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Yang Z, Li G, Zhang Y, Li F, Zhou T, Ye J, Wang X, Zhang X, Sun Z, Tao X, Wu M, Wu J, Li Y. Crop antiviral defense: Past and future perspective. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2680-3. [PMID: 39190125 DOI: 10.1007/s11427-024-2680-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 07/09/2024] [Indexed: 08/28/2024]
Abstract
Viral pathogens not only threaten the health and life of humans and animals but also cause enormous crop yield losses and contribute to global food insecurity. To defend against viral pathogens, plants have evolved an intricate immune system to perceive and cope with such attacks. Although most of the fundamental studies were carried out in model plants, more recent research in crops has provided new insights into the antiviral strategies employed by crop plants. We summarize recent advances in understanding the biological roles of cellular receptors, RNA silencing, RNA decay, hormone signaling, autophagy, and ubiquitination in manipulating crop host-mediated antiviral responses. The potential functions of circular RNAs, the rhizosphere microbiome, and the foliar microbiome of crops in plant-virus interactions will be fascinating research directions in the future. These findings will be beneficial for the development of modern crop improvement strategies.
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Affiliation(s)
- Zhirui Yang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Guangyao Li
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongliang Zhang
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Fangfang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Tao Zhou
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Jian Ye
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xianbing Wang
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiaoming Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100049, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zongtao Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Xiaorong Tao
- Department of Plant Pathology, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ming Wu
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jianguo Wu
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yi Li
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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López-Virgen AG, Dautt-Castro M, Ulloa-Llanes LK, Casas-Flores S, Contreras-Vergara CA, Hernández-Oñate MA, Sotelo-Mundo RR, Vélez-de la Rocha R, Islas-Osuna MA. Genome-wide identification of gene families related to miRNA biogenesis in Mangifera indica L. and their possible role during heat stress. PeerJ 2024; 12:e17737. [PMID: 39035161 PMCID: PMC11260077 DOI: 10.7717/peerj.17737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 06/23/2024] [Indexed: 07/23/2024] Open
Abstract
Mango is a popular tropical fruit that requires quarantine hot water treatment (QHWT) for postharvest sanitation, which can cause abiotic stress. Plants have various defense mechanisms to cope with stress; miRNAs mainly regulate the expression of these defense responses. Proteins involved in the biogenesis of miRNAs include DICER-like (DCL), ARGONAUTE (AGO), HYPONASTIC LEAVES 1 (HYL1), SERRATE (SE), HUA ENHANCER1 (HEN1), HASTY (HST), and HEAT-SHOCK PROTEIN 90 (HSP90), among others. According to our analysis, the mango genome contains five DCL, thirteen AGO, six HYL, two SE, one HEN1, one HST, and five putative HSP90 genes. Gene structure prediction and domain identification indicate that sequences contain key domains for their respective gene families, including the RNase III domain in DCL and PAZ and PIWI domains for AGOs. In addition, phylogenetic analysis indicates the formation of clades that include the mango sequences and their respective orthologs in other flowering plant species, supporting the idea these are functional orthologs. The analysis of cis-regulatory elements of these genes allowed the identification of MYB, ABRE, GARE, MYC, and MeJA-responsive elements involved in stress responses. Gene expression analysis showed that most genes are induced between 3 to 6 h after QHWT, supporting the early role of miRNAs in stress response. Interestingly, our results suggest that mango rapidly induces the production of miRNAs after heat stress. This research will enable us to investigate further the regulation of gene expression and its effects on commercially cultivated fruits, such as mango, while maintaining sanitary standards.
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Affiliation(s)
- Andrés G. López-Virgen
- CTAOV, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, México
| | - Mitzuko Dautt-Castro
- CTAOV, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, México
| | - Lourdes K. Ulloa-Llanes
- CTAOV, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, México
| | - Sergio Casas-Flores
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, San Luis Potosi, San Luis Potosi, México
| | | | | | - Rogerio R. Sotelo-Mundo
- CTAOA, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, México
| | - Rosabel Vélez-de la Rocha
- Unidad Culiacán, Centro de Investigación en Alimentación y Desarrollo, A.C., Culiacán, Sinaloa, México
| | - Maria A. Islas-Osuna
- CTAOV, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, México
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Zaheer U, Munir F, Salum YM, He W. Function and regulation of plant ARGONAUTE proteins in response to environmental challenges: a review. PeerJ 2024; 12:e17115. [PMID: 38560454 PMCID: PMC10979746 DOI: 10.7717/peerj.17115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/26/2024] [Indexed: 04/04/2024] Open
Abstract
Environmental stresses diversely affect multiple processes related to the growth, development, and yield of many crops worldwide. In response, plants have developed numerous sophisticated defense mechanisms at the cellular and subcellular levels to react and adapt to biotic and abiotic stressors. RNA silencing, which is an innate immune mechanism, mediates sequence-specific gene expression regulation in higher eukaryotes. ARGONAUTE (AGO) proteins are essential components of the RNA-induced silencing complex (RISC). They bind to small noncoding RNAs (sRNAs) and target complementary RNAs, causing translational repression or triggering endonucleolytic cleavage pathways. In this review, we aim to illustrate the recently published molecular functions, regulatory mechanisms, and biological roles of AGO family proteins in model plants and cash crops, especially in the defense against diverse biotic and abiotic stresses, which could be helpful in crop improvement and stress tolerance in various plants.
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Affiliation(s)
- Uroosa Zaheer
- Plant Protection, State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Faisal Munir
- Plant Protection, State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yussuf Mohamed Salum
- Plant Protection, State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Weiyi He
- Plant Protection, State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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Naim D, Ahsan A, Imtiaj A, Mollah NH. Genome-wide identification and in silico characterization of major RNAi gene families in date palm (Phoenix dactylifera). BMC Genom Data 2024; 25:31. [PMID: 38491426 PMCID: PMC10943882 DOI: 10.1186/s12863-024-01217-x] [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: 05/13/2023] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Dates contain various minerals that are essential for good health. The major RNA interference (RNAi) gene families play a vital role in plant growth and development by controlling the expression of protein-coding genes against different biotic and abiotic stresses. However, these gene families for date palm are not yet studied. Therefore, this study has explored major RNAi genes and their characteristics in date palm. RESULTS We have identified 4 PdDCLs, 7 PdAGOs, and 3 PdRDRs as RNAi proteins from the date palm genome by using AtRNAi genes as query sequences in BLASTp search. Domain analysis of predicted RNAi genes has revealed the Helicase_C, Dicer_dimer, PAZ, RNase III, and Piwi domains that are associated with the gene silencing mechanisms. Most PdRNAi proteins have been found in the nucleus and cytosol associated with the gene silencing actions. The gene ontology (GO) enrichment analysis has revealed some important GO terms including RNA interference, dsRNA fragmentation, and ribonuclease_III activity that are related to the protein-coding gene silencing mechanisms. Gene regulatory network (GRN) analysis has identified PAZ and SNF2 as the transcriptional regulators of PdRNAi genes. Top-ranked 10 microRNAs including Pda-miR156b, Pda-miR396a, Pda-miR166a, Pda-miR167d, and Pda-miR529a have been identified as the key post-transcriptional regulators of PdRNAi genes that are associated with different biotic/abiotic stresses. The cis-acting regulatory element analysis of PdRNAi genes has detected some vital cis-acting elements including ABRE, MBS, MYB, MYC, Box-4, G-box, I-box, and STRE that are linked with different abiotic stresses. CONCLUSION The results of this study might be valuable resources for the improvement of different characteristics in date palm by further studies in wet-lab.
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Affiliation(s)
- Darun Naim
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, 6205, Rajshahi, Bangladesh
- Department of Botany, Faculty of Biological Sciences, University of Rajshahi, 6205, Rajshahi, Bangladesh
| | - Asif Ahsan
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, 6205, Rajshahi, Bangladesh
| | - Ahmed Imtiaj
- Department of Botany, Faculty of Biological Sciences, University of Rajshahi, 6205, Rajshahi, Bangladesh
| | - Nurul Haque Mollah
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, 6205, Rajshahi, Bangladesh.
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Hasan MN, Mosharaf MP, Uddin KS, Das KR, Sultana N, Noorunnahar M, Naim D, Mollah MNH. Genome-Wide Identification and Characterization of Major RNAi Genes Highlighting Their Associated Factors in Cowpea ( Vigna unguiculata (L.) Walp.). BIOMED RESEARCH INTERNATIONAL 2023; 2023:8832406. [PMID: 38046903 PMCID: PMC10691899 DOI: 10.1155/2023/8832406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/07/2023] [Accepted: 10/30/2023] [Indexed: 12/05/2023]
Abstract
In different regions of the world, cowpea (Vigna unguiculata (L.) Walp.) is an important vegetable and an excellent source of protein. It lessens the malnutrition of the underprivileged in developing nations and has some positive effects on health, such as a reduction in the prevalence of cancer and cardiovascular disease. However, occasionally, certain biotic and abiotic stresses caused a sharp fall in cowpea yield. Major RNA interference (RNAi) genes like Dicer-like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) are essential for the synthesis of their associated factors like domain, small RNAs (sRNAs), transcription factors, micro-RNAs, and cis-acting factors that shield plants from biotic and abiotic stresses. In this study, applying BLASTP search and phylogenetic tree analysis with reference to the Arabidopsis RNAi (AtRNAi) genes, we discovered 28 VuRNAi genes, including 7 VuDCL, 14 VuAGO, and 7 VuRDR genes in cowpea. We looked at the domains, motifs, gene structures, chromosomal locations, subcellular locations, gene ontology (GO) terms, and regulatory factors (transcription factors, micro-RNAs, and cis-acting elements (CAEs)) to characterize the VuRNAi genes and proteins in cowpea in response to stresses. Predicted VuDCL1, VuDCL2(a, b), VuAGO7, VuAGO10, and VuRDR6 genes might have an impact on cowpea growth, development of the vegetative and flowering stages, and antiviral defense. The VuRNAi gene regulatory features miR395 and miR396 might contribute to grain quality improvement, immunity boosting, and pathogen infection resistance under salinity and drought conditions. Predicted CAEs from the VuRNAi genes might play a role in plant growth and development, improving grain quality and production and protecting plants from biotic and abiotic stresses. Therefore, our study provides crucial information about the functional roles of VuRNAi genes and their associated components, which would aid in the development of future cowpeas that are more resilient to biotic and abiotic stress. The manuscript is available as a preprint at this link: doi:10.1101/2023.02.15.528631v1.
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Affiliation(s)
- Mohammad Nazmol Hasan
- Department of Statistics, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Md Parvez Mosharaf
- School of Business, Faculty of Business, Education, Law and Arts, University of Southern Queensland, Toowoomba, QLD 4350, Australia
| | - Khandoker Saif Uddin
- Department of Quantitative Science (Statistics), International University of Business Agriculture and Technology (IUBAT), Uttara, Bangladesh
| | - Keya Rani Das
- Department of Statistics, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Nasrin Sultana
- Department of Statistics, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Mst. Noorunnahar
- Department of Statistics, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Darun Naim
- Department of Botany, Faculty of Biological Sciences, University of Rajshahi, Rajshahi 6205, Bangladesh
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md. Nurul Haque Mollah
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh
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Elhefnawi HT, Abdel Salam Rashed M, Atta A, Alshegaihi RM, Alwutayd KM, Abd El-Moneim D, Magdy M. Genomic assembly, characterization, and quantification of DICER-like gene family in Okra plants under dehydration conditions. PeerJ 2023; 11:e16232. [PMID: 38025717 PMCID: PMC10668803 DOI: 10.7717/peerj.16232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 09/14/2023] [Indexed: 12/01/2023] Open
Abstract
Background Okra is a plant farmed for its pods, leaves, and stems all of which are edible. It is famous for its ability to tolerate long desiccation periods. It belongs to the Malvaceae family and is a sister species to hibiscus, cotton, and cacao plants. Methods In the current study, okra plants were used as a model to sequence, assemble, and analyze the evolutionary and functional characteristics of the Dicer-like protein gene family (DCL) based on DNAseq and qPCR techniques. Results Four Dicer-like (DCL) single-copy genes of the okra plant Abelmoschus esculentus (L.) Moench (AeDCL) were successfully assembled. The lengths of the AeDCL copies were 8,494, 5,214, 4,731, and 9,329 bp. The detected exons in these samples ranged from a single exon in AeDCL3 to 24 exons in AeDCL4. AeDCLs had five functional domains of two DEAD-like helicase superfamilies, N and C; one Dicer domain; one ribonuclease III domain (a and b); and one double-stranded RNA-binding domain. The PAZ domain was completely annotated only for AeDCL1 and AeDCL3. All AeDCLs were up-regulated under drought conditions, with leaves showing more extensive fold changes than roots. The study focused on a comprehensive genome-wide identification and analysis of the DCL gene family in naturally drought-tolerant okra plants, an orphan crop that can be used as a model for further genomic and transcriptomic studies on drought-tolerance mechanisms in plants.
