| | - Mukram Mohamed Mackeen
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
- School of Chemical Sciences and Food Technology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
| | - Ratnam Wickneswari
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
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16
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Pertl-Obermeyer H, Lackner P, Schulze WX, Hoepflinger MC, Hoeftberger M, Foissner I, Obermeyer G. Dissecting the subcellular membrane proteome reveals enrichment of H+ (co-)transporters and vesicle trafficking proteins in acidic zones of Chara internodal cells. PLoS One 2018; 13:e0201480. [PMID: 30157181 PMCID: PMC6114288 DOI: 10.1371/journal.pone.0201480] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 07/16/2018] [Indexed: 02/06/2023] Open
Abstract
The Characeae are multicellular green algae with very close relationship to land plants. Their internodal cells have been the subject of numerous (electro-)physiological studies. When exposed to light, internodal cells display alternating bands of low and high pH along their surface in order to facilitate carbon uptake required for photosynthesis. Here we investigated for the first time the subcellular membrane protein composition of acidic and alkaline regions in internodal cells of Chara australis R. Br. using MS-proteomics. The identified peptides were annotated to Chara unigenes using a custom-made Chara database generated from a transcriptome analysis and to orthologous Arabidopsis genes using TAIR (The Arabidopsis Information Resource) database. Apart from providing the first public-available, functionally-annotated sequence database for Chara australis, the proteome study, which is supported by immunodetection, identified several membrane proteins associated with acidic regions that contain a high density of specific plasma membrane (PM) invaginations, the charasomes, which locally increase the membrane area to overcome diffusion limitation in membrane transport. An increased abundance of PM H+ ATPases at charasomes is consistent with their role in the acidification of the environment, but the characean PM H+ ATPase sequence suggests a different regulation compared to higher plant PM H+ ATPases. A higher abundance of H+ co-transporters in the charasome-rich, acidic regions possibly reflects enhanced uptake of ions and nutrients. The increase in mitochondrial proteins confirms earlier findings about the accumulation of cortical mitochondria in the acidic zones. The significant enrichment of clathrin heavy chains and clathrin adaptor proteins as well as other proteins involved in trafficking indicate a higher activity of membrane transport in the charasome-rich than in charasome-poor areas. New and unexpected data, for instance the upregulation and abundance of vacuolar transporters correlating with the charasome-rich, acidic cell regions account for new perspectives in the formation of charasomes.
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Affiliation(s)
- Heidi Pertl-Obermeyer
- Molecular Plant Biophysics and Biochemistry, Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Peter Lackner
- Bioinformatics of Allergens, Department of Biosciences, University of Salzburg, Salzburg, Austria
| | | | - Marion C. Hoepflinger
- Plant Cell Dynamics, Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Margit Hoeftberger
- Plant Cell Dynamics, Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Ilse Foissner
- Plant Cell Dynamics, Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Gerhard Obermeyer
- Molecular Plant Biophysics and Biochemistry, Department of Biosciences, University of Salzburg, Salzburg, Austria
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17
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Govender N, Senan S, Mohamed-Hussein ZA, Wickneswari R. A gene co-expression network model identifies yield-related vicinity networks in Jatropha curcas shoot system. Sci Rep 2018; 8:9211. [PMID: 29907786 PMCID: PMC6003958 DOI: 10.1038/s41598-018-27493-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 06/04/2018] [Indexed: 11/18/2022] Open
Abstract
The plant shoot system consists of reproductive organs such as inflorescences, buds and fruits, and the vegetative leaves and stems. In this study, the reproductive part of the Jatropha curcas shoot system, which includes the aerial shoots, shoots bearing the inflorescence and inflorescence were investigated in regard to gene-to-gene interactions underpinning yield-related biological processes. An RNA-seq based sequencing of shoot tissues performed on an Illumina HiSeq. 2500 platform generated 18 transcriptomes. Using the reference genome-based mapping approach, a total of 64 361 genes was identified in all samples and the data was annotated against the non-redundant database by the BLAST2GO Pro. Suite. After removing the outlier genes and samples, a total of 12 734 genes across 17 samples were subjected to gene co-expression network construction using petal, an R library. A gene co-expression network model built with scale-free and small-world properties extracted four vicinity networks (VNs) with putative involvement in yield-related biological processes as follow; heat stress tolerance, floral and shoot meristem differentiation, biosynthesis of chlorophyll molecules and laticifers, cell wall metabolism and epigenetic regulations. Our VNs revealed putative key players that could be adapted in breeding strategies for J. curcas shoot system improvements.
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Affiliation(s)
- Nisha Govender
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia.
