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Guo K, Huang Z, Wang C, Liu X, Chen Y, Fang J, Jin W, Xu J, Wu F, Zhou X. Nematicidal effects of silencing arginine kinase in the pine wood nematode, Bursaphelenchus xylophilus, determined using a dsRNA-like siRNA assembly. Int J Biol Macromol 2024; 279:135401. [PMID: 39245109 DOI: 10.1016/j.ijbiomac.2024.135401] [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: 07/24/2024] [Revised: 09/04/2024] [Accepted: 09/05/2024] [Indexed: 09/10/2024]
Abstract
The pine wood nematode Bursaphelenchus xylophilus is a highly invasive species responsible for the widespread pine wilt disease. Double-stranded RNA (dsRNA) biopesticides represent a novel strategy for controlling plant-parasitic nematodes. The B. xylophilus arginine kinase (BxAK) features a conserved ATP-binding domain and exhibits nematode-specific divergence in the phylogenetic tree. Notably, whole-mount in situ hybridization signals are evident in the nematode head and middle sections, particularly in the juvenile stage before sex differentiation. In this study, we developed a novel dsRNA-like small interfering RNA (siRNA) assembly that specifically targets BxAK and presents highly nematicidal effects. The RNA interference (RNAi) efficiency achieved a 95.9 % reduction in second-stage juveniles. In bioassays, the median lethal concentrations of this siRNA assembly against B. xylophilus were 168.5 ng/μl for juveniles and 603.8 ng/μl for adults within 48 h. Moreover, transcriptomic results revealed significantly downregulated expression levels of genes related to metabolism and development, suggesting that the mode of action of BxAK silencing is related to disruptions in energy homeostasis and juvenile development. In conclusion, BxAK is a molecular target for controlling B. xylophilus, and our siRNA assembly significantly enhances RNAi efficiency and lowers the lethal concentration required, making it a promising candidate for future biocontrol applications.
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Affiliation(s)
- Kai Guo
- State key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, People's Republic of China
| | - Ziqian Huang
- State key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, People's Republic of China
| | - Chunyu Wang
- State key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, People's Republic of China
| | - Xuemeng Liu
- State key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, People's Republic of China
| | - Ye Chen
- State key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, People's Republic of China
| | - Jiadi Fang
- State key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, People's Republic of China
| | - Weibo Jin
- Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China
| | - Jinfeng Xu
- Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China
| | - Fangli Wu
- Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China.
| | - Xiang Zhou
- State key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, People's Republic of China.
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Kamaraju D, Chatterjee M, Papolu PK, Shivakumara TN, Sreevathsa R, Hada A, Rao U. Host-induced RNA interference targeting the neuromotor gene FMRFamide-like peptide-14 (Mi-flp14) perturbs Meloidogyne incognita parasitic success in eggplant. PLANT CELL REPORTS 2024; 43:178. [PMID: 38907748 DOI: 10.1007/s00299-024-03259-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 06/04/2024] [Indexed: 06/24/2024]
Abstract
KEY MESSAGE The study demonstrates the successful management of Meloidogyne incognita in eggplant using Mi-flp14 RNA interference, showing reduced nematode penetration and reproduction without off-target effects across multiple generations. Root-knot nematode, Meloidogyne incognita, causes huge yield losses worldwide. Neuromotor function in M. incognita governed by 19 neuropeptides is vital for parasitism and parasite biology. The present study establishes the utility of Mi-flp14 for managing M. incognita in eggplant in continuation of our earlier proof of concept in tobacco (US patent US2015/0361445A1). Mi-flp14 hairpin RNA construct was used for generating 19 independent transgenic eggplant events. PCR and Southern hybridization analysis confirmed transgene integration and its orientation, while RT-qPCR and Northern hybridization established the generation of dsRNA and siRNA of Mi-flp14. In vitro and in vivo bio-efficacy analysis of single-copy events against M. incognita showed reduced nematode penetration and development at various intervals that negatively impacted reproduction. Interestingly, M. incognita preferred wild-type plants over the transgenics even when unbiased equal opportunity was provided for the infection. A significant reduction in disease parameters was observed in transgenic plants viz., galls (40-48%), females (40-50%), egg masses (35-40%), eggs/egg mass (50-55%), and derived multiplication factor (60-65%) compared to wild type. A unique demonstration of perturbed expression of Mi-flp14 in partially penetrated juveniles and female nematodes established successful host-mediated RNAi both at the time of penetration even before the nematodes started withdrawing plant nutrients and later stage, respectively. The absence of off-target effects in transgenic plants was supported by the normal growth phenotype of the plants and T-DNA integration loci. Stability in the bio-efficacy against M. incognita across T1- to T4-generation transgenic plants established the utility of silencing Mi-flp14 for nematode management. This study demonstrates the significance of targeting Mi-flp14 in eggplant for nematode management, particularly to address global agricultural challenges posed by M. incognita.