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Affiliation(s)
| | | | - Ayman Atta
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Rana M. Alshegaihi
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Khairiah Mubarak Alwutayd
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Diaa Abd El-Moneim
- Department of Plant Production (Genetic Branch), Faculty of Environmental Agricultural Sciences, Arish University, El-Arish, Egypt
| | - Mahmoud Magdy
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
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Liu M, Wu H, Hong N, Kang B, Peng B, Liu L, Gu Q. Argonaute 1 and 5 proteins play crucial roles in the defence against cucumber green mottle mosaic virus in watermelon. MOLECULAR PLANT PATHOLOGY 2023; 24:961-972. [PMID: 37118922 PMCID: PMC10346368 DOI: 10.1111/mpp.13344] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/04/2023] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
RNA silencing, a core part of plants' antiviral defence, requires the ARGONAUTE, DICER-like, and RNA-dependent RNA polymerase proteins. However, how these proteins contribute to watermelon's RNA interference (RNAi) pathway response to cucumber green mottle mosaic virus (CGMMV) has not been characterized. Here, we identify seven ClAGO, four ClDCL, and 11 ClRDR genes in watermelon and analyse their expression profiles when infected with CGMMV. ClAGO1 and ClAGO5 expression levels were highly induced by CGMMV infection. The results of ClAGO1 and ClAGO5 overexpression and silencing experiments suggest that these genes play central roles in watermelon's antiviral defence. Furthermore, co-immunoprecipitation and bimolecular fluorescence complementation experiments showed that ClAGO1 interacts with ClAGO5 in vivo, suggesting that ClAGO1 and ClAGO5 co-regulate watermelon defence against CGMMV infection. We also identified the ethylene response factor (ERF) binding site in the promoters of the ClAGO1 and ClAGO5 genes, and ethylene (ETH) treatment significantly increased ClAGO5 expression. Two ERF genes (Cla97C08G147180 and Cla97C06G122830) closely related to ClAGO5 expression were identified using co-expression analysis. Subcellular localization revealed that two ERFs and ClAGO5 predominantly localize at the nucleus, suggesting that enhancement of resistance to CGMMV by ETH is probably achieved through ClAGO5 but not ClAGO1. Our findings reveal aspects of the mechanisms underlying RNA silencing in watermelon against CGMMV.
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Affiliation(s)
- Mei Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
- Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Huijie Wu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Ni Hong
- Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Baoshan Kang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Bin Peng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Liming Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Qinsheng Gu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
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Podder A, Ahmed FF, Suman MZH, Mim AY, Hasan K. Genome-wide identification of DCL, AGO and RDR gene families and their associated functional regulatory element analyses in sunflower (Helianthus annuus). PLoS One 2023; 18:e0286994. [PMID: 37294803 PMCID: PMC10256174 DOI: 10.1371/journal.pone.0286994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/27/2023] [Indexed: 06/11/2023] Open
Abstract
RNA interference (RNAi) regulates a variety of eukaryotic gene expressions that are engaged in response to stress, growth, and the conservation of genomic stability during developmental phases. It is also intimately connected to the post-transcriptional gene silencing (PTGS) process and chromatin modification levels. The entire process of RNA interference (RNAi) pathway gene families mediates RNA silencing. The main factors of RNA silencing are the Dicer-Like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) gene families. To the best of our knowledge, genome-wide identification of RNAi gene families like DCL, AGO, and RDR in sunflower (Helianthus annuus) has not yet been studied despite being discovered in some species. So, the goal of this study is to find the RNAi gene families like DCL, AGO, and RDR in sunflower based on bioinformatics approaches. Therefore, we accomplished an inclusive in silico investigation for genome-wide identification of RNAi pathway gene families DCL, AGO, and RDR through bioinformatics approaches such as (sequence homogeneity, phylogenetic relationship, gene structure, chromosomal localization, PPIs, GO, sub-cellular localization). In this study, we have identified five DCL (HaDCLs), fifteen AGO (HaAGOs), and ten RDR (HaRDRs) in the sunflower genome database corresponding to the RNAi genes of model plant Arabidopsis thaliana based on genome-wide analysis and a phylogenetic method. The analysis of the gene structure that contains exon-intron numbers, conserved domain, and motif composition analyses for all HaDCL, HaAGO, and HaRDR gene families indicated almost homogeneity among the same gene family. The protein-protein interaction (PPI) network analysis illustrated that there exists interconnection among identified three gene families. The analysis of the Gene Ontology (GO) enrichment showed that the detected genes directly contribute to the RNA gene-silencing and were involved in crucial pathways. It was observed that the cis-acting regulatory components connected to the identified genes were shown to be responsive to hormone, light, stress, and other functions. That was found in HaDCL, HaAGO, and HaRDR genes associated with the development and growth of plants. Finally, we are able to provide some essential information about the components of sunflower RNA silencing through our genome-wide comparison and integrated bioinformatics analysis, which open the door for further research into the functional mechanisms of the identified genes and their regulatory elements.
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Affiliation(s)
- Anamika Podder
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Fee Faysal Ahmed
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md. Zahid Hasan Suman
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Afsana Yeasmin Mim
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Khadiza Hasan
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, Bangladesh
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Li Y, Ma E, Yang K, Zhao B, Li Y, Wan P. Genome-wide analysis of key gene families in RNA silencing and their responses to biotic and drought stresses in adzuki bean. BMC Genomics 2023; 24:195. [PMID: 37046231 PMCID: PMC10091639 DOI: 10.1186/s12864-023-09274-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 03/25/2023] [Indexed: 04/14/2023] Open
Abstract
BACKGROUND In plants, RNA silencing is an important conserved mechanism to regulate gene expression and combat against abiotic and biotic stresses. Dicer-like (DCL) and Argonaute (AGO) proteins and RNA-dependent RNA polymerase (RDR) are the core elements involved in gene silencing and their gene families have been explored in many plants. However, these genes and their responses to stresses have not yet been well characterized in adzuki bean. RESULTS A total of 11 AGO, 7 DCL and 6 RDR proteins were identified, and phylogenetic analyses of these proteins showed that they clustered into six, four and four clades respectively. The expression patterns of these genes in susceptible or resistant adzuki bean cultivars challenged with drought, bean common mosaic virus and Podosphaera xanthii infections were further validated by quantitative RT-PCR. The different responses of these proteins under abiotic and biotic stresses indicated their specialized regulatory mechanisms. CONCLUSIONS In this study, 24 genes of the DCL, AGO and RDR gene families in adzuki bean were identified, and the sequence characterization, structure of the encoded proteins, evolutionary relationship with orthologues in other legumes and gene expression patterns under drought and biotic stresses were primarily explored, which enriched our understanding of these genes in adzuki bean. Our findings provide a foundation for the comparative genomic analyses of RNA silencing elements in legume plants and further new insights into the functional complexity of RNA silencing in the response to various stresses in adzuki bean.
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Affiliation(s)
- Yongqiang Li
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture Rural Affairs, College of Biological Science and Resources Environment, Beijing University of Agriculture, HuilongguanBeinonglu 7, Changping District, Beijing, 102206, China.
| | - Enze Ma
- Beijing Key Laboratory of New Technology in Agricultural Application, College of Plant Science and Technology, Beijing University of Agriculture, HuilongguanBeinonglu 7, Changping District, Beijing, 102206, China
| | - Kai Yang
- Beijing Key Laboratory of New Technology in Agricultural Application, College of Plant Science and Technology, Beijing University of Agriculture, HuilongguanBeinonglu 7, Changping District, Beijing, 102206, China
| | - Bo Zhao
- Beijing Key Laboratory of New Technology in Agricultural Application, College of Plant Science and Technology, Beijing University of Agriculture, HuilongguanBeinonglu 7, Changping District, Beijing, 102206, China
| | - Yisong Li
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture Rural Affairs, College of Biological Science and Resources Environment, Beijing University of Agriculture, HuilongguanBeinonglu 7, Changping District, Beijing, 102206, China
| | - Ping Wan
- Beijing Key Laboratory of New Technology in Agricultural Application, College of Plant Science and Technology, Beijing University of Agriculture, HuilongguanBeinonglu 7, Changping District, Beijing, 102206, China.
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Zeng Q, Long G, Yang H, Zhou C, Yang X, Wang Z, Jin D. SfDicer1 participates in the regulation of molting development and reproduction in the white-backed planthopper, Sogatella furcifera. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 191:105347. [PMID: 36963929 DOI: 10.1016/j.pestbp.2023.105347] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/12/2023] [Accepted: 01/21/2023] [Indexed: 06/18/2023]
Abstract
Dicer1 plays a vital role in the formation of mature miRNA and regulates the growth, development, and reproduction of insects. However, it remains to be clarified whether Dicer1 is involved in regulating the biological processes underlying molting and reproduction of Sogatella furcifera (Horváth). Herein, SfDicer1 expression fluctuated in all the developmental stages of S. furcifera and increased as molting progressed. SfDicer1 exhibited high expression in the integument, head, fat body, and ovary of the insects. SfDicer1 dsRNA injection into 1-day-old fourth instar nymphs of S. furcifera substantially decreased the survival rate and expression of the lethal phenotypes of wing malformation and molting defects and significantly inhibited the expression of four conserved miRNAs associated with molting development. Subsequently, following the knockdown of SfDicer1 in the newly emerged (1-12 h) females of S. furcifera, SfVg and SfVgR expression levels were decreased, thereby delaying ovarian development, decreasing the number of eggs, and considerably reducing the hatching rate compared with those of the control. Finally, after silencing SfDicer1 for 48 h, the comparative transcriptome analysis of differentially expressed genes revealed considerable enrichment of the Gene Ontology terms structural constituent of cuticle, structural molecule activity, chitin metabolic process, amino sugar metabolic process, and intracellular anatomical structure, indicating that SfDicer1 inhibition affects the transcription of genes associated with growth and development. Thus, our results suggest that SfDicer1 is essential in the molting, survival, ovarian development, and fecundity of S. furcifera and is a suitable target gene for developing an RNAi-based strategy targeting the most destructive rice insect pest.
