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Chenna S, Ivanov M, Nielsen TK, Chalenko K, Olsen E, Jørgensen K, Sandelin A, Marquardt S. A data-driven genome annotation approach for cassava. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38831668 DOI: 10.1111/tpj.16856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 05/13/2024] [Accepted: 05/17/2024] [Indexed: 06/05/2024]
Abstract
Genome annotation files play a critical role in dictating the quality of downstream analyses by providing essential predictions for gene positions and structures. These files are pivotal in decoding the complex information encoded within DNA sequences. Here, we generated experimental data resolving RNA 5'- and 3'-ends as well as full-length RNAs for cassava TME12 sticklings in ambient temperature and cold. We used these data to generate genome annotation files using the TranscriptomeReconstructoR (TR) tool. A careful comparison to high-quality genome annotations suggests that our new TR genome annotations identified additional genes, resolved the transcript boundaries more accurately and identified additional RNA isoforms. We enhanced existing cassava genome annotation files with the information from TR that maintained the different transcript models as RNA isoforms. The resultant merged annotation was subsequently utilized for comprehensive analysis. To examine the effects of genome annotation files on gene expression studies, we compared the detection of differentially expressed genes during cold using the same RNA-seq data but alternative genome annotation files. We found that our merged genome annotation that included cold-specific TR gene models identified about twice as many cold-induced genes. These data indicate that environmentally induced genes may be missing in off-the-shelf genome annotation files. In conclusion, TR offers the opportunity to enhance crop genome annotations with implications for the discovery of differentially expressed candidate genes during plant-environment interactions.
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Affiliation(s)
- Swetha Chenna
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, Frederiskberg C, 1871, Denmark
| | - Maxim Ivanov
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, Frederiskberg C, 1871, Denmark
| | - Tue Kjærgaard Nielsen
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, Frederiskberg C, 1871, Denmark
| | - Karina Chalenko
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, Frederiskberg C, 1871, Denmark
| | - Evy Olsen
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, Frederiskberg C, 1871, Denmark
| | - Kirsten Jørgensen
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, Frederiskberg C, 1871, Denmark
| | - Albin Sandelin
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N, DK2200, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N, DK2200, Denmark
| | - Sebastian Marquardt
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, Frederiskberg C, 1871, Denmark
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2
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Wang B, Ji M, Fang H, Gu H, Mehari TG, Han J, Feng W, Huo X, Zhang J, Chen Y, Zhang J, Ditta A, Khan MKR, Paterson AH, Chee PW, Wang K. An analysis of lncRNAs related to fiber quality and the discovery of their target genes in a Gossypium hirsutum line with Gossypium mustelinum introgression. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:40. [PMID: 38296887 DOI: 10.1007/s00122-024-04541-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/04/2024] [Indexed: 02/02/2024]
Abstract
KEY MESSAGE Analysis of fiber quality lncRNAs and their target genes from a pair of Gossypium mustelinum near-isogenic lines provide new prospects for improving the fiber quality of Upland cotton. Long noncoding RNAs (lncRNAs) are an important part of genome transcription and play roles in a wide range of biological processes in plants. In this research, a pair of near-isogenic cotton lines, namely, a Gossypium mustelinum introgression line (IL9) with outstanding fiber quality and its recurrent Upland cotton parent (PD94042), were used as the experimental materials. Cotton fibers were selected for lncRNA sequencing at 17 and 21 days post-anthesis. A total of 2693 differentially expressed genes were identified. In total, 5841 lncRNAs were ultimately screened, from which 163 differentially expressed lncRNAs were identified. Target genes of the lncRNAs were predicted by two different methods: cis and trans. Some of the target genes were related to cell components, membrane components, plant hormone signal transduction and catalytic metabolism, and the results indicated that there might also be important effects on the development of fiber. Four differentially expressed target genes related to fiber quality (Gomus.D05G015100, Gomus.A05G281300, Gomus.A12G023400 and Gomus.A10G226800) were screened through gene function annotation, and the functions of these four genes were verified through virus-induced gene silencing (VIGS). Compared to the negative controls, plants in which any of these four genes were silenced showed significant reductions in fiber strength. In addition, the plants in which the Gomus.A12G023400 gene was silenced showed a significant reduction in fiber uniformity, whereas the plants in which Gomus.A05G281300 was silenced showed a significant increase in fiber fineness as measured via micronaire. Our results showed that these genes play different roles during fiber development, impacting fiber quality.