- Center for Bioinformatics Research, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia.
| | - Siju Senan
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Zeti-Azura Mohamed-Hussein
- Center for Bioinformatics Research, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Ratnam Wickneswari
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
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18
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Li R, Reddy VA, Jin J, Rajan C, Wang Q, Yue G, Lim CH, Chua NH, Ye J, Sarojam R. Comparative transcriptome analysis of oil palm flowers reveals an EAR-motif-containing R2R3-MYB that modulates phenylpropene biosynthesis. BMC PLANT BIOLOGY 2017; 17:219. [PMID: 29169327 PMCID: PMC5701422 DOI: 10.1186/s12870-017-1174-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 11/13/2017] [Indexed: 05/14/2023]
Abstract
BACKGROUND Oil palm is the most productive oil crop and the efficiency of pollination has a direct impact on the yield of oil. Pollination by wind can occur but maximal pollination is mediated by the weevil E. kamerunicus. These weevils complete their life cycle by feeding on male flowers. Attraction of weevils to oil palm flowers is due to the emission of methylchavicol by both male and female flowers. In search for male flowers, the weevils visit female flowers by accident due to methylchavicol fragrance and deposit pollen. Given the importance of methylchavicol emission on pollination, we performed comparative transcriptome analysis of oil palm flowers and leaves to identify candidate genes involved in methylchavicol production in flowers. RESULTS RNA sequencing (RNA-Seq) of male open flowers, female open flowers and leaves was performed using Illumina HiSeq 2000 platform. Analysis of the transcriptome data revealed that the transcripts of methylchavicol biosynthesis genes were strongly up-regulated whereas transcripts encoding genes involved in lignin production such as, caffeic acid O-methyltransferase (COMT) and Ferulate-5-hydroxylase (F5H) were found to be suppressed in oil palm flowers. Among the transcripts encoding transcription factors, an EAR-motif-containing R2R3-MYB transcription factor (EgMYB4) was found to be enriched in oil palm flowers. We determined that EgMYB4 can suppress the expression of a monolignol pathway gene, EgCOMT, in vivo by binding to the AC elements present in the promoter region. EgMYB4 was further functionally characterized in sweet basil which also produces phenylpropenes like oil palm. Transgenic sweet basil plants showed significant reduction in lignin content but produced more phenylpropenes. CONCLUSIONS Our results suggest that EgMYB4 possibly restrains lignin biosynthesis in oil palm flowers thus allowing enhanced carbon flux into the phenylpropene pathway. This study augments our understanding of the diverse roles that EAR-motif-containing MYBs play to fine tune the metabolic flux along the various branches of core phenylpropanoid pathway. This will aid in metabolic engineering of plant aromatic compounds.
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Affiliation(s)
- Ran Li
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, 117604 Singapore
- Present Address: Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Vaishnavi Amarr Reddy
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, 117604 Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, 117543 Singapore
| | - Jingjing Jin
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, 117604 Singapore
| | - Chakaravarthy Rajan
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, 117604 Singapore
- Present Address: Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Qian Wang
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, 117604 Singapore
- Present Address: College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang, China
| | - Genhua Yue
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, 117604 Singapore
| | - Chin Huat Lim
- R&D Department, Wilmar International Plantation, Palembang, Indonesia
| | - Nam-Hai Chua
- Laboratory of Plant Molecular Biology, Rockefeller University, New York, NY 10065 USA
| | - Jian Ye
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, 117604 Singapore
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Rajani Sarojam
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, 117604 Singapore
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19
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Abstract
Shoot and inflorescence are central physiological and developmental tissues of plants. Flowering is one of the most important agronomic traits for improvement of crop yield. To analyze the vegetative to reproductive tissue transition in Jatropha curcas, gene expression profiles were generated from shoot and inflorescence tissues. RNA isolated from both tissues was sequenced using the Ilumina HiSeq 2500 platform. Differential gene expression analysis identified key biological processes associated with vegetative to reproductive tissue transition. The present data for J. curcas may inform the design of breeding strategies particularly with respect to reproductive tissue transition. The raw data of this study has been deposited in the NCBI's Sequence Read Archive (SRA) database with the accession number SRP090662.
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20
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Gonzalez-Ibeas D, Martinez-Garcia PJ, Famula RA, Delfino-Mix A, Stevens KA, Loopstra CA, Langley CH, Neale DB, Wegrzyn JL. Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana). G3 (BETHESDA, MD.) 2016; 6:3787-3802. [PMID: 27799338 PMCID: PMC5144951 DOI: 10.1534/g3.116.032805] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 07/13/2016] [Indexed: 02/06/2023]
Abstract
Sugar pine (Pinus lambertiana Douglas) is within the subgenus Strobus with an estimated genome size of 31 Gbp. Transcriptomic resources are of particular interest in conifers due to the challenges presented in their megagenomes for gene identification. In this study, we present the first comprehensive survey of the P. lambertiana transcriptome through deep sequencing of a variety of tissue types to generate more than 2.5 billion short reads. Third generation, long reads generated through PacBio Iso-Seq have been included for the first time in conifers to combat the challenges associated with de novo transcriptome assembly. A technology comparison is provided here to contribute to the otherwise scarce comparisons of second and third generation transcriptome sequencing approaches in plant species. In addition, the transcriptome reference was essential for gene model identification and quality assessment in the parallel project responsible for sequencing and assembly of the entire genome. In this study, the transcriptomic data were also used to address questions surrounding lineage-specific Dicer-like proteins in conifers. These proteins play a role in the control of transposable element proliferation and the related genome expansion in conifers.