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Affiliation(s)
- Qinghui Zeng
- Institute of Entomology, Guizhou University; Guizhou Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, and Scientific Observing and Experimental Station of Crop Pests in Guiyang, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Guiyang 550025, China
| | - Guiyun Long
- Institute of Entomology, Guizhou University; Guizhou Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, and Scientific Observing and Experimental Station of Crop Pests in Guiyang, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Guiyang 550025, China
| | - Hong Yang
- Institute of Entomology, Guizhou University; Guizhou Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, and Scientific Observing and Experimental Station of Crop Pests in Guiyang, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Guiyang 550025, China.
| | - Cao Zhou
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Xibin Yang
- Institute of Entomology, Guizhou University; Guizhou Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, and Scientific Observing and Experimental Station of Crop Pests in Guiyang, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Guiyang 550025, China
| | - Zhao Wang
- College of Environment and Life Sciences, Kaili University, Kaili 556011, China
| | - Daochao Jin
- Institute of Entomology, Guizhou University; Guizhou Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, and Scientific Observing and Experimental Station of Crop Pests in Guiyang, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Guiyang 550025, China
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11
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Yun S, Zhang X. Genome-wide identification, characterization and expression analysis of AGO, DCL, and RDR families in Chenopodium quinoa. Sci Rep 2023; 13:3647. [PMID: 36871121 PMCID: PMC9985633 DOI: 10.1038/s41598-023-30827-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 03/02/2023] [Indexed: 03/06/2023] Open
Abstract
RNA interference is a highly conserved mechanism wherein several types of non-coding small RNAs regulate gene expression at the transcriptional or post-transcriptional level, modulating plant growth, development, antiviral defence, and stress responses. Argonaute (AGO), DCL (Dicer-like), and RNA-dependent RNA polymerase (RDR) are key proteins in this process. Here, these three protein families were identified in Chenopodium quinoa. Further, their phylogenetic relationships with Arabidopsis, their domains, three-dimensional structure modelling, subcellular localization, and functional annotation and expression were analysed. Whole-genome sequence analysis predicted 21 CqAGO, eight CqDCL, and 11 CqRDR genes in quinoa. All three protein families clustered into phylogenetic clades corresponding to those of Arabidopsis, including three AGO clades, four DCL clades, and four RDR clades, suggesting evolutionary conservation. Domain and protein structure analyses of the three gene families showed almost complete homogeneity among members of the same group. Gene ontology annotation revealed that the predicted gene families might be directly involved in RNAi and other important pathways. Largely, these gene families showed significant tissue-specific expression patterns, RNA-sequencing (RNA-seq) data revealed that 20 CqAGO, seven CqDCL, and ten CqRDR genes tended to have preferential expression in inflorescences. Most of them being downregulated in response to drought, cold, salt and low phosphate stress. To our knowledge, this is the first study to elucidate these key protein families involved in the RNAi pathway in quinoa, which are significant for understanding the mechanisms underlying stress responses in this plant.
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Affiliation(s)
- Shiyu Yun
- Institute of Industrial Crops, Shanxi Agricultural University, Taiyuan, 030031, China
| | - Xin Zhang
- Institute of Industrial Crops, Shanxi Agricultural University, Taiyuan, 030031, China.
- State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Taiyuan, 030031, China.
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12
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Jing X, Xu L, Huai X, Zhang H, Zhao F, Qiao Y. Genome-Wide Identification and Characterization of Argonaute, Dicer-like and RNA-Dependent RNA Polymerase Gene Families and Their Expression Analyses in Fragaria spp. Genes (Basel) 2023; 14:genes14010121. [PMID: 36672862 PMCID: PMC9859564 DOI: 10.3390/genes14010121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/19/2022] [Accepted: 12/29/2022] [Indexed: 01/04/2023] Open
Abstract
In the growth and development of plants, some non-coding small RNAs (sRNAs) not only mediate RNA interference at the post-transcriptional level, but also play an important regulatory role in chromatin modification at the transcriptional level. In these processes, the protein factors Argonaute (AGO), Dicer-like (DCL), and RNA-dependent RNA polymerase (RDR) play very important roles in the synthesis of sRNAs respectively. Though they have been identified in many plants, the information about these gene families in strawberry was poorly understood. In this study, using a genome-wide analysis and a phylogenetic approach, 13 AGO, six DCL, and nine RDR genes were identified in diploid strawberry Fragaria vesca. We also identified 33 AGO, 18 DCL, and 28 RDR genes in octoploid strawberry Fragaria × ananassa, studied the expression patterns of these genes in various tissues and developmental stages of strawberry, and researched the response of these genes to some hormones, finding that almost all genes respond to the five hormone stresses. This study is the first report of a genome-wide analysis of AGO, DCL, and RDR gene families in Fragaria spp., in which we provide basic genomic information and expression patterns for these genes. Additionally, this study provides a basis for further research on the functions of these genes and some evidence for the evolution between diploid and octoploid strawberries.
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Affiliation(s)
- Xiaotong Jing
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Linlin Xu
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Xinjia Huai
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Hong Zhang
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Fengli Zhao
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Yushan Qiao
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
- Correspondence:
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13
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Xiang R, Ahmad B, Liang C, Shi X, Yang L, Du G, Wang L. Systematic genome-wide and expression analysis of RNA-directed DNA methylation pathway genes in grapes predicts their involvement in multiple biological processes. FRONTIERS IN PLANT SCIENCE 2022; 13:1089392. [PMID: 36570893 PMCID: PMC9780290 DOI: 10.3389/fpls.2022.1089392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
RNA-directed DNA methylation (RdDM) is an important epigenetic pathway in plants and mediates transcriptional silencing by siRNAs. Different gene families have role in the regulation of the RdDM pathway and there is a lack of information about these gene families in the grapes (Vitis vinifera L.). Here, we mentioned the genome-wide identification, bioinformatics analysis, evolutionary history, and expression profiling of VvRdDM pathway genes against various stresses, hormonal treatments as well as in different organs. Sixty VvRdDM genes belonging to fourteen different families were identified. All the genes were unevenly distributed and chromosome 4 contained the highest number of genes (7). Most of the genes showed similar exon-intron and motif distribution patterns within the same subfamilies. Out of 14 families, only members of 4 families underwent duplication events during the evolutionary process and 50% of members of the AGO family are the result of duplication events. Based on Ka/Ks ratio all duplicated gene pairs have a negative mode of selection. VvRdDM pathway genes showed differential spatiotemporal expression patterns against different hormone and stress treatments. Further, with multiple transcriptome analysis, some VvRdDM genes showed a broad spectrum of high expression in different organs at various stages, and VvRdDM genes also displayed different expression in seeded and seedless cultivars during different phases of seed development. This proposed that VvRdDM genes may play multiple roles in grape growth and development, especially in seed development. qRT-PCR analysis of selected genes further verified the critical roles of RdDM genes in multiple biological processes, especially in seed development/ovule abortion i.e., VvIDN2a, VvDRD1a, VvRDR1a, and VvRDR6. Our study provides detailed information about VvRdDM genes in perspective of gene structure and evolution, as well as expression pattern against different stress, hormones and in different plants parts. It provides new candidate gene resources for further functional characterization and molecular breeding of grapes.
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Affiliation(s)
- Rui Xiang
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Bilal Ahmad
- College of Horticulture, Hebei Agricultural University, Baoding, China
- Department of Horticulture, Muhammad Nawaz Sharif (MNS)-University of Agriculture Multan, Multan, Pakistan
| | - Chen Liang
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Xiaoxin Shi
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Lili Yang
- Shijiazhuang Fruit Research Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Guoqiang Du
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Li Wang
- College of Horticulture, Hebei Agricultural University, Baoding, China
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14
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Hao Y, Dong Z, Zhao Y, Tang W, Wang X, Li J, Wang L, Hu Y, Fang L, Guan X, Gu F, Liu Z, Zhang Z. Phylogenomic analysis of cytochrome P450 multigene family and its differential expression analysis in pepper ( Capsicum annuum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:1078377. [PMID: 36561456 PMCID: PMC9763298 DOI: 10.3389/fpls.2022.1078377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Plant cytochrome P450 is a multifamily enzyme widely involved in biochemical reactions for the synthesis of antioxidants, pigments, structural polymers, and defense-related compounds. Pepper (Capsicum annuum L.) is an economically important plant. A comprehensive identification and characterization of P450 genes would provide valuable information on the evolutionary relationships of genes and their functional characteristics. In this study, we identified P450 genes in pepper with the aid of bioinformatics methods to investigate the phylogenetic relation, gene structure, chromosomal localization, duplicated events, and collinearity among Solanaceae species. We identified and classified 478 genes of P450 from the pepper genome into two major clades and nine subfamilies through phylogenetic analysis. Massive duplication events were found in the P450 gene family, which may explain the expansion of the P450 gene family. In addition, we also found that these duplication genes may have undergone strict purification selection during evolution. Gene expression analysis showed that some P450 genes that belong to clan 71 in pepper may play an important role in placenta and pericarp development. Through quantitative real-time polymerase chain reaction and transcriptome analysis, we also found that many P450 genes were related to defensive and phytohormone response in pepper. These findings provide insight for further studies to identify the biological functions of the P450 genes in pepper.
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Affiliation(s)
- Yupeng Hao
- Hainan Institute, Zhejiang University, Sanya, China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zeyu Dong
- Hainan Institute, Zhejiang University, Sanya, China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yongyan Zhao
- Hainan Institute, Zhejiang University, Sanya, China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Wenchen Tang
- Hainan Institute, Zhejiang University, Sanya, China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | | | - Jun Li
- Hainan Institute, Zhejiang University, Sanya, China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Luyao Wang
- Hainan Institute, Zhejiang University, Sanya, China
| | - Yan Hu
- Hainan Institute, Zhejiang University, Sanya, China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Lei Fang
- Hainan Institute, Zhejiang University, Sanya, China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Xueying Guan
- Hainan Institute, Zhejiang University, Sanya, China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Fenglin Gu
- Spice and Beverage Research Institute, Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, China
| | - Ziji Liu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Haikou, China
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15
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Host-induced gene silencing of PcCesA3 and PcOSBP1 confers resistance to Phytophthora capsici in Nicotiana benthamiana through NbDCL3 and NbDCL4 processed small interfering RNAs. Int J Biol Macromol 2022; 222:1665-1675. [PMID: 36167102 DOI: 10.1016/j.ijbiomac.2022.09.178] [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: 07/21/2022] [Revised: 09/16/2022] [Accepted: 09/17/2022] [Indexed: 11/24/2022]
Abstract
Host-induced gene silencing (HIGS) is a RNA-based system depend on the biological macromolecules generated in plants to control diseases. However, the effector proteins active in the HIGS are uncertain, which impedes its further application, especially for oomycete that lack efficient HIGS targets. Phytophthora capsici is an important oomycete causes blight in over 70 crops. Here, we comprehensively screened efficient HIGS vectors targeting PcCesA3 or PcOSBP1 in P. capsici to better control it and explore the characteristics of efficient HIGS vectors. Among the 26 vectors with different lengths and structures, we found that hairpin vectors with a 70 nt loop and ~ 500 bp stem showed the highest control efficacy, with the expressing of the screened vectors, the infection and fertility of P. capsici were greatly inhibited in transgenic Nicotiana benthamiana. Based on these efficient vectors, we demonstrated that the amount of HIGS vector generated small interfering RNAs (siRNAs) was positively related to gene silencing efficiency and resistance, and that NbDCL3 and NbDCL4 were the key effectors producing siRNAs. This work discovers the principles for efficient HIGS vectors design, and elucidates the molecular mechanism of HIGS, which could benefit the control of many other plant diseases based on HIGS.