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Affiliation(s)
- Baohua Wang
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China.
| | - Meijun Ji
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
| | - Hui Fang
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
| | - Haijing Gu
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
| | | | - Jinlei Han
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
| | - Wenxiang Feng
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
| | - Xuehan Huo
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs of China, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China
| | - Jingxia Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs of China, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China
| | - Yu Chen
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs of China, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China
| | - Jun Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs of China, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China
| | - Allah Ditta
- Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology, Faisalabad, 38000, Pakistan
| | - Muhammad K R Khan
- Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology, Faisalabad, 38000, Pakistan
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA.
| | - Peng W Chee
- Department of Crop and Soil Sciences, University of Georgia, Tifton, GA, 31793, USA.
| | - Kai Wang
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China.
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3
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Magar ND, Shah P, Barbadikar KM, Bosamia TC, Madhav MS, Mangrauthia SK, Pandey MK, Sharma S, Shanker AK, Neeraja CN, Sundaram RM. Long non-coding RNA-mediated epigenetic response for abiotic stress tolerance in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108165. [PMID: 38064899 DOI: 10.1016/j.plaphy.2023.108165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 02/15/2024]
Abstract
Plants perceive environmental fluctuations as stress and confront several stresses throughout their life cycle individually or in combination. Plants have evolved their sensing and signaling mechanisms to perceive and respond to a variety of stresses. Epigenetic regulation plays a critical role in the regulation of genes, spatiotemporal expression of genes under stress conditions and imparts a stress memory to encounter future stress responses. It is quintessential to integrate our understanding of genetics and epigenetics to maintain plant fitness, achieve desired genetic gains with no trade-offs, and durable long-term stress tolerance. The long non-coding RNA >200 nts having no coding potential (or very low) play several roles in epigenetic memory, contributing to the regulation of gene expression and the maintenance of cellular identity which include chromatin remodeling, imprinting (dosage compensation), stable silencing, facilitating nuclear organization, regulation of enhancer-promoter interactions, response to environmental signals and epigenetic switching. The lncRNAs are involved in a myriad of stress responses by activation or repression of target genes and hence are potential candidates for deploying in climate-resilient breeding programs. This review puts forward the significant roles of long non-coding RNA as an epigenetic response during abiotic stresses in plants and the prospects of deploying lncRNAs for designing climate-resilient plants.
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Affiliation(s)
- Nakul D Magar
- Biotechnology Section, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India; Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250004, India
| | - Priya Shah
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, 502324, India
| | - Kalyani M Barbadikar
- Biotechnology Section, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India.
| | - Tejas C Bosamia
- Plant Omics Division, CSIR-Central Salt and Marine Chemicals Research Institute, Gujarat, 364002, India
| | - M Sheshu Madhav
- Biotechnology Section, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | | | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, 502324, India
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250004, India
| | - Arun K Shanker
- Plant Physiology, ICAR-Central Research Institute for Dryland Agriculture, Hyderabad, 500059, India
| | - C N Neeraja
- Biotechnology Section, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | - R M Sundaram
- Biotechnology Section, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
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4
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Pacheco JM, Gabarain VB, Lopez LE, Lehuedé TU, Ocaranza D, Estevez JM. Understanding signaling pathways governing the polar development of root hairs in low-temperature, nutrient-deficient environments. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102386. [PMID: 37352652 DOI: 10.1016/j.pbi.2023.102386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/04/2023] [Accepted: 05/07/2023] [Indexed: 06/25/2023]
Abstract
Plants exposed to freezing and above-freezing low temperatures must employ a variety of strategies to minimize fitness loss. There is a considerable knowledge gap regarding how mild low temperatures (around 10 °C) affect plant growth and developmental processes, even though the majority of the molecular mechanisms that plants use to adapt to extremely low temperatures are well understood. Root hairs (RH) have become a useful model system for studying how plants regulate their growth in response to both cell-intrinsic cues and environmental inputs. Here, we'll focus on recent advances in the molecular mechanisms underpinning Arabidopsis thaliana RH growth at mild low temperatures and how these discoveries may influence our understanding of nutrient sensing mechanisms by the roots. This highlights how intricately linked mechanisms are necessary for plant development to take place under specific circumstances and to produce a coherent response, even at the level of a single RH cell.