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Affiliation(s)
- Daniel Gonzalez-Ibeas
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269
| | | | - Randi A Famula
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Annette Delfino-Mix
- United States Department of Agriculture Forest Service, Institute of Forest Genetics, Placerville, California 95667
| | - Kristian A Stevens
- Department of Evolution and Ecology, University of California, Davis, California 95616
| | - Carol A Loopstra
- Department of Ecosystem Science and Management, Texas A&M University, College Station, Texas 77843
| | - Charles H Langley
- Department of Evolution and Ecology, University of California, Davis, California 95616
| | - David B Neale
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269
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21
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Ramírez Rivera NG, García-Salinas C, Aragão FJL, Díaz de la Garza RI. Metabolic engineering of folate and its precursors in Mexican common bean (Phaseolus vulgaris L.). PLANT BIOTECHNOLOGY JOURNAL 2016; 14:2021-32. [PMID: 26997331 PMCID: PMC5043471 DOI: 10.1111/pbi.12561] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 03/05/2016] [Accepted: 03/12/2016] [Indexed: 05/24/2023]
Abstract
Folate (vitamin B9) deficiency causes several health problems globally. However, folate biofortification of major staple crops is one alternative that can be used to improve vitamin intakes in populations at risk. We increased the folate levels in common bean by engineering the pteridine branch required for their biosynthesis. GTP cyclohydrolase I from Arabidopsis (AtGchI) was stably introduced into three common bean Pinto cultivars by particle bombardment. Seed-specific overexpression of AtGCHI caused significant increases of up to 150-fold in biosynthetic pteridines in the transformed lines. The pteridine boost enhanced folate levels in raw desiccated seeds by up to threefold (325 μg in a 100 g portion), which would represent 81% of the adult recommended daily allowance. Unexpectedly, the engineering also triggered a general increase in PABA levels, the other folate precursor. This was not observed in previous engineering studies and was probably caused by a feedforward mechanism that remains to be elucidated. Results from this work also show that common bean grains accumulate considerable amounts of oxidized pteridines that might represent products of folate degradation in desiccating seeds. Our study uncovers a probable different regulation of folate homoeostasis in these legume grains than that observed in other engineering works. Legumes are good sources of folates, and this work shows that they can be engineered to accumulate even greater amounts of folate that, when consumed, can improve folate status. Biofortification of common bean with folates and other micronutrients represents a promising strategy to improve the nutritional status of populations around the world.
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Affiliation(s)
- Naty G Ramírez Rivera
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Monterrey, Nuevo León, México
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22
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Cervera A, Urbina D, de la Peña M. Retrozymes are a unique family of non-autonomous retrotransposons with hammerhead ribozymes that propagate in plants through circular RNAs. Genome Biol 2016; 17:135. [PMID: 27339130 PMCID: PMC4918200 DOI: 10.1186/s13059-016-1002-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 06/07/2016] [Indexed: 11/16/2022] Open
Abstract
Background Catalytic RNAs, or ribozymes, are regarded as fossils of a prebiotic RNA world that have remained in the genomes of modern organisms. The simplest ribozymes are the small self-cleaving RNAs, like the hammerhead ribozyme, which have been historically considered biological oddities restricted to some RNA pathogens. Recent data, however, indicate that small self-cleaving ribozymes are widespread in genomes, although their functions are still unknown. Results We reveal that hammerhead ribozyme sequences in plant genomes form part of a new family of small non-autonomous retrotransposons with hammerhead ribozymes, referred to as retrozymes. These elements contain two long terminal repeats of approximately 350 bp, each harbouring a hammerhead ribozyme that delimitates a variable region of 600–1000 bp with no coding capacity. Retrozymes are actively transcribed, which gives rise to heterogeneous linear and circular RNAs that accumulate differentially depending on the tissue or developmental stage of the plant. Genomic and transcriptomic retrozyme sequences are highly heterogeneous and share almost no sequence homology among species except the hammerhead ribozyme motif and two small conserved domains typical of Ty3-gypsy long terminal repeat retrotransposons. Moreover, we detected the presence of RNAs of both retrozyme polarities, which suggests events of independent RNA-RNA rolling-circle replication and evolution, similarly to that of infectious circular RNAs like viroids and viral satellite RNAs. Conclusions Our work reveals that circular RNAs with hammerhead ribozymes are frequently occurring molecules in plant and, most likely, metazoan transcriptomes, which explains the ubiquity of these genomic ribozymes and suggests a feasible source for the emergence of circular RNA plant pathogens. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1002-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amelia Cervera
- IBMCP (CSIC-UPV). C/Ingeniero Fausto Elio s/n, 46022, Valencia, Spain
| | - Denisse Urbina
- IBMCP (CSIC-UPV). C/Ingeniero Fausto Elio s/n, 46022, Valencia, Spain
| | - Marcos de la Peña
- IBMCP (CSIC-UPV). C/Ingeniero Fausto Elio s/n, 46022, Valencia, Spain.