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Comprehensive In Silico Analysis of RNA Silencing-Related Genes and Their Regulatory Elements in Wheat (Triticum aestivum L.). BIOMED RESEARCH INTERNATIONAL 2022; 2022:4955209. [PMID: 36177060 PMCID: PMC9513535 DOI: 10.1155/2022/4955209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 08/09/2022] [Accepted: 08/13/2022] [Indexed: 11/17/2022]
Abstract
Dicer-like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) are known as the three major gene families that act as the critical components of RNA interference or silencing mechanisms through the noncoding small RNA molecules (miRNA and siRNA) to regulate the expressions of protein-coding genes in eukaryotic organisms. However, most of their characteristics including structures, chromosomal location, subcellular locations, regulatory elements, and gene networking were not rigorously studied. Our analysis identified 7 TaDCL, 39 TaAGO, and 16 TaRDR genes as RNA interference (RNAi) genes from the wheat genome. Phylogenetic analysis of predicted RNAi proteins with the RNAi proteins of Arabidopsis and rice showed that the predicted proteins of TaDCL, TaAGO, and TaRDR groups are clustered into four, eight, and four subgroups, respectively. Domain, 3D protein structure, motif, and exon-intron structure analyses showed that these proteins conserve identical characteristics within groups and maintain differences between groups. The nonsynonymous/synonymous mutation ratio (Ka/Ks) < 1 suggested that these protein sequences conserve some purifying functions. RNAi genes networking with TFs revealed that ERF, MIKC-MADS, C2H2, BBR-BPC, MYB, and Dof are the key transcriptional regulators of the predicted RNAi-related genes. The cis-regulatory element (CREs) analysis detected some important CREs of RNAi genes that are significantly associated with light, stress, and hormone responses. Expression analysis based on an online database exhibited that almost all of the predicted RNAi genes are expressed in different tissues and organs. A case-control study from the gene expression level showed that some RNAi genes significantly responded to the drought and heat stresses. Overall results would therefore provide an excellent basis for in-depth molecular investigation of these genes and their regulatory elements for wheat crop improvement against different stressors.
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Fu M, Chen Y, Li H, Wang L, Liu R, Liu Z. Genome-Wide Identification and Expression Analyses of the Cotton AGO Genes and Their Potential Roles in Fiber Development and Stress Response. Genes (Basel) 2022; 13:genes13081492. [PMID: 36011401 PMCID: PMC9408788 DOI: 10.3390/genes13081492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/09/2022] [Accepted: 08/19/2022] [Indexed: 11/19/2022] Open
Abstract
Argonaute proteins (AGOs) are indispensable components of RNA silencing. However, systematic characterization of the AGO genes have not been completed in cotton until now. In this study, cotton AGO genes were identified and analyzed with respect to their evolution and expression profile during biotic and abiotic stresses. We identified 14 GaAGO, 14 GrAGO, and 28 GhAGO genes in the genomes of Gossypium arboreum, Gossypium raimondii, and Gossypium hirsutum. Cotton AGO proteins were classified into four subgroups. Structural and functional conservation were observed in the same subgroups based on the analysis of the gene structure and conserved domains. Twenty-four duplicated gene pairs were identified in GhAGO genes, and all of them exhibited strong purifying selection during evolution. Moreover, RNA-seq analysis showed that most of the GhAGO genes exhibit high expression levels in the fiber initiation and elongation processes. Furthermore, the expression profiles of GhAGO genes tested by quantitative real-time polymerase chain reaction (qPCR) demonstrated that they were sensitive to Verticillium wilt infection and salt and drought stresses. Overall, our results will pave the way for further functional investigation of the cotton AGO gene family, which may be involved in fiber development and stress response.
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Affiliation(s)
| | | | | | | | | | - Zhanji Liu
- Correspondence: ; Tel.: +86-531-6665-9992
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18
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Gong Q, Wang Y, Jin Z, Hong Y, Liu Y. Transcriptional and post-transcriptional regulation of RNAi-related gene expression during plant-virus interactions. STRESS BIOLOGY 2022; 2:33. [PMID: 37676459 PMCID: PMC10441928 DOI: 10.1007/s44154-022-00057-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 08/14/2022] [Indexed: 09/08/2023]
Abstract
As sessile organisms, plants encounter diverse invasions from pathogens including viruses. To survive and thrive, plants have evolved multilayered defense mechanisms to combat virus infection. RNAi, also known as RNA silencing, is an across-kingdom innate immunity and gene regulatory machinery. Molecular framework and crucial roles of RNAi in antiviral defense have been well-characterized. However, it is largely unknown that how RNAi is transcriptionally regulated to initiate, maintain and enhance cellular silencing under normal or stress conditions. Recently, insights into the transcriptional and post-transcriptional regulation of RNAi-related genes in different physiological processes have been emerging. In this review, we integrate these new findings to provide updated views on how plants modulate RNAi machinery at the (post-) transcriptional level to respond to virus infection.
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Affiliation(s)
- Qian Gong
- MOE Key Laboratory of Bioinformatics and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Yunjing Wang
- MOE Key Laboratory of Bioinformatics and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Zhenhui Jin
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
- School of Science and the Environment, University of Worcester, Worcester, WR2 6AJ, UK
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
- School of Science and the Environment, University of Worcester, Worcester, WR2 6AJ, UK
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Yule Liu
- MOE Key Laboratory of Bioinformatics and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
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Impact of Exogenous Application of Potato Virus Y-Specific dsRNA on RNA Interference, Pattern-Triggered Immunity and Poly(ADP-ribose) Metabolism. Int J Mol Sci 2022; 23:ijms23147915. [PMID: 35887257 PMCID: PMC9317112 DOI: 10.3390/ijms23147915] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 02/06/2023] Open
Abstract
In this work we developed and exploited a spray-induced gene silencing (SIGS)-based approach to deliver double-stranded RNA (dsRNA), which was found to protect potato against potato virus Y (PVY) infection. Given that dsRNA can act as a defence-inducing signal that can trigger sequence-specific RNA interference (RNAi) and non-specific pattern-triggered immunity (PTI), we suspected that these two pathways may be invoked via exogeneous application of dsRNA, which may account for the alterations in PVY susceptibility in dsRNA-treated potato plants. Therefore, we tested the impact of exogenously applied PVY-derived dsRNA on both these layers of defence (RNAi and PTI) and explored its effect on accumulation of a homologous virus (PVY) and an unrelated virus (potato virus X, PVX). Here, we show that application of PVY dsRNA in potato plants induced accumulation of both small interfering RNAs (siRNAs), a hallmark of RNAi, and some PTI-related gene transcripts such as WRKY29 (WRKY transcription factor 29; molecular marker of PTI), RbohD (respiratory burst oxidase homolog D), EDS5 (enhanced disease susceptibility 5), SERK3 (somatic embryogenesis receptor kinase 3) encoding brassinosteroid-insensitive 1-associated receptor kinase 1 (BAK1), and PR-1b (pathogenesis-related gene 1b). With respect to virus infections, PVY dsRNA suppressed only PVY replication but did not exhibit any effect on PVX infection in spite of the induction of PTI-like effects in the presence of PVX. Given that RNAi-mediated antiviral immunity acts as the major virus resistance mechanism in plants, it can be suggested that dsRNA-based PTI alone may not be strong enough to suppress virus infection. In addition to RNAi- and PTI-inducing activities, we also showed that PVY-specific dsRNA is able to upregulate production of a key enzyme involved in poly(ADP-ribose) metabolism, namely poly(ADP-ribose) glycohydrolase (PARG), which is regarded as a positive regulator of biotic stress responses. These findings offer insights for future development of innovative approaches which could integrate dsRNA-induced RNAi, PTI and modulation of poly(ADP-ribose) metabolism in a co-ordinated manner, to ensure a high level of crop protection.
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Belal MA, Ezzat M, Zhang Y, Xu Z, Cao Y, Han Y. Integrative Analysis of the DICER-like (DCL) Genes From Peach (Prunus persica): A Critical Role in Response to Drought Stress. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.923166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
DICER-likes (DCLs) proteins are the core component for non-coding RNA (ncRNA) biogenesis, playing essential roles in some biological processes. The DCL family has been characterized in model plants, such as Arabidopsis, rice, and poplar. However, the evolutionary aspect and the expression mechanism under drought stress were scarce and have never been reported and characterized in one of the most important worldwide cultivated fruit trees, peach (Prunus persica). Eight DCLs genes in the Prunus persica genome were detected, in addition to 51 DCLs in the other seven Rosaceae genomes. The phylogenetic analysis with Arabidopsis thaliana and RTL1 gene as outgroups suggested that DCL members are divided into four clades: DCL1, DCL2, DCL3, and DCL4 with several gene gain/loss events of DCL gene copies through the evolutionary tract of the Rosacea family. The number of homologous DCL copies within each clade, along with the chromosomal location indicated gene duplication event of the DCL2 gene occurred once for the subfamily Amygdaloideae and twice for Pyrus communis and Prunus dulics and trice for the P. persica on Chromosome number 7 genes. Another duplication event was found for the DCL3 gene that occurred once for all the eight Rosaceae species with no match in A. thaliana. The DCL genetic similarity and activity was evaluated using BLASTp and previously published RNA-seq data among different tissues and over different time points of peach trees exposed to drought conditions. Finally, the expression pattern of PrupeDCLs in response to drought stress was identified, and two of these members, Prupe.7G047900 and Prupe.6G363600, were found as main candidate genes for response to drought stress. Our data presented here provide useful information for a better understanding of the molecular evolution of DCL genes in Rosaceae genomes, and the function of DCLs in P. persica.
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Koeda S, Mori N, Horiuchi R, Watanabe C, Nagano AJ, Shiragane H. PepYLCIV and PepYLCAV resistance gene Pepy-2 encodes DFDGD-Class RNA-dependent RNA polymerase in Capsicum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2437-2452. [PMID: 35652932 DOI: 10.1007/s00122-022-04125-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
A begomovirus resistance gene Pepy-2 encoding the DFDGD-Class RNA-dependent RNA polymerase 3a was identified in pepper (C. annuum) through the forward and reverse genetic analyses. In several countries throughout the world, the whitefly-transmitted begomovirus causes massive yield losses in pepper (Capsicum spp.) production. Although introgression of the genetic resistance against begomovirus to commercial cultivars is strongly required, the recently discovered recessive resistance gene pepy-1, which encodes the messenger RNA surveillance factor Pelota, is the only begomovirus resistance gene identified in Capsicum so far. In this study, we fine-mapped another begomovirus resistance gene from PG1-1 (C. annuum), which is resistant to pepper yellow leaf curl Indonesia virus (PepYLCIV) and pepper yellow leaf curl Aceh virus (PepYLCAV), to further speed up the marker-assisted breeding of begomovirus resistance in peppers. A single dominant locus, Pepy-2, conferring resistance against PepYLCIV in PG1-1 was identified on chromosome 7 by screening recombinants from the F2 and F3 segregating populations derived from a cross between PG1-1 and begomovirus susceptible SCM334. In the target region spanning 722 kb, a strong candidate gene, the RNA-dependent RNA polymerase 3a (CaRDR3a), was identified. The whole-genome and transcriptome sequences of PG1-1 and SCM334 revealed a single Guanine (G) deletion in CaRDR3a first exon, causing a frameshift resulting in loss-of-function in SCM334. In addition, multiple loss-of-function alleles of CaRDR3a were identified in the reference sequences of C. annuum, C. chinense, and C. baccatum in the public database. Furthermore, virus-induced gene silencing of CaRDR3a in PG1-1 resulted in the loss of resistance against PepYLCIV. PG1-1 and the DNA marker developed in this study will be useful to breeders using Pepy-2 in their breeding programs.
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Affiliation(s)
- Sota Koeda
- Graduate School of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan.