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Affiliation(s)
- Javier Martínez Pacheco
- Fundación Instituto Leloir and IIBBA-CONICET. Av. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina; ANID - Millennium Science Initiative Program - Millennium Nucleus for the DeveIopment of Super Adaptable Plants (MN-SAP), Santiago 8370146, Chile
| | - Victoria Berdion Gabarain
- Fundación Instituto Leloir and IIBBA-CONICET. Av. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina; ANID - Millennium Science Initiative Program - Millennium Nucleus for the DeveIopment of Super Adaptable Plants (MN-SAP), Santiago 8370146, Chile
| | - Leonel E Lopez
- Fundación Instituto Leloir and IIBBA-CONICET. Av. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina; ANID - Millennium Science Initiative Program - Millennium Nucleus for the DeveIopment of Super Adaptable Plants (MN-SAP), Santiago 8370146, Chile
| | - Tomás Urzúa Lehuedé
- ANID - Millennium Science Initiative Program - Millennium Nucleus for the DeveIopment of Super Adaptable Plants (MN-SAP), Santiago 8370146, Chile; ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile; Centro de Biotecnología Vegetal (CBV), Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370146, Chile
| | - Darío Ocaranza
- ANID - Millennium Science Initiative Program - Millennium Nucleus for the DeveIopment of Super Adaptable Plants (MN-SAP), Santiago 8370146, Chile; Centro de Biotecnología Vegetal (CBV), Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370146, Chile
| | - José M Estevez
- Fundación Instituto Leloir and IIBBA-CONICET. Av. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina; ANID - Millennium Science Initiative Program - Millennium Nucleus for the DeveIopment of Super Adaptable Plants (MN-SAP), Santiago 8370146, Chile; ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile; Centro de Biotecnología Vegetal (CBV), Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370146, Chile.
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5
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Sun N, Bu Y, Wu X, Ma X, Yang H, Du L, Li X, Xiao J, Lin J, Jing Y. Comprehensive analysis of lncRNA-mRNA regulatory network in Populus associated with xylem development. JOURNAL OF PLANT PHYSIOLOGY 2023; 287:154055. [PMID: 37506405 DOI: 10.1016/j.jplph.2023.154055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/01/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023]
Abstract
Long noncoding RNAs (lncRNAs) play essential roles in numerous biological processes in plants, such as regulating the gene expression. However, only a few studies have looked into their potential functions in xylem development. High-throughput sequencing of P. euramericana 'Zhonglin46' developing and mature xylem was performed in this study. Through sequencing analysis, 14,028 putative lncRNA transcripts were identified, including 4525 differentially expressed lncRNAs (DELs). Additional research revealed that in mature xylem, a total of 2320 DELs were upregulated and 2205 were downregulated compared to developing xylem. Meanwhile, there were a total of 8122 differentially expressed mRNAs (DEMs) that were upregulated and 16,424 that were downregulated in mature xylem compared with developing xylem. The cis- and trans-target genes of DELs were analyzed for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, which indicated that these DELs participate in controlling the phenylpropanoid and lignin biosynthesis pathway as well as the starch and sucrose metabolism pathway. Among the cis-regulated DELs, LNC_006291, LNC_006292, and LNC_006532 all participate in regulating multiple HCT gene family membranes. As targets, POPTR_001G045900v3 (CCR2) and POPTR_018G063500v3 (SUS) both have only one cis-regulatory lncRNA, referred to as LNC_000057 and LNC_006212, respectively. Moreover, LNC_004484 and two DELs named LNC_008014 and LNC_010781 were revealed to be important nodes in the co-expression network of trans-lncRNAs and mRNAs associated to the lignin biosynthesis pathway and cellulose and xylan biosynthetic pathways, respectively. Finally, quantitative real-time PCR (qRT-PCR) was used to confirme 34 pairs of lncRNA-mRNA. Taken together, these findings may help to clarify the regulatory role that lncRNAs play in xylem development and wood formation.