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23
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Gangwar M, Sood H, Chauhan RS. Genomics and relative expression analysis identifies key genes associated with high female to male flower ratio in Jatropha curcas L. Mol Biol Rep 2016; 43:305-22. [PMID: 26878857 DOI: 10.1007/s11033-016-3953-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 02/09/2016] [Indexed: 02/02/2023]
Abstract
Jatropha curcas, has been projected as a major source of biodiesel due to high seed oil content (42 %). A major roadblock for commercialization of Jatropha-based biodiesel is low seed yield per inflorescence, which is affected by low female to male flower ratio (1:25-30). Molecular dissection of female flower development by analyzing genes involved in phase transitions and floral organ development is, therefore, crucial for increasing seed yield. Expression analysis of 42 genes implicated in floral organ development and sex determination was done at six floral developmental stages of a J. curcas genotype (IC561235) with inherently higher female to male flower ratio (1:8-10). Relative expression analysis of these genes was done on low ratio genotype. Genes TFL1, SUP, AP1, CRY2, CUC2, CKX1, TAA1 and PIN1 were associated with reproductive phase transition. Further, genes CUC2, TAA1, CKX1 and PIN1 were associated with female flowering while SUP and CRY2 in female flower transition. Relative expression of these genes with respect to low female flower ratio genotype showed up to ~7 folds increase in transcript abundance of SUP, TAA1, CRY2 and CKX1 genes in intermediate buds but not a significant increase (~1.25 folds) in female flowers, thereby suggesting that these genes possibly play a significant role in increased transition towards female flowering by promoting abortion of male flower primordia. The outcome of study has implications in feedstock improvement of J. curcas through functional validation and eventual utilization of key genes associated with female flowering.
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Affiliation(s)
- Manali Gangwar
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, 173234, Solan, Himachal Pradesh, India
| | - Hemant Sood
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, 173234, Solan, Himachal Pradesh, India
| | - Rajinder Singh Chauhan
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, 173234, Solan, Himachal Pradesh, India.
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Botelho SR, Martins TP, Duarte MF, Barbosa AV, Lau D, Fernandes FR, Sanches MM. Development of methodologies for virus detection in soybean and wheat seeds. MethodsX 2016; 3:62-8. [PMID: 27408831 PMCID: PMC4929247 DOI: 10.1016/j.mex.2016.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 01/13/2016] [Indexed: 11/22/2022] Open
Abstract
Seeds that contain large amounts of oil, starch, fibers and phenols are the most difficult tissues for RNA extraction. Currently, there are some reports of virus detection in seeds using commercial kits for RNA extraction. However, individual seeds were used, which may not be always suitable for analyses that deal with large amounts of seeds. Sangha [1] described a simple, quick and efficient protocol for RNA extraction and downstream applications in a group of seeds of jatropha (Jatropha curcas), mustard (Brassica sp.) and rice (Oryza sativa). We tested this protocol for soybean (Glycine max), maize (Zea mays), wheat (Triticum aestivum) and triticale (×Triticosecale) seeds and further reverse transcription PCR (RT-PCR)/quantitative real-time PCR (qPCR) in order to have a faster and more practical method for virus detection from seeds than the traditional scheme of seed planting and subsequent Elisa/RT-PCR from leaves. The essential points in the method are:•Some modifications in the protocol [1] were done in order to increase performance: Wheat and triticale seeds are incubated with water prior to maceration. An amount of 1.2 g of dry soybean seeds is used to maceration.•RT-PCR is used for detection of Wheat streak mosaic virus from wheat seeds and RT-qPCR for detection of Soybean mosaic virus from soybean seeds.•The method may be tested for other viruses, however, pre-validation will be needed.