- Faculty of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan.
| | - Namiko Mori
- Graduate School of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan
| | - Ryo Horiuchi
- Faculty of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan
| | - Chiho Watanabe
- Faculty of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan
| | - Atsushi J Nagano
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2914, Japan
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22
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Tsai WA, Shafiei-Peters JR, Mitter N, Dietzgen RG. Effects of Elevated Temperature on the Susceptibility of Capsicum Plants to Capsicum Chlorosis Virus Infection. Pathogens 2022; 11:pathogens11020200. [PMID: 35215143 PMCID: PMC8879237 DOI: 10.3390/pathogens11020200] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 02/01/2023] Open
Abstract
Capsicum, an important vegetable crop in Queensland, Australia, is vulnerable to both elevated temperatures and capsicum chlorosis virus (CaCV). Thus, it is imperative to understand the genetic responses of capsicum plants (Capsicum annuum) to CaCV under elevated temperature conditions. Here, we challenged susceptible plants (cv. Yolo Wonder) with CaCV and investigated the effects of elevated temperature on symptom expression, the accumulation of virus-derived short interfering RNA (vsiRNA) and viral RNA, and the expression of plant defense-associated genes. CaCV-inoculated plants initially showed more severe symptoms and higher viral concentrations at a higher temperature (HT, 35 °C) than at ambient temperature (AT, 25 °C). However, symptom recovery and reduced viral RNA accumulation were seen in the CaCV-infected plants grown at HT at later stages of infection. We also observed that HT enhanced the accumulation of vsiRNAs and that, concurrently, RNA interference (RNAi)-related genes, including Dicer-like2 (DCL2), DCL4, RNA-dependent RNA polymerase 1 (RdRp1), RdRp6, and Argonaute2 (AGO2), were upregulated early during infection. Moreover, continuous high levels of vsiRNAs were observed during later stages of CaCV infection at HT. Overall, our investigation suggests that HT facilitates CaCV replication during early infection stages. However, this appears to lead to an early onset of antiviral RNA silencing, resulting in a subsequent recovery from CaCV in systemic leaves.
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23
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Jiao Y, Zhao X, Hao K, Gao X, Xing D, Wang Z, An M, Xia Z, Wu Y. Characterization of small interfering RNAs derived from pepper mild mottle virus in infected pepper plants by high-throughput sequencing. Virus Res 2022; 307:198607. [PMID: 34688783 DOI: 10.1016/j.virusres.2021.198607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/12/2021] [Accepted: 10/17/2021] [Indexed: 11/25/2022]
Abstract
Pepper mild mottle virus (PMMoV) infects pepper plants and induces severe yield losses in China. However, the molecular interaction between PMMoV and pepper plants is largely unknown. RNA silencing is a eukaryotically conserved mechanism against viruses mediated by virus-derived small interfering RNAs (vsiRNAs) in plants. In this study, the profiles of vsiRNAs from PMMoV in infected pepper plants were obtained by high-throughput sequencing. The results showed that vsiRNAs were predominantly 21 and 22 nucleotides (nts) in length, and had a U bias at the 5'-terminal. The single-nucleotide resolution maps revealed that vsiRNAs were heterogeneously distributed throughout PMMoV genomic RNAs and hotspots of sense and antisense strands were mainly located in the RdRp and CP coding regions. The host transcripts targeted by vsiRNAs were predicted and they are mainly involved in physiological pathways related to stress response, cell regulation, and metabolism process. In addition, PMMoV infection induced significant up-regulation of CaAGO1a/1b/2, CaDCL2 and CaRDR1 gene transcripts in pepper plants, which are important components involved in antiviral RNA silencing pathway. Taken together, our results suggest the possible roles of vsiRNAs in PMMoV-pepper interactions.
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Affiliation(s)
- Yubing Jiao
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Xiuxiang Zhao
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Kaiqiang Hao
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Xinran Gao
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Dan Xing
- Institute of Pepper, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Zhiping Wang
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Mengnan An
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Zihao Xia
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China.
| | - Yuanhua Wu
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China.
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24
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Chang L, Tzean Y, Hsin KT, Lin CY, Wang CN, Yeh HH. Stress associated proteins coordinate the activation of comprehensive antiviral immunity in Phalaenopsis orchids. THE NEW PHYTOLOGIST 2022; 233:145-155. [PMID: 34614215 DOI: 10.1111/nph.17776] [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: 04/28/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Viruses cause severe damage on crops, and identification of key gene(s) that can comprehensively activate antiviral immunity will provide insights for designing effective antiviral strategies. Salicylic acid (SA)-mediated antiviral immunity and RNA interference (RNAi) are two independently discovered antiviral pathways. Previously, we identified the orchid stress-associated protein (SAP), Pha13, which serves as a hub in SA-mediated antiviral immunity. As SAPs exist as a protein family, whether duplicated SAPs have redundant or distinctive functions in antiviral immunity remains elusive. We performed functional assays on orchid Pha21, a homolog of Pha13, using transient and transgenic approaches on orchid, Arabidopsis and Nicotiana benthamiana to overexpress and/or silence Pha21. The SA treatment induced the expression of both Pha13 and Pha21, whereas Pha21 was found to play a key role in the initiation of the RNAi pathway in Phalaenopsis orchids. We demonstrated that Pha21-mediated antiviral immunity and enhancement of the RNAi pathway is conserved between dicotyledons and monocotyledons. We provide new insight that orchid SAPs confer distinctive functions to coordinate both SA-signaling and RNAi for comprehensive activation of antiviral immunity, and this information will help us develop antiviral strategies on crops.
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Affiliation(s)
- Li Chang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Yuh Tzean
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Kuan-Ting Hsin
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Chia-Ying Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Chun-Neng Wang
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Hsin-Hung Yeh
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, 10617, Taiwan
- Institute of Biotechnology, National Taiwan University, Taipei, 10617, Taiwan
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25
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Mai J, Liao L, Ling R, Guo X, Lin J, Mo B, Chen W, Yu Y. Study on RNAi-based herbicide for Mikania micrantha. Synth Syst Biotechnol 2021; 6:437-445. [PMID: 34901482 PMCID: PMC8637008 DOI: 10.1016/j.synbio.2021.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 10/10/2021] [Accepted: 11/09/2021] [Indexed: 01/26/2023] Open
Abstract
The invasive plant Mikania micrantha Kunth (M. micrantha) from South America poses a significant threat to the stability and biodiversity of ecosystems. However, an effective and economical method to control M. micrantha is still lacking. RNA interference (RNAi) has been widely studied and applied in agriculture for trait improvement. Spray-induced gene silencing (SIGS) can produce RNAi silencing effects without introducing heritable modifications to the plant genome and is becoming a novel nontransformation strategy for plant protection. In this study, the genes encoding chlorophyll a/b-binding proteins were selected as targets of RNAi, based on high-throughput sequencing of M. micrantha transcriptome and bioinformatic analyses of sequence specificity. Three types of RNAi molecules, double-stranded RNA, RNAi nanomicrosphere, and short hairpin RNA (shRNA), with their corresponding short interfering RNA sequences were designed and synthesized for SIGS vector construction, from which each RNAi molecule was transcribed and extracted to be sprayed on M. micrantha leaves. Whereas water-treated control leaves remained green, leaves treated with RNAi molecules turned yellow and eventually wilted. Quantitative real-time PCR showed that the expression levels of target genes were significantly reduced in the RNAi-treated groups compared with those of the control, suggesting that all three types of RNAi herbicides effectively silenced the endogenous target genes, which are essential for the growth of M. micrantha. We also found that shRNA showed better silencing efficiency than the other two molecules. Taken together, our study successfully designed three types of RNAi-based herbicides that specifically silenced endogenous target genes and controlled the growth of M. micrantha. Moreover, we identified a gene family encoding chlorophyll a/b-binding proteins that is important for the growth and development of M. micrantha and could serve as potential targets for controlling the spread of M. micrantha.
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Key Words
- Chlorophyll a/b-binding protein
- GMOs, genetically modified organisms
- HIGS, host-induced gene silencing
- Invasive plant
- LHCs, light-harvesting complexes
- Mikania micrantha
- Nucleic acid bioherbicide
- RNA interference
- RNAi, RNA interference
- RNP, RNAi nanomicrosphere
- SEM, scanning electron microscope
- SIGS, Spray-induced gene silencing
- Spray-induced gene silencing
- dsRNA, double-stranded RNA
- qRT-PCR, Quantitative real-time PCR
- shRNA, short hairpin RNA
- siRNA, short interfering RNA
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Affiliation(s)
- Jiantao Mai
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, 1066 Xueyuan Avenue, Shenzhen, 518000, PR China
| | - Lingling Liao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, 1066 Xueyuan Avenue, Shenzhen, 518000, PR China
| | - Rongsong Ling
- Institute for Advanced Study, Shenzhen University, 3688 Nanhai Avenue, Shenzhen, 518000, PR China
| | - Xiaolong Guo
- College of Materials Science and Engineering, Shenzhen University, 1066 Xueyuan Avenue, Shenzhen, 518000, PR China
| | - Jingying Lin
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, 1066 Xueyuan Avenue, Shenzhen, 518000, PR China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, 1066 Xueyuan Avenue, Shenzhen, 518000, PR China
| | - Weizhao Chen
- Shenzhen Key Laboratory for Microbial Gene Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, PR China
| | - Yu Yu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, 1066 Xueyuan Avenue, Shenzhen, 518000, PR China
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26
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Gao X, Jia ZQ, Tao HZ, Xu Y, Li YZ, Liu YT. Use of deep sequencing to profile small RNAs derived from tomato spotted wilt orthotospovirus and hippeastrum chlorotic ringspot orthotospovirus in infected Capsicum annuum. Virus Res 2021; 309:198648. [PMID: 34910964 DOI: 10.1016/j.virusres.2021.198648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/16/2021] [Accepted: 11/23/2021] [Indexed: 10/19/2022]
Abstract
Virus-derived small RNAs are one of the key factors of RNA silencing in plant defence against viruses. We obtained virus-derived small interfering RNA profiles from Tomato spotted wilt orthotospovirus and Hippeastrum chlorotic ringspot orthotospovirus infected Capsicum annuum XX19 and XY11 by deep sequencing one day after inoculation. The vsiRNAs data were mapped to the TSWV and HCRV genomes, and the results showed that the vsiRNAs measured 19-24 nucleotides in length. Most of the vsiRNAs were mapped to the S segment of the viral genome. For XX19 and XY11 infected with HCRV, the distribution range of vsiRNAs in S RNA was 52.06-55.20%, while for XX19 and XY11 infected with TSWV, the distribution range of vsiRNAs in S RNA was 87.76-89.07%. The first base at the 5' end of the siRNA from TSWV and HCRV was primarily biased towards A, U, or C. Compared with mock-inoculated XX19 and XY11, the expression level of CaRDR1 was upregulated in TSWV- and HCRV-inoculated XX19 and XY11. CaAGO2 and CaAGO5 were upregulated in XY11 against HCRV infection, and CaRDR2 was downregulated in TSWV-infected XY11 and XX19. The profile of HCRV and TSWV vsiRNA verified in this study could be useful for selecting key vsiRNA such as those in disease-resistant varieties by artificially synthesizing amiRNA.
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Affiliation(s)
- Xue Gao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Zhi-Qiang Jia
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Hong-Zheng Tao
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China; School of Life Science and Technology, Honghe University, Mengzi, 661199, China
| | - Ye Xu
- College of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Yong-Zhong Li
- College of Tobacco Science, Yunnan Agricultural University, Kunming 650201, China.
| | - Ya-Ting Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China.
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27
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Wang Y, Gong Q, Wu Y, Huang F, Ismayil A, Zhang D, Li H, Gu H, Ludman M, Fátyol K, Qi Y, Yoshioka K, Hanley-Bowdoin L, Hong Y, Liu Y. A calmodulin-binding transcription factor links calcium signaling to antiviral RNAi defense in plants. Cell Host Microbe 2021; 29:1393-1406.e7. [PMID: 34352216 DOI: 10.1016/j.chom.2021.07.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/20/2021] [Accepted: 07/06/2021] [Indexed: 10/20/2022]
Abstract
RNA interference (RNAi) is an across-kingdom gene regulatory and defense mechanism. However, little is known about how organisms sense initial cues to mobilize RNAi. Here, we show that wounding to Nicotiana benthamiana cells during virus intrusion activates RNAi-related gene expression through calcium signaling. A rapid wound-induced elevation in calcium fluxes triggers calmodulin-dependent activation of calmodulin-binding transcription activator-3 (CAMTA3), which activates RNA-dependent RNA polymerase-6 and Bifunctional nuclease-2 (BN2) transcription. BN2 stabilizes mRNAs encoding key components of RNAi machinery, notably AGONAUTE1/2 and DICER-LIKE1, by degrading their cognate microRNAs. Consequently, multiple RNAi genes are primed for combating virus invasion. Calmodulin-, CAMTA3-, or BN2-knockdown/knockout plants show increased susceptibility to geminivirus, cucumovirus, and potyvirus. Notably, Geminivirus V2 protein can disrupt the calmodulin-CAMTA3 interaction to counteract RNAi defense. These findings link Ca2+ signaling to RNAi and reveal versatility of host antiviral defense and viral counter-defense.