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Affiliation(s)
- Na Sun
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Yufen Bu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Xinyuan Wu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Xiaocen Ma
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Haobo Yang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Liang Du
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Xiaojuan Li
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Jianwei Xiao
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Jinxing Lin
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Yanping Jing
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
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6
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Liu J, Wei L, Feng S. Research progress of non-coding RNAs in vegetable responses to abiotic stresses. Gene 2023:147537. [PMID: 37301448 DOI: 10.1016/j.gene.2023.147537] [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: 05/13/2023] [Revised: 05/25/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023]
Abstract
Vegetable crops play a crucial role in agricultural production, providing essential vitamins and minerals necessary for a healthy diet. Recently, there has been growing interest in cultivating vegetable varieties with outstanding agricultural and economic traits. However, vegetable production is often exposed to various abiotic stresses like soil drought, temperature fluctuations, and heavy metal stress, which can negatively impact yield and quality. While previous research has investigated the physiological responses of vegetable crops to such stressors, less attention has been given to genetic networks. Plants respond to environmental stress mainly by adapting first and then reacting, thereby enhancing their resistance to stress. Typically, different abiotic stresses trigger epigenetic changes, which can regulate non-coding RNAs. Therefore, studying the epigenetic mechanisms of vegetable crop responses to abiotic stress can provide insights into the molecular response mechanisms of plants under stress. This knowledge has practical applications in breeding vegetable crops for resistance. This article summarizes the primary research findings on the regulation of non-coding RNAs and their expression levels in vegetable crops exposed to abiotic stresses to guide molecular breeding approaches for vegetable crops.
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Affiliation(s)
- Jipeng Liu
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China
| | - Liang Wei
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China
| | - Shengjun Feng
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China.
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7
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Pradhan UK, Meher PK, Naha S, Rao AR, Gupta A. ASLncR: a novel computational tool for prediction of abiotic stress-responsive long non-coding RNAs in plants. Funct Integr Genomics 2023; 23:113. [PMID: 37000299 DOI: 10.1007/s10142-023-01040-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 04/01/2023]
Abstract
Abiotic stresses are detrimental to plant growth and development and have a major negative impact on crop yields. A growing body of evidence indicates that a large number of long non-coding RNAs (lncRNAs) are key to many abiotic stress responses. Thus, identifying abiotic stress-responsive lncRNAs is essential in crop breeding programs in order to develop crop cultivars resistant to abiotic stresses. In this study, we have developed the first machine learning-based computational model for predicting abiotic stress-responsive lncRNAs. The lncRNA sequences which were responsive and non-responsive to abiotic stresses served as the two classes of the dataset for binary classification using the machine learning algorithms. The training dataset was created using 263 stress-responsive and 263 non-stress-responsive sequences, whereas the independent test set consists of 101 sequences from both classes. As the machine learning model can adopt only the numeric data, the Kmer features ranging from sizes 1 to 6 were utilized to represent lncRNAs in numeric form. To select important features, four different feature selection strategies were utilized. Among the seven learning algorithms, the support vector machine (SVM) achieved the highest cross-validation accuracy with the selected feature sets. The observed 5-fold cross-validation accuracy, AU-ROC, and AU-PRC were found to be 68.84, 72.78, and 75.86%, respectively. Furthermore, the robustness of the developed model (SVM with the selected feature) was evaluated using an independent test dataset, where the overall accuracy, AU-ROC, and AU-PRC were found to be 76.23, 87.71, and 88.49%, respectively. The developed computational approach was also implemented in an online prediction tool ASLncR accessible at https://iasri-sg.icar.gov.in/aslncr/ . The proposed computational model and the developed prediction tool are believed to supplement the existing effort for the identification of abiotic stress-responsive lncRNAs in plants.