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Affiliation(s)
- Divya Kamaraju
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, 751024, India
| | - Madhurima Chatterjee
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Pradeep K Papolu
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | | | - Rohini Sreevathsa
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Alkesh Hada
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
- Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), The Volcani Center, 7505101, Bet Dagan, Israel.
| | - Uma Rao
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
- Engrave Biolabs Pvt Ltd. , Shanthipuram, Kukatpally, Hyderabad, 500072, India.
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Rui L, Wen TY, Qiu YJ, Yang D, Ye JR, Wu XQ. A pioneer nematode effector suppresses plant reactive oxygen species burst by interacting with the class III peroxidase. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38808618 DOI: 10.1111/pce.14939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/02/2024] [Accepted: 04/27/2024] [Indexed: 05/30/2024]
Abstract
Bursaphelenchus xylophilus is the pathogen of pine wilt disease, which can devastate the pine forest ecosystem. Usually, plant cells generate reactive oxygen species (ROS) as a defensive substance or signalling molecules to resist the infection of nematodes. However, little is known about how B. xylophilus effectors mediate the plant ROS metabolism. Here, we identified a pioneer B. xylophilus Prx3-interacting effector 1 (BxPIE1) expressed in the dorsal gland cells and the intestine. Silencing of the BxPIE1 gene resulted in reduced nematode reproduction and a delay in disease progression during parasitic stages, with the upregulation of pathogenesis-related (PR) genes PtPR-3 (class Ⅳ chitinase) and PtPR-9 (peroxidase). The protein-protein interaction assays further demonstrated that BxPIE1 interacts with a Pinus thunbergii class III peroxidase (PtPrx3), which produces H2O2 under biotic stress. The expression of BxPIE1 and PtPrx3 was upregulated during the infection stage. Furthermore, BxPIE1 effectively inhibited H2O2 generating from class III peroxidase and ascorbate can recover the virulence of siBxPIE1-treated B. xylophilus by scavenging H2O2. Taken together, BxPIE1 is an important virulence factor, revealing a novel mechanism utilized by nematodes to suppress plant immunity.
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Affiliation(s)
- Lin Rui
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, China
| | - Tong-Yue Wen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, China
| | - Yi-Jun Qiu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, China
| | - Dan Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, China
| | - Jian-Ren Ye
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, China
| | - Xiao-Qin Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, China
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Yang J, Zhou S, Yang Z, Shi X, Liu H, Yang Z, Peng D, Ding Z, Ye S. Silencing of the T-type voltage-gated calcium channel α 1 subunit by fungus-mediated RNAi altered the structure of F-actin and caused defective behaviors in Ditylenchus destructor. Mol Biol Rep 2024; 51:673. [PMID: 38787479 DOI: 10.1007/s11033-024-09626-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND T-type calcium channels, characterized as low-voltage activated (LVA) calcium channels, play crucial physiological roles across a wide range of tissues, including both the neuronal and nonneuronal systems. Using in situ hybridization and RNA interference (RNAi) techniques in vitro, we previously identified the tissue distribution and physiological function of the T-type calcium channel α1 subunit (DdCα1G) in the plant-parasitic nematode Ditylenchus destructor. METHODS AND RESULTS To further characterize the functional role of DdCα1G, we employed a combination of immunohistochemistry and fungus-mediated RNAi and found that DdCα1G was clearly distributed in stylet-related tissue, oesophageal gland-related tissue, secretory-excretory duct-related tissue and male spicule-related tissue. Silencing DdCα1G led to impairments in the locomotion, feeding, reproductive ability and protein secretion of nematodes. To confirm the defects in behavior, we used phalloidin staining to examine muscle changes in DdCα1G-RNAi nematodes. Our observations demonstrated that defective behaviors are associated with related muscular atrophy. CONCLUSION Our findings provide a deeper understanding of the physiological functions of T-type calcium channels in plant-parasitic nematodes. The T-type calcium channel can be considered a promising target for sustainable nematode management practices.