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Affiliation(s)
- Yunjing Wang
- MOE Key Laboratory of Bioinformatics and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Qian Gong
- MOE Key Laboratory of Bioinformatics and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Yuyao Wu
- MOE Key Laboratory of Bioinformatics and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Fan Huang
- MOE Key Laboratory of Bioinformatics and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Asigul Ismayil
- MOE Key Laboratory of Bioinformatics and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Danfeng Zhang
- MOE Key Laboratory of Bioinformatics and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Huangai Li
- MOE Key Laboratory of Bioinformatics and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Hanqing Gu
- MOE Key Laboratory of Bioinformatics and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Márta Ludman
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi Albert u. 4, Gödöllő 2100, Hungary
| | - Károly Fátyol
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi Albert u. 4, Gödöllő 2100, Hungary
| | - Yijun Qi
- MOE Key Laboratory of Bioinformatics and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Keiko Yoshioka
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh NC 27695, USA
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; School of Science and the Environment, University of Worcester, Worcester WR2 6AJ, UK
| | - Yule Liu
- MOE Key Laboratory of Bioinformatics and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
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28
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Ahmed FF, Hossen MI, Sarkar MAR, Konak JN, Zohra FT, Shoyeb M, Mondal S. Genome-wide identification of DCL, AGO and RDR gene families and their associated functional regulatory elements analyses in banana (Musa acuminata). PLoS One 2021; 16:e0256873. [PMID: 34473743 PMCID: PMC8412350 DOI: 10.1371/journal.pone.0256873] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/17/2021] [Indexed: 12/15/2022] Open
Abstract
RNA silencing is mediated through RNA interference (RNAi) pathway gene families, i.e., Dicer-Like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) and their cis-acting regulatory elements. The RNAi pathway is also directly connected with the post-transcriptional gene silencing (PTGS) mechanism, and the pathway controls eukaryotic gene regulation during growth, development, and stress response. Nevertheless, genome-wide identification of RNAi pathway gene families such as DCL, AGO, and RDR and their regulatory network analyses related to transcription factors have not been studied in many fruit crop species, including banana (Musa acuminata). In this study, we studied in silico genome-wide identification and characterization of DCL, AGO, and RDR genes in bananas thoroughly via integrated bioinformatics approaches. A genome-wide analysis identified 3 MaDCL, 13 MaAGO, and 5 MaRDR candidate genes based on multiple sequence alignment and phylogenetic tree related to the RNAi pathway in banana genomes. These genes correspond to the Arabidopsis thaliana RNAi silencing genes. The analysis of the conserved domain, motif, and gene structure (exon-intron numbers) for MaDCL, MaAGO, and MaRDR genes showed higher homogeneity within the same gene family. The Gene Ontology (GO) enrichment analysis exhibited that the identified RNAi genes could be involved in RNA silencing and associated metabolic pathways. A number of important transcription factors (TFs), e.g., ERF, Dof, C2H2, TCP, GATA and MIKC_MADS families, were identified by network and sub-network analyses between TFs and candidate RNAi gene families. Furthermore, the cis-acting regulatory elements related to light-responsive (LR), stress-responsive (SR), hormone-responsive (HR), and other activities (OT) functions were identified in candidate MaDCL, MaAGO, and MaRDR genes. These genome-wide analyses of these RNAi gene families provide valuable information related to RNA silencing, which would shed light on further characterization of RNAi genes, their regulatory elements, and functional roles, which might be helpful for banana improvement in the breeding program.
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Affiliation(s)
- Fee Faysal Ahmed
- Faculty of Science, Department of Mathematics, Jashore University of Science and Technology, Jashore, Bangladesh
- * E-mail:
| | - Md. Imran Hossen
- Faculty of Science, Department of Mathematics, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md. Abdur Rauf Sarkar
- Faculty of Biological Science and Technology, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Jesmin Naher Konak
- Faculty of Life Science, Department of Biochemistry and Molecular Biology, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Fatema Tuz Zohra
- Faculty of Agriculture, Laboratory of Fruit Science, Saga University, Honjo-machi, Saga, Japan
| | - Md. Shoyeb
- Faculty of Biological Science and Technology, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Samiran Mondal
- Faculty of Science, Department of Mathematics, Jashore University of Science and Technology, Jashore, Bangladesh
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29
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Cervantes-Pérez SA, Yong-Villalobos L, Florez-Zapata NMV, Oropeza-Aburto A, Rico-Reséndiz F, Amasende-Morales I, Lan T, Martínez O, Vielle-Calzada JP, Albert VA, Herrera-Estrella L. Atypical DNA methylation, sRNA-size distribution, and female gametogenesis in Utricularia gibba. Sci Rep 2021; 11:15725. [PMID: 34344949 PMCID: PMC8333044 DOI: 10.1038/s41598-021-95054-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 07/20/2021] [Indexed: 12/27/2022] Open
Abstract
The most studied DNA methylation pathway in plants is the RNA Directed DNA Methylation (RdDM), a conserved mechanism that involves the role of noncoding RNAs to control the expansion of the noncoding genome. Genome-wide DNA methylation levels have been reported to correlate with genome size. However, little is known about the catalog of noncoding RNAs and the impact on DNA methylation in small plant genomes with reduced noncoding regions. Because of the small length of intergenic regions in the compact genome of the carnivorous plant Utricularia gibba, we investigated its repertoire of noncoding RNA and DNA methylation landscape. Here, we report that, compared to other angiosperms, U. gibba has an unusual distribution of small RNAs and reduced global DNA methylation levels. DNA methylation was determined using a novel strategy based on long-read DNA sequencing with the Pacific Bioscience platform and confirmed by whole-genome bisulfite sequencing. Moreover, some key genes involved in the RdDM pathway may not represented by compensatory paralogs or comprise truncated proteins, for example, U. gibba DICER-LIKE 3 (DCL3), encoding a DICER endonuclease that produces 24-nt small-interfering RNAs, has lost key domains required for complete function. Our results unveil that a truncated DCL3 correlates with a decreased proportion of 24-nt small-interfering RNAs, low DNA methylation levels, and developmental abnormalities during female gametogenesis in U. gibba. Alterations in female gametogenesis are reminiscent of RdDM mutant phenotypes in Arabidopsis thaliana. It would be interesting to further study the biological implications of the DCL3 truncation in U. gibba, as it could represent an initial step in the evolution of RdDM pathway in compact genomes.
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Affiliation(s)
- Sergio Alan Cervantes-Pérez
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824, Irapuato, Guanajuato, Mexico
| | - Lenin Yong-Villalobos
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824, Irapuato, Guanajuato, Mexico.,Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Department, Texas Tech University, Lubbock, TX, 79409, USA
| | - Nathalia M V Florez-Zapata
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824, Irapuato, Guanajuato, Mexico.,Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Avenida Paseo Bolívar (Circunvalar) #16-20, Bogotá, DC, 111311, Colombia
| | - Araceli Oropeza-Aburto
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824, Irapuato, Guanajuato, Mexico
| | - Félix Rico-Reséndiz
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824, Irapuato, Guanajuato, Mexico
| | - Itzel Amasende-Morales
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824, Irapuato, Guanajuato, Mexico
| | - Tianying Lan
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | - Octavio Martínez
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824, Irapuato, Guanajuato, Mexico
| | - Jean Philippe Vielle-Calzada
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824, Irapuato, Guanajuato, Mexico
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA.,School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824, Irapuato, Guanajuato, Mexico. .,Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Department, Texas Tech University, Lubbock, TX, 79409, USA.
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Genome-Wide Identification and Evolutionary Analysis of Argonaute Genes in Hexaploid Bread Wheat. BIOMED RESEARCH INTERNATIONAL 2021; 2021:9983858. [PMID: 34239939 PMCID: PMC8233069 DOI: 10.1155/2021/9983858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 05/16/2021] [Accepted: 06/08/2021] [Indexed: 01/02/2023]
Abstract
Argonaute (AGO) proteins play a pivotal role in plant growth and development as the core components of RNA-induced silencing complex (RISC). However, no systematic characterization of AGO genes in wheat has been reported to date. In this study, a total number of 69 TaAGO genes in the hexaploid bread wheat (Triticum aestivum cv. Chinese Spring) genome, divided into 10 subfamilies, were identified. Compared to all wheat genes, TaAGOs showed a significantly lower evolutionary rate, which is consistent with their high conservation in eukaryotes. However, the homoeolog retention was remarkably higher than the average, implying the nonredundant biological importance of TaAGO genes in bread wheat. Further homoeologous gene expression bias analyses revealed that TaAGOs may have undergone neofunctionalization after polyploidization and duplication through the divergent expression of homoeologous gene copies, to provide new opportunities for the generation of adaptive traits. Moreover, quantitative real-time polymerase chain reaction (qRT-PCR) analyses indicated that TaAGO gene expression was involved in response to heat, drought, and salt stresses. Our results would provide a theoretical basis for future studies on the biological functions of TaAGO genes in wheat and other gramineous species.
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Genome-wide identification, evolutionary relationship and expression analysis of AGO, DCL and RDR family genes in tea. Sci Rep 2021; 11:8679. [PMID: 33883595 PMCID: PMC8060290 DOI: 10.1038/s41598-021-87991-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/07/2021] [Indexed: 12/05/2022] Open
Abstract
Three gene families in plants viz. Argonaute (AGOs), Dicer-like (DCLs) and RNA dependent RNA polymerase (RDRs) constitute the core components of small RNA mediated gene silencing machinery. The present study endeavours to identify members of these gene families in tea and to investigate their expression patterns in different tissues and various stress regimes. Using genome-wide analysis, we have identified 18 AGOs, 5 DCLs and 9 RDRs in tea, and analyzed their phylogenetic relationship with orthologs of Arabidopsis thaliana. Gene expression analysis revealed constitutive expression of CsAGO1 in all the studied tissues and stress conditions, whereas CsAGO10c showed most variable expression among all the genes. CsAGO10c gene was found to be upregulated in tissues undergoing high meristematic activity such as buds and roots, as well as in Exobasidium vexans infected samples. CsRDR2 and two paralogs of CsAGO4, which are known to participate in biogenesis of hc-siRNAs, showed similarities in their expression levels in most of the tea plant tissues. This report provides first ever insight into the important gene families involved in biogenesis of small RNAs in tea. The comprehensive knowledge of these small RNA biogenesis purveyors can be utilized for tea crop improvement aimed at stress tolerance and quality enhancement.