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Affiliation(s)
- Upendra Kumar Pradhan
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, 110012, India
| | - Prabina Kumar Meher
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, 110012, India.
| | - Sanchita Naha
- Division of Computer Applications, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, 110012, India
| | | | - Ajit Gupta
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, 110012, India
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8
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Long Non-Coding RNAs of Plants in Response to Abiotic Stresses and Their Regulating Roles in Promoting Environmental Adaption. Cells 2023; 12:cells12050729. [PMID: 36899864 PMCID: PMC10001313 DOI: 10.3390/cells12050729] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/10/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
Abiotic stresses triggered by climate change and human activity cause substantial agricultural and environmental problems which hamper plant growth. Plants have evolved sophisticated mechanisms in response to abiotic stresses, such as stress perception, epigenetic modification, and regulation of transcription and translation. Over the past decade, a large body of literature has revealed the various regulatory roles of long non-coding RNAs (lncRNAs) in the plant response to abiotic stresses and their irreplaceable functions in environmental adaptation. LncRNAs are recognized as a class of ncRNAs that are longer than 200 nucleotides, influencing a variety of biological processes. In this review, we mainly focused on the recent progress of plant lncRNAs, outlining their features, evolution, and functions of plant lncRNAs in response to drought, low or high temperature, salt, and heavy metal stress. The approaches to characterize the function of lncRNAs and the mechanisms of how they regulate plant responses to abiotic stresses were further reviewed. Moreover, we discuss the accumulating discoveries regarding the biological functions of lncRNAs on plant stress memory as well. The present review provides updated information and directions for us to characterize the potential functions of lncRNAs in abiotic stresses in the future.
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Guo X, Yu X, Xu Z, Zhao P, Zou L, Li W, Geng M, Zhang P, Peng M, Ruan M. CC-type glutaredoxin, MeGRXC3, associates with catalases and negatively regulates drought tolerance in cassava (Manihot esculenta Crantz). PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2389-2405. [PMID: 36053917 PMCID: PMC9674314 DOI: 10.1111/pbi.13920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/05/2022] [Accepted: 08/27/2022] [Indexed: 06/15/2023]
Abstract
Glutaredoxins (GRXs) are essential for reactive oxygen species (ROS) homeostasis in responses of plants to environment changes. We previously identified several drought-responsive CC-type GRXs in cassava, an important tropical crop. However, how CC-type GRX regulates ROS homeostasis of cassava under drought stress remained largely unknown. Here, we report that a drought-responsive CC-type GRX, namely MeGRXC3, was associated with activity of catalase in the leaves of 100 cultivars (or unique unnamed genotypes) of cassava under drought stress. MeGRXC3 negatively regulated drought tolerance by modulating drought- and abscisic acid-induced stomatal closure in transgenic cassava. It antagonistically regulated hydrogen peroxide (H2 O2 ) accumulation in epidermal cells and guard cells. Moreover, MeGRXC3 interacted with two catalases of cassava, MeCAT1 and MeCAT2, and regulated their activity in vivo. Additionally, MeGRXC3 interacts with a cassava TGA transcription factor, MeTGA2, in the nucleus, and regulates the expression of MeCAT7 through a MeTGA2-MeMYB63 pathway. Overall, we demonstrated the roles of MeGRXC3 in regulating activity of catalase at both transcriptional and post-translational levels, therefore involving in ROS homeostasis and stomatal movement in responses of cassava to drought stress. Our study provides the first insights into how MeGRXC3 may be used in molecular breeding of cassava crops.