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Affiliation(s)
| | - Thais P. Martins
- Embrapa Genetic Resources and Biotechnology, Brasilia, DF, Brazil
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Gu K, Tian D, Mao H, Wu L, Yin Z. Development of marker-free transgenic Jatropha curcas producing curcin-deficient seeds through endosperm-specific RNAi-mediated gene silencing. BMC PLANT BIOLOGY 2015; 15:242. [PMID: 26450182 PMCID: PMC4599812 DOI: 10.1186/s12870-015-0625-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/22/2015] [Indexed: 05/04/2023]
Abstract
BACKGROUND Jatropha curcas L. is a potential biofuel plant and its seed oil is suitable for biodiesel production. Despite this promising application, jatropha seeds contain two major toxic components, namely phorbol esters and curcins. These compounds would reduce commercial value of seed cake and raise safety and environment concerns on jatropha plantation and processing. Curcins are Type I ribosome inactivating proteins. Several curcin genes have been identified in the jatropha genome. Among which, the Curcin 1 (C1) gene is identified to be specifically expressed in endosperm, whereas the Curcin 2A (C2A) is mainly expressed in young leaves. RESULTS A marker-free RNAi construct carrying a β-estradiol-regulated Cre/loxP system and a C1 promoter-driven RNAi cassette for C1 gene was made and used to generate marker-free transgenic RNAi plants to specifically silence the C1 gene in the endosperm of J. curcas. Plants of transgenic line L1, derived from T0-1, carry two copies of marker-free RNAi cassette, whereas plants of L35, derived from T0-35, harbored one copy of marker-free RNAi cassette and three copies of closely linked and yet truncated Hpt genes. The C1 protein content in endosperm of L1 and L35 seeds was greatly reduced or undetectable, while the C2A proteins in young leaves of T0-1 and T0-35 plants were unaffected. In addition, the C1 mRNA transcripts were undetectable in the endosperm of T3 seeds of L1 and L35. The results demonstrated that the expression of the C1 gene was specifically down-regulated or silenced by the double-stranded RNA-mediated RNA interference generated from the RNAi cassette. CONCLUSION The C1 promoter-driven RNAi cassette for the C1 gene in transgenic plants was functional and heritable. Both C1 transcripts and C1 proteins were greatly down-regulated or silenced in the endosperm of transgenic J. curcas. The marker-free transgenic plants and curcin-deficient seeds developed in this study provided a solution for the toxicity of curcins in jatropha seeds and addressed the safety concerns of the marker genes in transgenic plants on the environments.
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Affiliation(s)
- Keyu Gu
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Republic of Singapore.
| | - Dongsheng Tian
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Republic of Singapore.
| | - Huizhu Mao
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Republic of Singapore.
| | - Lifang Wu
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Republic of Singapore.
- Present address: Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, China.
| | - Zhongchao Yin
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Republic of Singapore.
- Department of Biological Sciences, National University of Singapore, 14 Science Drive, Singapore, 117543, Republic of Singapore.
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore.
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Lang V, Usadel B, Obermeyer G. De novo sequencing and analysis of the lily pollen transcriptome: an open access data source for an orphan plant species. PLANT MOLECULAR BIOLOGY 2015; 87:69-80. [PMID: 25341867 DOI: 10.1007/s11103-014-0261-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 10/14/2014] [Indexed: 06/04/2023]
Abstract
Pollen grains of Lilium longiflorum are a long-established model system for pollen germination and tube tip growth. Due to their size, protein content and almost synchronous germination in synthetic media, they provide a simple system for physiological measurements as well as sufficient material for biochemical studies like protein purifications, enzyme assays, organelle isolation or determination of metabolites during germination and pollen tube elongation. Despite recent progresses in molecular biology techniques, sequence information of expressed proteins or transcripts in lily pollen is still scarce. Using a next generation sequencing strategy (RNAseq), the lily pollen transcriptome was investigated resulting in more than 50 million high quality reads with a length of 90 base pairs. Sequenced transcripts were assembled and annotated, and finally visualized with MAPMAN software tools and compared with other RNAseq or genome data including Arabidopsis pollen, Lilium vegetative tissues and the Amborella trichopoda genome. All lily pollen sequence data are provided as open access files with suitable tools to search sequences of interest.
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Affiliation(s)
- Veronika Lang
- Molecular Plant Biophysics and Biochemistry, Depatment of Molecular Biology, University of Salzburg, Billrothstr.11, 5020, Salzburg, Austria
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27
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An improved method for extraction of high-quality total RNA from oil seeds. Biotechnol Lett 2014; 37:927-33. [PMID: 25534638 DOI: 10.1007/s10529-014-1752-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 12/11/2014] [Indexed: 10/24/2022]
Abstract
Seeds of oilseed plants that contain large amounts of oil, polysaccharides, proteins and polyphenols are not amenable to conventional RNA isolation protocols. The presence of these substances affects the quality and quantity of isolated nucleic acids. Here, a rapid and efficient RNA isolation protocol that, in contrast to other methods tested, allows high purify, integrity and yield of total RNA from seeds of sesame, corn, sunflower, flax and rapeseed was developed. The average yields of total RNA from 70 mg oil seeds ranged from 84 to 310 µg with A260/A280 between 1.9 and 2.08. The RNA isolated with this protocol was verified to be suitable for PCR, quantitative real-time PCR, semi-quantitative RT-PCR, cDNA synthesis and expression analysis.
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28
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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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29
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Abstract
RNA-seq has emerged as the technology of choice to quantify gene expression. This technology is a convenient accurate tool to quantify diurnal changes in gene expression, gene discovery, differential use of promoters, and splice variants for all genes expressed in a single tissue. Thus, RNA-seq experiments provide sequence information and absolute expression values about transcripts in addition to relative quantification available with microarrays or qRT-PCR. The depth of information by sequencing requires careful assessment of RNA intactness and DNA contamination. Although the RNA-seq is comparatively recent, a standard analysis framework has emerged with the packages of Bowtie2, TopHat, and Cufflinks. With rising popularity of RNA-seq tools have become manageable for researchers without much bioinformatical knowledge or programming skills. Here, we present a workflow for a RNA-seq experiment from experimental planning to biological data extraction.