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Mosharaf MP, Rahman H, Ahsan MA, Akond Z, Ahmed FF, Islam MM, Moni MA, Mollah MNH. In silico identification and characterization of AGO, DCL and RDR gene families and their associated regulatory elements in sweet orange (Citrus sinensis L.). PLoS One 2020; 15:e0228233. [PMID: 33347517 PMCID: PMC7751981 DOI: 10.1371/journal.pone.0228233] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 12/07/2020] [Indexed: 12/30/2022] Open
Abstract
RNA interference (RNAi) plays key roles in post-transcriptional and chromatin modification levels as well as regulates various eukaryotic gene expressions which are involved in stress responses, development and maintenance of genome integrity during developmental stages. The whole mechanism of RNAi pathway is directly involved with the gene-silencing process by the interaction of Dicer-Like (DCL), Argonaute (AGO) and RNA-dependent RNA polymerase (RDR) gene families and their regulatory elements. However, these RNAi gene families and their sub-cellular locations, functional pathways and regulatory components were not extensively investigated in the case of economically and nutritionally important fruit plant sweet orange (Citrus sinensis L.). Therefore, in silico characterization, gene diversity and regulatory factor analysis of RNA silencing genes in C. sinensis were conducted by using the integrated bioinformatics approaches. Genome-wide comparison analysis based on phylogenetic tree approach detected 4 CsDCL, 8 CsAGO and 4 CsRDR as RNAi candidate genes in C. sinensis corresponding to the RNAi genes of model plant Arabidopsis thaliana. The domain and motif composition and gene structure analyses for all three gene families exhibited almost homogeneity within the same group members. The Gene Ontology enrichment analysis clearly indicated that the predicted genes have direct involvement into the gene-silencing and other important pathways. The key regulatory transcription factors (TFs) MYB, Dof, ERF, NAC, MIKC_MADS, WRKY and bZIP were identified by their interaction network analysis with the predicted genes. The cis-acting regulatory elements associated with the predicted genes were detected as responsive to light, stress and hormone functions. Furthermore, the expressed sequence tag (EST) analysis showed that these RNAi candidate genes were highly expressed in fruit and leaves indicating their organ specific functions. Our genome-wide comparison and integrated bioinformatics analyses provided some necessary information about sweet orange RNA silencing components that would pave a ground for further investigation of functional mechanism of the predicted genes and their regulatory factors.
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Affiliation(s)
- Md. Parvez Mosharaf
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
| | - Hafizur Rahman
- Department of Microbiology, Rajshahi Institute of Biosciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Asif Ahsan
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
| | - Zobaer Akond
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
- Institute of Environmental Science, University of Rajshahi, Rajshahi, Bangladesh
- Agricultural Statistics and ICT Division, Bangladesh Agricultural Research Institute (BARI), Gazipur, Bangladesh
| | - Fee Faysal Ahmed
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
- Department of Mathematics, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md. Mazharul Islam
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
| | - Mohammad Ali Moni
- The University of Sydney, Sydney Medical School, School of Medical Sciences, Discipline of Biomedical Science, Sydney, New South Wales, Australia
| | - Md. Nurul Haque Mollah
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
- * E-mail:
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Cao Y, Xu X, Jiang L. Integrative analysis of the RNA interference toolbox in two Salicaceae willow species, and their roles in stress response in poplar (Populus trichocarpa Torr. & Gray). Int J Biol Macromol 2020; 162:1127-1139. [DOI: 10.1016/j.ijbiomac.2020.06.235] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/31/2020] [Accepted: 06/24/2020] [Indexed: 10/24/2022]
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Genome-Wide Identification and Coexpression Network Analysis of DNA Methylation Pathway Genes and Their Differentiated Functions in Ginkgo biloba L. FORESTS 2020. [DOI: 10.3390/f11101076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
DNA methylation plays a vital role in diverse biological processes. DNA methyltransferases (DNMTs) genes and RNA-directed DNA methylation (RdDM)-related genes are key genes responsible for establishing and maintaining genome DNA methylation in plants. In the present study, we systematically identified nine GbDNMTs in Ginkgo biloba, including the three common families of GbMET1a/1b, GbCMT2, and GbDRMa/b/2a/2b/2c, and a fourth family—GbDNMT3—which is absent in most angiosperms. We also identified twenty RdDM-related genes, including four GbDCLs, six GbAGOs, and ten GbRDRs. Expression analysis of the genes showed the different patterns of individual genes, and 15 of 29 genes displayed expression change under five types of abiotic stress. Gene coexpression analysis and weighted gene co-expression network analysis (WGCNA) using 126 public transcriptomic datasets revealed that these genes were clustered into two groups. In group I, genes covered members from all six families which were preferentially expressed in the ovulate strobile and fruit. A gene ontology (GO) enrichment analysis of WGCNA modules indicated that group I genes were most correlated with the biological process of cell proliferation. Group II only consisted of RdDM-related genes, including GbDRMs, GbAGOs, and GbRDRs, but no GbDCLs, and these genes were specifically expressed in the cambium, suggesting that they may function in a dicer-like (DCL)-independent RdDM pathway in specific tissues. The gene module related to group II was most enriched in signal transduction, cell communication, and the response to the stimulus. These results demonstrate that gene family members could be conserved or diverged across species, and multi-member families in the same pathway may cluster into different modules to function differentially. The study provides insight into the DNA methylation genes and their possible functions in G. biloba, laying a foundation for the further study of DNA methylation in gymnosperms.
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Srideepthi R, Krishna MSR, Suneetha P, Krishna RS, Karthikeyan S. Genome-wide identification, characterization and expression analysis of non-RD receptor like kinase gene family under Colletotrichum truncatum stress conditions in hot pepper. Genetica 2020; 148:283-296. [PMID: 32918190 DOI: 10.1007/s10709-020-00104-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 09/08/2020] [Indexed: 11/24/2022]
Abstract
Receptor like kinases (RLKs) are preserved upstream signaling molecules which regulate several biological processes from plant development to various stress adaptation programs. Non arginine aspartate (non-RD) a prominent class of RLKs plays a significant role in disease resistance and apoptosis in plants. In present investigation, a comprehensive in silico analysis for non-RD Kinase gene family as well as identification of gene structures, sequence similarity, chromosomal localization, gene duplication analysis, promoter analysis, transcript expression profiles and phylogenic studies were done. In this study, twenty-six genes were observed on nine out of twelve chromosomes. All these genes were clustered into five subfamilies under large monophyletic group termed as Interleukin-1 Receptor-Associated Kinase (IRAK) family. Some of the important physiochemical properties of twenty-six proteins are determined and ranged in the following order: (a) Amino acids size ranged from (620 to 1781) (b) Molecular weight ranged as of (70.11 to 197.11 KDa) and (c) Theoretical PI ranged from (5.69 to 8.63) respectively. Structural diversity in genomic structure among non-RD kinase gene family was identified and presence of pathogen induced cis regulatory elements including STRE, MYC, MYB, and W box were found. Expression profiles revealed the potential ability of three genes CaRLK1 from LRRXII and CaRLK15,16 from stress antifung subfamily were pointedly upregulated beyond the severe stress time period (9 DAI) in anthracnose resistant genotype PBC-80 in response to Colletotrichum truncatum infection. Subsequently, in silico studies from the available genome sequencing data helped us to identify candidate genes tangled in inducing disease resistance.
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Affiliation(s)
- R Srideepthi
- Koneru Lakshmaiah Education Foundation, Guntur, India
| | - M S R Krishna
- Koneru Lakshmaiah Education Foundation, Guntur, India.
| | - P Suneetha
- Professor Jaya Shanker Telangana State Agricultural University, Hyderabad, India
| | - R Sai Krishna
- ICAR- National Rice Research Institute, Cuttack, India
| | - S Karthikeyan
- Koneru Lakshmaiah Education Foundation, Guntur, India
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Cui DL, Meng JY, Ren XY, Yue JJ, Fu HY, Huang MT, Zhang QQ, Gao SJ. Genome-wide identification and characterization of DCL, AGO and RDR gene families in Saccharum spontaneum. Sci Rep 2020; 10:13202. [PMID: 32764599 PMCID: PMC7413343 DOI: 10.1038/s41598-020-70061-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 07/23/2020] [Indexed: 12/25/2022] Open
Abstract
RNA silencing is a conserved mechanism in eukaryotic organisms to regulate gene expression. Argonaute (AGO), Dicer-like (DCL) and RNA-dependent RNA polymerase (RDR) proteins are critical components of RNA silencing, but how these gene families’ functions in sugarcane were largely unknown. Most stress-resistance genes in modern sugarcane cultivars (Saccharum spp.) were originated from wild species of Saccharum, for example S. spontaneum. Here, we used genome-wide analysis and a phylogenetic approach to identify four DCL, 21 AGO and 11 RDR genes in the S. spontaneum genome (termed SsDCL, SsAGO and SsRDR, respectively). Several genes, particularly some of the SsAGOs, appeared to have undergone tandem or segmental duplications events. RNA-sequencing data revealed that four SsAGO genes (SsAGO18c, SsAGO18b, SsAGO10e and SsAGO6b) and three SsRDR genes (SsRDR2b, SsRDR2d and SsRDR3) tended to have preferential expression in stem tissue, while SsRDR5 was preferentially expressed in leaves. qRT-PCR analysis showed that SsAGO10c, SsDCL2 and SsRDR6b expressions were strongly upregulated, whereas that of SsAGO18b, SsRDR1a, SsRDR2b/2d and SsRDR5 was significantly depressed in S. spontaneum plants exposed to PEG-induced dehydration stress or infected with Xanthomonas albilineans, causal agent of leaf scald disease of sugarcane, suggesting that these genes play important roles in responses of S. spontaneum to biotic and abiotic stresses.
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Affiliation(s)
- Dong-Li Cui
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jian-Yu Meng
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Xiao-Yan Ren
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jing-Jing Yue
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Hua-Ying Fu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Mei-Ting Huang
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Qing-Qi Zhang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
| | - San-Ji Gao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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Genome-Wide Identification of RNA Silencing-Related Genes and Their Expressional Analysis in Response to Heat Stress in Barley ( Hordeum vulgare L.). Biomolecules 2020; 10:biom10060929. [PMID: 32570964 PMCID: PMC7356095 DOI: 10.3390/biom10060929] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/10/2020] [Accepted: 06/15/2020] [Indexed: 12/16/2022] Open
Abstract
Barley (Hordeum vulgare L.) is an economically important crop cultivated in temperate climates all over the world. Adverse environmental factors negatively affect its survival and productivity. RNA silencing is a conserved pathway involved in the regulation of growth, development and stress responses. The key components of RNA silencing are the Dicer-like proteins (DCLs), Argonautes (AGOs) and RNA-dependent RNA polymerases (RDRs). Despite its economic importance, there is no available comprehensive report on barley RNA silencing machinery and its regulation. In this study, we in silico identified five DCL (HvDCL), eleven AGO (HvAGO) and seven RDR (HvRDR) genes in the barley genome. Genomic localization, phylogenetic analysis, domain organization and functional/catalytic motif identification were also performed. To understand the regulation of RNA silencing, we experimentally analysed the transcriptional changes in response to moderate, persistent or gradient heat stress treatments: transcriptional accumulation of siRNA- but not miRNA-based silencing factor was consistently detected. These results suggest that RNA silencing is dynamically regulated and may be involved in the coordination of development and environmental adaptation in barley. In summary, our work provides information about barley RNA silencing components and will be a ground for the selection of candidate factors and in-depth functional/mechanistic analyses.