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Affiliation(s)
- Xin Guo
- Key Laboratory of Biology and Genetic Resources of Tropical CropsInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
- Hainan Key Laboratory for Protection and Utilization of Tropical BioresourcesHainan Institute for Tropical Agricultural ResourcesHaikouChina
| | - Xiaoling Yu
- Key Laboratory of Biology and Genetic Resources of Tropical CropsInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
- Hainan Key Laboratory for Protection and Utilization of Tropical BioresourcesHainan Institute for Tropical Agricultural ResourcesHaikouChina
| | - Ziyin Xu
- College of Tropical CropsHainan UniversityHaikouChina
| | - Pingjuan Zhao
- Key Laboratory of Biology and Genetic Resources of Tropical CropsInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
- Hainan Key Laboratory for Protection and Utilization of Tropical BioresourcesHainan Institute for Tropical Agricultural ResourcesHaikouChina
| | - Liangping Zou
- Key Laboratory of Biology and Genetic Resources of Tropical CropsInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
- Hainan Key Laboratory for Protection and Utilization of Tropical BioresourcesHainan Institute for Tropical Agricultural ResourcesHaikouChina
| | - Wenbin Li
- Key Laboratory of Biology and Genetic Resources of Tropical CropsInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
- Hainan Key Laboratory for Protection and Utilization of Tropical BioresourcesHainan Institute for Tropical Agricultural ResourcesHaikouChina
| | - Mengting Geng
- College of Tropical CropsHainan UniversityHaikouChina
| | - Peng Zhang
- National Key Laboratory of Plant Molecular GeneticsCAS Center for Excellence in Molecular Plant SciencesShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Ming Peng
- Key Laboratory of Biology and Genetic Resources of Tropical CropsInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
- Hainan Key Laboratory for Protection and Utilization of Tropical BioresourcesHainan Institute for Tropical Agricultural ResourcesHaikouChina
| | - Mengbin Ruan
- Key Laboratory of Biology and Genetic Resources of Tropical CropsInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
- Hainan Key Laboratory for Protection and Utilization of Tropical BioresourcesHainan Institute for Tropical Agricultural ResourcesHaikouChina
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10
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Wei L, Zhang R, Zhang M, Xia G, Liu S. Functional analysis of long non-coding RNAs involved in alkaline stress responses in wheat. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5698-5714. [PMID: 35595260 DOI: 10.1093/jxb/erac211] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Saline-alkali soil is a major environmental problem affecting crop productivity. One of the most effective approaches to combat it is to breed stress-tolerant plants through genetic engineering. Shanrong No. 4 (SR4) is an alkaline-tolerant cultivar of bread wheat (Triticum aestivum) derived from asymmetric somatic hybridization between the common wheat cultivar Jinan 177 (JN177) and tall wheatgrass. In this study, we aimed to explore the structure and function of alkalinity stress-responsive long non-coding RNAs (lncRNAs) in wheat. Sequencing was employed to identify the lncRNAs associated with stress tolerance and their corresponding targets. Approximately 19 000 novel lncRNA sequences were detected in SR4 and JN177. Upon exposure to alkaline stress, SR4 differentially expressed 5691 lncRNAs, whilst JN177 differentially expressed 5932. We selected five of them (L0760, L6247, L0208, L2098, and L3065) and generated seedlings of transiently knocked down strains using the virus-induced gene-silencing method. Knockdown of L0760 and L2098 caused the plants to exhibit sensitivity to alkaline stress, whereas knockdown of L6247, L0208, and L3065 increased the ability of plants to tolerate alkaline stress. We constructed lncRNA-miRNA-target-mRNA networks and alkali-response-related lncRNA-target-mRNA association networks to analyse the functions of lncRNAs. Collectively, our results demonstrate that lncRNAs may perform different roles under alkaline stress conditions.
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Affiliation(s)
- Lin Wei
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Rong Zhang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Min Zhang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Guangmin Xia
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Shuwei Liu
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
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11
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Sadhukhan A, Prasad SS, Mitra J, Siddiqui N, Sahoo L, Kobayashi Y, Koyama H. How do plants remember drought? PLANTA 2022; 256:7. [PMID: 35687165 DOI: 10.1007/s00425-022-03924-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 05/21/2022] [Indexed: 06/15/2023]
Abstract
Plants develop both short-term and transgenerational memory of drought stress through epigenetic regulation of transcription for a better response to subsequent exposure. Recurrent spells of droughts are more common than a single drought, with intermittent moist recovery intervals. While the detrimental effects of the first drought on plant structure and physiology are unavoidable, if survived, plants can memorize the first drought to present a more robust response to the following droughts. This includes a partial stomatal opening in the watered recovery interval, higher levels of osmoprotectants and ABA, and attenuation of photosynthesis in the subsequent exposure. Short-term drought memory is regulated by ABA and other phytohormone signaling with transcriptional memory behavior in various genes. High levels of methylated histones are deposited at the drought-tolerance genes. During the recovery interval, the RNA polymerase is stalled to be activated by a pause-breaking factor in the subsequent drought. Drought leads to DNA demethylation near drought-response genes, with genetic control of the process. Progenies of the drought-exposed plants can better adapt to drought owing to the inheritance of particular methylation patterns. However, a prolonged watered recovery interval leads to loss of drought memory, mediated by certain demethylases and chromatin accessibility factors. Small RNAs act as critical regulators of drought memory by altering transcript levels of drought-responsive target genes. Further studies in the future will throw more light on the genetic control of drought memory and the interplay of genetic and epigenetic factors in its inheritance. Plants from extreme environments can give queues to understanding robust memory responses at the ecosystem level.