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Affiliation(s)
- Canan Külahoglu
- iGrad Plant, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
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30
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Jia H, McCarty DR, Suzuki M. Distinct roles of LAFL network genes in promoting the embryonic seedling fate in the absence of VAL repression. PLANT PHYSIOLOGY 2013; 163:1293-305. [PMID: 24043445 PMCID: PMC3813651 DOI: 10.1104/pp.113.220988] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 09/08/2013] [Indexed: 05/18/2023]
Abstract
The transition between seed and seedling phases of development is coordinated by an interaction between the closely related ABSCISIC ACID-INSENSITIVE3 (ABI3), FUSCA3 (FUS3), and LEAFY COTYLEDON2 (LEC2; AFL) and VIVIPAROUS1/ABI3-LIKE (VAL) clades of the B3 transcription factor family that respectively activate and repress the seed maturation program. In the val1 val2 double mutant, derepression of the LEC1, LEC1-LIKE (L1L), and AFL (LAFL) network is associated with misexpression of embryonic characteristics resulting in arrested seedling development. We show that while the frequency of the embryonic fate in val1 val2 seedlings depends on the developmental timing of seed rescue, VAL proteins repress LAFL genes during germination, but not during seed development. Quantitative analysis of LAFL mutants that suppress the val1 val2 seedling phenotype revealed distinct roles of LAFL genes in promoting activation of the LAFL network. LEC2 and FUS3 are both essential for coordinate activation of the network, whereas effects of LEC1, L1L, and ABI3 are additive. Suppression of the val1 val2 seedling phenotype by the B3 domain-deficient abi3-12 mutation indicates that ABI3 activation of the LAFL network requires the B3 DNA-binding domain. In the VAL-deficient background, coordinate regulation of the LAFL network is observed over a wide range of genetic and developmental conditions. Our findings highlight distinct functional roles and interactions of LAFL network genes that are uncovered in the absence of VAL repressors.
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31
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Obermeyer G, Fragner L, Lang V, Weckwerth W. Dynamic adaption of metabolic pathways during germination and growth of lily pollen tubes after inhibition of the electron transport chain. PLANT PHYSIOLOGY 2013; 162:1822-33. [PMID: 23660836 PMCID: PMC3729764 DOI: 10.1104/pp.113.219857] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 05/08/2013] [Indexed: 05/19/2023]
Abstract
Investigation of the metabolome and the transcriptome of pollen of lily (Lilium longiflorum) gave a comprehensive overview of metabolic pathways active during pollen germination and tube growth. More than 100 different metabolites were determined simultaneously by gas chromatography coupled to mass spectrometry, and expressed genes of selected metabolic pathways were identified by next-generation sequencing of lily pollen transcripts. The time-dependent changes in metabolite abundances, as well as the changes after inhibition of the mitochondrial electron transport chain, revealed a fast and dynamic adaption of the metabolic pathways in the range of minutes. The metabolic state prior to pollen germination differed clearly from the metabolic state during pollen tube growth, as indicated by principal component analysis of all detected metabolites and by detailed observation of individual metabolites. For instance, the amount of sucrose increased during the first 60 minutes of pollen culture but decreased during tube growth, while glucose and fructose showed the opposite behavior. Glycolysis, tricarbonic acid cycle, glyoxylate cycle, starch, and fatty acid degradation were activated, providing energy during pollen germination and tube growth. Inhibition of the mitochondrial electron transport chain by antimycin A resulted in an immediate production of ethanol and a fast rearrangement of metabolic pathways, which correlated with changes in the amounts of the majority of identified metabolites, e.g. a rapid increase in γ-aminobutyric acid indicated the activation of a γ-aminobutyric acid shunt in the tricarbonic acid cycle, while ethanol fermentation compensated the reduced ATP production after inhibition of the oxidative phosphorylation.
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Affiliation(s)
- Gerhard Obermeyer
- Molecular Plant Biophysics and Biochemistry, Department of Molecular Biology, University of Salzburg, 5020 Salzburg, Austria.
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32
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Lan T, Yao B, Shen Y, Wang X. Isolation of high-quality total RNA from lipid-rich seeds. Anal Biochem 2013; 438:11-3. [PMID: 23524018 DOI: 10.1016/j.ab.2013.03.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Revised: 03/11/2013] [Accepted: 03/12/2013] [Indexed: 11/25/2022]
Abstract
Obtaining high-quality RNA from lipid-rich seeds has been a challenge, since lipids can interfere with tissue disruption and block cells from extraction buffer, and polysaccharides, polyphenols, and other secondary metabolites can bind or coprecipitate with RNA. Using an improved CTAB-based extraction buffer and modified grinding and incubation method, we developed a protocol that is able to minimize the negative effects caused by lipids and other compounds. Using this protocol, we obtained high-quality and high-quantity RNA from six species of lipid-rich seeds within 3 hours. The isolated RNA was demonstrated to be suitable for downstream applications.