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Moura MO, Fausto AKS, Fanelli A, Guedes FADF, Silva TDF, Romanel E, Vaslin MFS. Genome-wide identification of the Dicer-like family in cotton and analysis of the DCL expression modulation in response to biotic stress in two contrasting commercial cultivars. BMC PLANT BIOLOGY 2019; 19:503. [PMID: 31729948 PMCID: PMC6858778 DOI: 10.1186/s12870-019-2112-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 10/31/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Dicer-like proteins (DCLs) are essential players in RNA-silencing mechanisms, acting in gene regulation via miRNAs and in antiviral protection in plants and have also been associated to other biotic and abiotic stresses. To the best of our knowledge, despite being identified in some crops, cotton DCLs haven't been characterized until now. In this work, we characterized the DCLs of three cotton species and analyzed their expression profiles during biotic stress. RESULTS As main results, 11 DCLs in the allotetraploid cotton Gossypium hirsutum, 7 and 6 in the diploid G. arboreum and G. raimondii, were identified, respectively. Among some DCLs duplications observed in these genomes, the presence of an extra DCL3 in the three cotton species were detected, which haven't been found in others eudicots. All the DCL types identified by in silico analysis in the allotetraploid cotton genome were able to generate transcripts, as observed by gene expression analysis in distinct tissues. Based on the importance of DCLs for plant defense against virus, responses of cotton DCLs to virus infection and/or herbivore attack using two commercial cotton cultivars (cv.), one susceptible (FM966) and another resistant (DO) to polerovirus CLRDV infection, were analyzed. Both cvs. Responded differently to virus infection. At the inoculation site, the resistant cv. showed strong induction of DCL2a and b, while the susceptible cv. showed a down-regulation of these genes, wherever DCL4 expression was highly induced. A time course of DCL expression in aerial parts far from inoculation site along infection showed that DCL2b and DCL4 were repressed 24 h after infection in the susceptible cotton. As CLRDV is aphid-transmitted, herbivore attack was also checked. Opposite expression pattern of DCL2a and b and DCL4 was observed for R and S cottons, showing that aphid feeding alone may induce DCL modulation. CONCLUSIONS Almost all the DCLs of the allotetraploide G. hirsutum cotton were found in their relative diploids. Duplications of DCL2 and DCL3 were found in the three species. All four classes of DCL responded to aphid attack and virus infection in G. hirsutum. DCLs initial responses against the virus itself and/or herbivore attack may be contributing towards virus resistance.
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Affiliation(s)
- Marianna O. Moura
- Departamento de Virologia, Instituto de Microbiologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-590 Brazil
| | - Anna Karoline S. Fausto
- Departamento de Virologia, Instituto de Microbiologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-590 Brazil
| | - Amanda Fanelli
- Departamento de Biotecnologia, Escola de Engenharia de Lorena/Universidade de São Paulo (EEL/USP), Lorena, SP 12602-810 Brazil
| | - Fernanda A. de F. Guedes
- Programa de Pós-graduação em Biotecnologia Vegetal, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-590 Brazil
| | - Tatiane da F. Silva
- Departamento de Biotecnologia, Escola de Engenharia de Lorena/Universidade de São Paulo (EEL/USP), Lorena, SP 12602-810 Brazil
| | - Elisson Romanel
- Departamento de Biotecnologia, Escola de Engenharia de Lorena/Universidade de São Paulo (EEL/USP), Lorena, SP 12602-810 Brazil
| | - Maite F. S. Vaslin
- Departamento de Virologia, Instituto de Microbiologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-590 Brazil
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Ali M, Gai WX, Khattak AM, Khan A, Haq SU, Ma X, Wei AM, Muhammad I, Jan I, Gong ZH. Knockdown of the chitin-binding protein family gene CaChiIV1 increased sensitivity to Phytophthora capsici and drought stress in pepper plants. Mol Genet Genomics 2019. [PMID: 31175439 DOI: 10.1007/s00438-019-01583-1587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Phytophthora capsici has been the most destructive pathogen of pepper plants (Capsicum annuum L.), possessing the ability to quickly overcome the host defense system. In this context, the chitin-binding protein (CBP) family member CaChiIV1 regulates the response to P. capsici and abiotic stresses. The relevance of functional characterization and regulation of CaChiIV1 has not been explored in horticultural crops, especially pepper plants. The target gene (CaChiIV1) was isolated from pepper plants and cloned; the encoded protein carries a chitin-binding domain (CBD) that is rich in cysteine residues and has a hinge region with an abundance of proline and glycine residues. Additionally, the conserved regions in the promoter have a remarkable motif, "TTGACC". The expression of CaChiIV1 was markedly regulated by methyl-jasmonate (MeJA), hydrogen peroxide (H2O2), melatonin, mannitol and P. capsici (PC and HX-9) infection. Knockdown of CaChiIV1 in pepper plants increased sensitivity to P. capsici (PC strain). Higher malondialdehyde (MDA) content and relative electrolyte leakage (REL) but lower antioxidant enzyme activities, chlorophyll content, root activity, and proline content were observed in CaChiIV1-silenced plants than in control plants. In conclusion, CaChiIV1-silenced pepper plants displayed increased susceptibility to P. capsici infection due to changes in expression of defense-related genes, thus showing its coregulation affect in particular conditions. Furthermore, antioxidant enzymes and proline content were largely diminished in CaChiIV1-silenced plants. Therefore, this evidence suggests that the CaChiIV1 gene plays a prominent role in the defense mechanism of pepper plants against P. capsici infection. In the future, the potential role of the CaChiIV1 gene in defense regulatory pathways and its coregulation with other pathogen-related genes should be identified.
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Affiliation(s)
- Muhammad Ali
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Wen-Xian Gai
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Abdul Mateen Khattak
- Department of Horticulture, The University of Agriculture, Peshawar, Khyber Pakhtunkhwa, Pakistan
- College of Information and Electrical Engineering, China Agricultural University, Beijing, People's Republic of China
| | - Abid Khan
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Saeed Ul Haq
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiao Ma
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ai-Min Wei
- Tianjin Vegetable Research Center, Tianjin, 300192, People's Republic of China
| | - Izhar Muhammad
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ibadullah Jan
- Department of Agriculture, University of Swabi, Khyber Pakhtunkhwa, Pakistan
| | - Zhen-Hui Gong
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Sabbione A, Daurelio L, Vegetti A, Talón M, Tadeo F, Dotto M. Genome-wide analysis of AGO, DCL and RDR gene families reveals RNA-directed DNA methylation is involved in fruit abscission in Citrus sinensis. BMC PLANT BIOLOGY 2019; 19:401. [PMID: 31510935 PMCID: PMC6739940 DOI: 10.1186/s12870-019-1998-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 08/29/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND Small RNAs regulate a wide variety of processes in plants, from organ development to both biotic and abiotic stress response. Being master regulators in genetic networks, their biogenesis and action is a fundamental aspect to characterize in order to understand plant growth and development. Three main gene families are critical components of RNA silencing: DICER-LIKE (DCL), ARGONAUTE (AGO) and RNA-DEPENDENT RNA POLYMERASE (RDR). Even though they have been characterized in other plant species, there is no information about these gene families in Citrus sinensis, one of the most important fruit species from both economical and nutritional reasons. While small RNAs have been implicated in the regulation of multiple aspects of plant growth and development, their role in the abscission process has not been characterized yet. RESULTS Using genome-wide analysis and a phylogenetic approach, we identified a total of 13 AGO, 5 DCL and 7 RDR genes. We characterized their expression patterns in root, leaf, flesh, peel and embryo samples using RNA-seq data. Moreover, we studied their role in fruit abscission through gene expression analysis in fruit rind compared to abscission zone from samples obtained by laser capture microdissection. Interestingly, we determined that the expression of several RNA silencing factors are down-regulated in fruit abscission zone, being particularly represented gene components of the RNA-dependent DNA Methylation pathway, indicating that repression of this process is necessary for fruit abscission to take place in Citrus sinensis. CONCLUSIONS The members of these 3 families present characteristic conserved domains and distinct expression patterns. We provide a detailed analysis of the members of these families and improved the annotation of some of these genes based on RNA-seq data. Our data suggests that the RNA-dependent DNA Methylation pathway is involved in the important fruit abscission process in C. sinensis.
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Affiliation(s)
- Agustín Sabbione
- Facultad de Ciencias Agrarias, Universidad Nacional del Litoral, Esperanza, Argentina
- Laboratorio de Investigaciones en Fisiología y Biología Molecular Vegetal (LIFiBVe), Cátedra de Fisiología Vegetal, Facultad de Ciencias Agrarias, Universidad Nacional del Litoral, Esperanza, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Lucas Daurelio
- Laboratorio de Investigaciones en Fisiología y Biología Molecular Vegetal (LIFiBVe), Cátedra de Fisiología Vegetal, Facultad de Ciencias Agrarias, Universidad Nacional del Litoral, Esperanza, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Abelardo Vegetti
- Facultad de Ciencias Agrarias, Universidad Nacional del Litoral, Esperanza, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Manuel Talón
- Centre de Genómica, Institut Valencià d’Investigacions Agràries (IVIA), Montcada, València, Spain
| | - Francisco Tadeo
- Centre de Genómica, Institut Valencià d’Investigacions Agràries (IVIA), Montcada, València, Spain
| | - Marcela Dotto
- Facultad de Ciencias Agrarias, Universidad Nacional del Litoral, Esperanza, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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Knockdown of the chitin-binding protein family gene CaChiIV1 increased sensitivity to Phytophthora capsici and drought stress in pepper plants. Mol Genet Genomics 2019; 294:1311-1326. [PMID: 31175439 DOI: 10.1007/s00438-019-01583-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/29/2019] [Indexed: 12/31/2022]
Abstract
Phytophthora capsici has been the most destructive pathogen of pepper plants (Capsicum annuum L.), possessing the ability to quickly overcome the host defense system. In this context, the chitin-binding protein (CBP) family member CaChiIV1 regulates the response to P. capsici and abiotic stresses. The relevance of functional characterization and regulation of CaChiIV1 has not been explored in horticultural crops, especially pepper plants. The target gene (CaChiIV1) was isolated from pepper plants and cloned; the encoded protein carries a chitin-binding domain (CBD) that is rich in cysteine residues and has a hinge region with an abundance of proline and glycine residues. Additionally, the conserved regions in the promoter have a remarkable motif, "TTGACC". The expression of CaChiIV1 was markedly regulated by methyl-jasmonate (MeJA), hydrogen peroxide (H2O2), melatonin, mannitol and P. capsici (PC and HX-9) infection. Knockdown of CaChiIV1 in pepper plants increased sensitivity to P. capsici (PC strain). Higher malondialdehyde (MDA) content and relative electrolyte leakage (REL) but lower antioxidant enzyme activities, chlorophyll content, root activity, and proline content were observed in CaChiIV1-silenced plants than in control plants. In conclusion, CaChiIV1-silenced pepper plants displayed increased susceptibility to P. capsici infection due to changes in expression of defense-related genes, thus showing its coregulation affect in particular conditions. Furthermore, antioxidant enzymes and proline content were largely diminished in CaChiIV1-silenced plants. Therefore, this evidence suggests that the CaChiIV1 gene plays a prominent role in the defense mechanism of pepper plants against P. capsici infection. In the future, the potential role of the CaChiIV1 gene in defense regulatory pathways and its coregulation with other pathogen-related genes should be identified.
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RNA Interference: A Natural Immune System of Plants to Counteract Biotic Stressors. Cells 2019; 8:cells8010038. [PMID: 30634662 PMCID: PMC6356646 DOI: 10.3390/cells8010038] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/01/2019] [Accepted: 01/07/2019] [Indexed: 02/06/2023] Open
Abstract
During plant-pathogen interactions, plants have to defend the living transposable elements from pathogens. In response to such elements, plants activate a variety of defense mechanisms to counteract the aggressiveness of biotic stressors. RNA interference (RNAi) is a key biological process in plants to inhibit gene expression both transcriptionally and post-transcriptionally, using three different groups of proteins to resist the virulence of pathogens. However, pathogens trigger an anti-silencing mechanism through the expression of suppressors to block host RNAi. The disruption of the silencing mechanism is a virulence strategy of pathogens to promote infection in the invaded hosts. In this review, we summarize the RNA silencing pathway, anti-silencing suppressors, and counter-defenses of plants to viral, fungal, and bacterial pathogens.
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Plant Defense Genes against Biotic Stresses. Int J Mol Sci 2018; 19:ijms19082446. [PMID: 30126226 PMCID: PMC6121480 DOI: 10.3390/ijms19082446] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 08/18/2018] [Indexed: 12/30/2022] Open
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