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Affiliation(s)
- Ayan Sadhukhan
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Karwar, Jodhpur, 342037, India.
| | - Shiva Sai Prasad
- Department of Agriculture, Koneru Lakshmaiah Education Foundation, Vaddeswaram, Guntur, Andhra Pradesh, 522502, India
| | - Jayeeta Mitra
- Department of Botany, Arunachal University of Studies, Arunachal Pradesh, Namsai, 792103, India
| | - Nadeem Siddiqui
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, Guntur, Andhra Pradesh, 522502, India
| | - Lingaraj Sahoo
- Department of Bioscience and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, India
| | - Yuriko Kobayashi
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan
| | - Hiroyuki Koyama
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan
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12
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Saeed F, Chaudhry UK, Bakhsh A, Raza A, Saeed Y, Bohra A, Varshney RK. Moving Beyond DNA Sequence to Improve Plant Stress Responses. Front Genet 2022; 13:874648. [PMID: 35518351 PMCID: PMC9061961 DOI: 10.3389/fgene.2022.874648] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 03/31/2022] [Indexed: 01/25/2023] Open
Abstract
Plants offer a habitat for a range of interactions to occur among different stress factors. Epigenetics has become the most promising functional genomics tool, with huge potential for improving plant adaptation to biotic and abiotic stresses. Advances in plant molecular biology have dramatically changed our understanding of the molecular mechanisms that control these interactions, and plant epigenetics has attracted great interest in this context. Accumulating literature substantiates the crucial role of epigenetics in the diversity of plant responses that can be harnessed to accelerate the progress of crop improvement. However, harnessing epigenetics to its full potential will require a thorough understanding of the epigenetic modifications and assessing the functional relevance of these variants. The modern technologies of profiling and engineering plants at genome-wide scale provide new horizons to elucidate how epigenetic modifications occur in plants in response to stress conditions. This review summarizes recent progress on understanding the epigenetic regulation of plant stress responses, methods to detect genome-wide epigenetic modifications, and disentangling their contributions to plant phenotypes from other sources of variations. Key epigenetic mechanisms underlying stress memory are highlighted. Linking plant response with the patterns of epigenetic variations would help devise breeding strategies for improving crop performance under stressed scenarios.
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Affiliation(s)
- Faisal Saeed
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Usman Khalid Chaudhry
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Allah Bakhsh
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Yasir Saeed
- Department of Plant Pathology, Faculty of Agriculture, University of Agriculture, Faisalabad, Pakistan
| | - Abhishek Bohra
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA, Australia
| | - Rajeev K. Varshney
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA, Australia
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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13
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McMahon J, Sayre R, Zidenga T. Cyanogenesis in cassava and its molecular manipulation for crop improvement. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1853-1867. [PMID: 34905020 DOI: 10.1093/jxb/erab545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
While cassava is one of the most important staple crops worldwide, it has received the least investment per capita consumption of any of the major global crops. This is in part due to cassava being a crop of subsistence farmers that is grown in countries with limited resources for crop improvement. While its starchy roots are rich in calories, they are poor in protein and other essential nutrients. In addition, they contain potentially toxic levels of cyanogenic glycosides which must be reduced to safe levels before consumption. Furthermore, cyanogens compromise the shelf life of harvested roots due to cyanide-induced inhibition of mitochondrial respiration, and associated production of reactive oxygen species that accelerate root deterioration. Over the past two decades, the genetic, biochemical, and developmental factors that control cyanogen synthesis, transport, storage, and turnover have largely been elucidated. It is now apparent that cyanogens contribute substantially to whole-plant nitrogen metabolism and protein synthesis in roots. The essential role of cyanogens in root nitrogen metabolism, however, has confounded efforts to create acyanogenic varieties. This review proposes alternative molecular approaches that integrate accelerated cyanogen turnover with nitrogen reassimilation into root protein that may offer a solution to creating a safer, more nutritious cassava crop.