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Affiliation(s)
- Tianying Lan
- Department of Biology, Chongqing University of Science and Technology, Chongqing 401331, People's Republic of China.
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33
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Mornkham T, Wangsomnuk PP, Fu YB, Wangsomnuk P, Jogloy S, Patanothai A. Extractions of High Quality RNA from the Seeds of Jerusalem Artichoke and Other Plant Species with High Levels of Starch and Lipid. PLANTS (BASEL, SWITZERLAND) 2013; 2:302-16. [PMID: 27137377 PMCID: PMC4844358 DOI: 10.3390/plants2020302] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 04/04/2013] [Accepted: 04/08/2013] [Indexed: 11/16/2022]
Abstract
Jerusalem artichoke (Helianthus tuberosus L.) is an important tuber crop. However, Jerusalem artichoke seeds contain high levels of starch and lipid, making the extraction of high-quality RNA extremely difficult and the gene expression analysis challenging. This study was aimed to improve existing methods for extracting total RNA from Jerusalem artichoke dry seeds and to assess the applicability of the improved method in other plant species. Five RNA extraction methods were evaluated on Jerusalem artichoke seeds and two were modified. One modified method with the significant improvement was applied to assay seeds of diverse Jerusalem artichoke accessions, sunflower, rice, maize, peanut and marigold. The effectiveness of the improved method to extract total RNA from seeds was assessed using qPCR analysis of four selected genes. The improved method of Ma and Yang (2011) yielded a maximum RNA solubility and removed most interfering substances. The improved protocol generated 29 to 41 µg RNA/30 mg fresh weight. An A260/A280 ratio of 1.79 to 2.22 showed their RNA purity. Extracted RNA was effective for downstream applications such as first-stranded cDNA synthesis, cDNA cloning and qPCR. The improved method was also effective to extract total RNA from seeds of sunflower, rice, maize and peanut that are rich in polyphenols, lipids and polysaccharides.
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Affiliation(s)
- Tanupat Mornkham
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand.
| | | | - Yong-Bi Fu
- Plant Gene Resources of Canada, Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK S7N 0X2, Canada.
| | - Pinich Wangsomnuk
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand.
| | - Sanun Jogloy
- Department of Plant Science and Agricultural Resources, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand.
| | - Aran Patanothai
- Department of Plant Science and Agricultural Resources, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand.
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34
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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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35
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Gu K, Yi C, Tian D, Sangha JS, Hong Y, Yin Z. Expression of fatty acid and lipid biosynthetic genes in developing endosperm of Jatropha curcas. BIOTECHNOLOGY FOR BIOFUELS 2012; 5:47. [PMID: 22809288 PMCID: PMC3457857 DOI: 10.1186/1754-6834-5-47] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 07/04/2012] [Indexed: 05/06/2023]
Abstract
BACKGROUND Temporal and spatial expression of fatty acid and lipid biosynthetic genes are associated with the accumulation of storage lipids in the seeds of oil plants. In jatropha (Jatropha curcas L.), a potential biofuel plant, the storage lipids are mainly synthesized and accumulated in the endosperm of seeds. Although the fatty acid and lipid biosynthetic genes in jatropha have been identified, the expression of these genes at different developing stages of endosperm has not been systemically investigated. RESULTS Transmission electron microscopy study revealed that the oil body formation in developing endosperm of jatropha seeds initially appeared at 28 days after fertilization (DAF), was actively developed at 42 DAF and reached to the maximum number and size at 56 DAF. Sixty-eight genes that encode enzymes, proteins or their subunits involved in fatty acid and lipid biosynthesis were identified from a normalized cDNA library of jatropha developing endosperm. Gene expression with quantitative reverse-transcription polymerase chain reaction analysis demonstrated that the 68 genes could be collectively grouped into five categories based on the patterns of relative expression of the genes during endosperm development. Category I has 47 genes and they displayed a bell-shaped expression pattern with the peak expression at 28 or 42 DAF, but low expression at 14 and 56 DAF. Category II contains 8 genes and expression of the 8 genes was constantly increased from 14 to 56 DAF. Category III comprises of 2 genes and both genes were constitutively expressed throughout endosperm development. Category IV has 9 genes and they showed a high expression at 14 and 28 DAF, but a decreased expression from 42 to 56 DAF. Category V consists of 2 genes and both genes showed a medium expression at 14 DAF, the lowest expression at 28 or 42 DAF, and the highest expression at 56 DAF. In addition, genes encoding enzymes or proteins with similar function were differentially expressed during endosperm development. CONCLUSION The formation of oil bodies in jatropha endosperm is developmentally regulated. The expression of the majority of fatty acid and lipid biosynthetic genes is highly consistent with the development of oil bodies and endosperm in jatropha seeds, while the genes encoding enzymes with similar function may be differentially expressed during endosperm development. These results not only provide the initial information on spatial and temporal expression of fatty acid and lipid biosynthetic genes in jatropha developing endosperm, but are also valuable to identify the rate-limiting genes for storage lipid biosynthesis and accumulation during seed development.