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14
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Drought tolerance improvement in Solanum lycopersicum: an insight into "OMICS" approaches and genome editing. 3 Biotech 2022; 12:63. [PMID: 35186660 PMCID: PMC8825918 DOI: 10.1007/s13205-022-03132-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/24/2022] [Indexed: 12/16/2022] Open
Abstract
Solanum lycopersicum (tomato) is an internationally acclaimed vegetable crop that is grown worldwide. However, drought stress is one of the most critical challenges for tomato production, and it is a crucial task for agricultural biotechnology to produce drought-resistant cultivars. Although breeders have done a lot of work on the tomato to boost quality and quantity of production and enhance resistance to biotic and abiotic stresses, conventional tomato breeding approaches have been limited to improving drought tolerance because of the intricacy of drought traits. Many efforts have been made to better understand the mechanisms involved in adaptation and tolerance to drought stress in tomatoes throughout the years. "Omics" techniques, such as genomics, transcriptomics, proteomics, and metabolomics in combination with modern sequencing technologies, have tremendously aided the discovery of drought-responsive genes. In addition, the availability of biotechnological tools, such as plant transformation and the recently developed genome editing system for tomatoes, has opened up wider opportunities for validating the function of drought-responsive genes and the generation of drought-tolerant varieties. This review highlighted the recent progresses for tomatoes improvement against drought stress through "omics" and "multi-omics" technologies including genetic engineering. We have also discussed the roles of non-coding RNAs and genome editing techniques for drought stress tolerance improvement in tomatoes.
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15
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Gelaw TA, Sanan-Mishra N. Non-Coding RNAs in Response to Drought Stress. Int J Mol Sci 2021; 22:12519. [PMID: 34830399 PMCID: PMC8621352 DOI: 10.3390/ijms222212519] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 02/06/2023] Open
Abstract
Drought stress causes changes in the morphological, physiological, biochemical and molecular characteristics of plants. The response to drought in different plants may vary from avoidance, tolerance and escape to recovery from stress. This response is genetically programmed and regulated in a very complex yet synchronized manner. The crucial genetic regulations mediated by non-coding RNAs (ncRNAs) have emerged as game-changers in modulating the plant responses to drought and other abiotic stresses. The ncRNAs interact with their targets to form potentially subtle regulatory networks that control multiple genes to determine the overall response of plants. Many long and small drought-responsive ncRNAs have been identified and characterized in different plant varieties. The miRNA-based research is better documented, while lncRNA and transposon-derived RNAs are relatively new, and their cellular role is beginning to be understood. In this review, we have compiled the information on the categorization of non-coding RNAs based on their biogenesis and function. We also discuss the available literature on the role of long and small non-coding RNAs in mitigating drought stress in plants.
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Affiliation(s)
- Temesgen Assefa Gelaw
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
- Department of Biotechnology, College of Natural and Computational Science, Debre Birhan University, Debre Birhan P.O. Box 445, Ethiopia
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
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Urquiaga MCDO, Thiebaut F, Hemerly AS, Ferreira PCG. From Trash to Luxury: The Potential Role of Plant LncRNA in DNA Methylation During Abiotic Stress. FRONTIERS IN PLANT SCIENCE 2021; 11:603246. [PMID: 33488652 PMCID: PMC7815527 DOI: 10.3389/fpls.2020.603246] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 12/07/2020] [Indexed: 05/27/2023]
Abstract
Remarkable progress has been made in elucidating important roles of plant non-coding RNAs. Among these RNAs, long noncoding RNAs (lncRNAs) have gained widespread attention, especially their role in plant environmental stress responses. LncRNAs act at different levels of gene expression regulation, and one of these mechanisms is by recruitment of DNA methyltransferases or demethylases to regulate the target gene transcription. In this mini-review, we highlight the function of lncRNAs, including their potential role in RNA-directed DNA Methylation (RdDM) silencing pathway and their potential function under abiotic stresses conditions. Moreover, we also present and discuss studies of lncRNAs in crops. Finally, we propose a path outlook for future research that may be important for plant breeding.
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Affiliation(s)
| | - Flávia Thiebaut
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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