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Affiliation(s)
- Keyu Gu
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Republic of Singapore
| | - Chengxin Yi
- JOil (S) Private Limited, 1 Research Link, National University of Singapore, Singapore, 117604, Republic of Singapore
| | - Dongsheng Tian
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Republic of Singapore
| | - Jatinder Singh Sangha
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Republic of Singapore
| | - Yan Hong
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Republic of Singapore
- JOil (S) Private Limited, 1 Research Link, National University of Singapore, Singapore, 117604, Republic of Singapore
| | - Zhongchao Yin
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Republic of Singapore
- Department of Biological Sciences, 14 Science Drive, National University of Singapore, Singapore, 117543, Republic of Singapore
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Sangha JS, Khan W, Ji X, Zhang J, Mills AAS, Critchley AT, Prithiviraj B. Carrageenans, sulphated polysaccharides of red seaweeds, differentially affect Arabidopsis thaliana resistance to Trichoplusia ni (cabbage looper). PLoS One 2011; 6:e26834. [PMID: 22046375 PMCID: PMC3203909 DOI: 10.1371/journal.pone.0026834] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 10/05/2011] [Indexed: 01/12/2023] Open
Abstract
Carrageenans are a collective family of linear, sulphated galactans found in a number of commercially important species of marine red alga. These polysaccharides are known to elicit defense responses in plant and animals and possess anti-viral properties. We investigated the effect of foliar application of ι-, κ- and λ-carrageenans (representing various levels of sulphation) on Arabidopsis thaliana in resistance to the generalist insect Trichoplusia ni (cabbage looper) which is known to cause serious economic losses in crop plants. Plants treated with ι- and κ-carrageenan showed reduced leaf damage, whereas those treated with λ- carrageenan were similar to that of the control. In a no-choice test, larval weight was reduced by more than 20% in ι- and κ- carrageenan treatments, but unaffected by λ-carrageenan. In multiple choice tests, carrageenan treated plants attracted fewer T. ni larvae by the fourth day following infestation as compared to the control. The application of carrageenans did not affect oviposition behaviour of T. ni. Growth of T. ni feeding on an artificial diet amended with carrageenans was not different from that fed with untreated control diet. ι-carrageenan induced the expression of defense genes; PR1, PDF1.2, and TI1, but κ- and λ-carrageenans did not. Besides PR1, PDF1.2, and TI1, the indole glucosinolate biosynthesis genes CYP79B2, CYP83B1 and glucosinolate hydrolysing QTL, ESM1 were up-regulated by ι-carrageenan treatment at 48 h post infestation. Gas chromatography-mass spectrometry analysis of carrageenan treated leaves showed increased concentrations of both isothiocyanates and nitriles. Taken together, these results show that carrageenans have differential effects on Arabidopsis resistance to T. ni and that the degree of sulphation of the polysaccharide chain may well mediate this effect.
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Affiliation(s)
- Jatinder S. Sangha
- Department of Environmental Sciences, Nova Scotia Agricultural College, Truro, Nova Scotia, Canada
| | - Wajahatullah Khan
- Department of Biochemistry, Genome Research Chair Unit, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Xiuhong Ji
- Institute for Nutrisciences and Health, National Research Council of Canada, Charlottetown, Prince Edward Island, Canada
| | - Junzeng Zhang
- Institute for Nutrisciences and Health, National Research Council of Canada, Charlottetown, Prince Edward Island, Canada
| | - Aaron A. S. Mills
- Department of Environmental Sciences, Nova Scotia Agricultural College, Truro, Nova Scotia, Canada
| | | | - Balakrishnan Prithiviraj
- Department of Environmental Sciences, Nova Scotia Agricultural College, Truro, Nova Scotia, Canada
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Kumar GRK, Eswaran N, Johnson TS. Isolation of high-quality RNA from various tissues of Jatropha curcas for downstream applications. Anal Biochem 2011; 413:63-5. [PMID: 21300020 DOI: 10.1016/j.ab.2011.01.046] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 01/31/2011] [Accepted: 01/31/2011] [Indexed: 11/13/2022]
Abstract
A method for isolating transcriptionally active RNA for downstream applications from diverse tissues of Jatropha curcas, a plant rich in latex, lipids, waxes, polysaccharide, polyphenols, and secondary metabolites, is described. The described method uses alkaline borate buffer during tissue homogenization to negate the formation of viscous gel observed in guanidium-salt-containing methods. By this method, quality RNA was extracted from leaf, immature inflorescence, endosperm, and root tissues with yields ranging from 1.80 to 7.80mg/100mg fresh weight (FW). The total RNA obtained was found to be suitable for poly(A)(+)RNA purification, complementary DNA (cDNA) synthesis, cloning of full-length cDNA, and cDNA library construction.
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Affiliation(s)
- G Raja Krishna Kumar
- Plant Metabolic Engineering Group, Reliance Life Sciences, Rabale, Navi Mumbai 400 701, India
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