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Affiliation(s)
- Jiahao Yang
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Siyu Zhou
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Ziqi Yang
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Xuqi Shi
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Haoran Liu
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Zhuhong Yang
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, 410128, China
- Hunan Provincial Engineering & Technology Research Center for Biopesticide and Formulation Processing, Changsha, Hunan, 410128, China
| | - Deliang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Zhong Ding
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, 410128, China.
- Hunan Provincial Engineering & Technology Research Center for Biopesticide and Formulation Processing, Changsha, Hunan, 410128, China.
| | - Shan Ye
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, 410128, China.
- Hunan Provincial Engineering & Technology Research Center for Biopesticide and Formulation Processing, Changsha, Hunan, 410128, China.
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Dutta TK, Akhil VS, Kundu A, Dash M, Phani V, Sirohi A, Somvanshi VS. Induced knockdown of Mg-odr-1 and Mg-odr-3 perturbed the host seeking behavior of Meloidogyne graminicola in rice. Heliyon 2024; 10:e26384. [PMID: 38420492 PMCID: PMC10900406 DOI: 10.1016/j.heliyon.2024.e26384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 01/18/2024] [Accepted: 02/12/2024] [Indexed: 03/02/2024] Open
Abstract
Root-knot nematode Meloidogyne graminicola is one of the most destructive plant parasites in upland as well as direct seeded rice. As an integral part of nematode biology, host finding behavior involves perceiving and responding to different chemical cues originating from the rhizosphere. A sustainable management tactic may include retardation of nematode chemoreception that would impair them to detect and discriminate the host stimuli. Deciphering the molecular basis of nematode chemoreception is vital to identify chokepoints for chemical or genetic interventions. However, compared to the well-characterized chemoreception mechanism in model nematode Caenorhabditis elegans, plant nematode chemoreception is yet underexplored. Herein, the full-length cDNA sequences of two chemotaxis-related genes (Mg-odr-1 and Mg-odr-3) were cloned from M. graminicola. Both the genes were markedly upregulated in the early developmental stages of M. graminicola suggesting their involvement in host finding processes. RNAi-induced independent knockdown of Mg-odr-1 and Mg-odr-3 caused behavioral aberration in second-stage juveniles of M. graminicola which in turn perturbed the nematodes' host finding ability and parasitic success inside rice roots. Additionally, nematodes' chemotactic response to different host root exudates, volatile and nonvolatile compounds was affected. Our results demonstrating the role of specific chemosensory genes in modulating M. graminicola host seeking behavior can enrich the existing knowledge of plant nematode chemoreception mechanism, and these genes can be targeted for novel nematicide development or in planta RNAi screens.
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Affiliation(s)
- Tushar K. Dutta
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Voodikala S. Akhil
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Artha Kundu
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Manoranjan Dash
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Victor Phani
- Department of Agricultural Entomology, Uttar Banga Krishi Viswavidyalaya (Majhian Campus), Balurghat, 733133, India
| | - Anil Sirohi
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Vishal S. Somvanshi
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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Thorat YE, Dutta TK, Jain PK, Subramaniam K, Sirohi A. A nematode-inducible promoter can effectively drives RNAi construct to confer Meloidogyne incognita resistance in tomato. PLANT CELL REPORTS 2023; 43:3. [PMID: 38117317 DOI: 10.1007/s00299-023-03114-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 10/30/2023] [Indexed: 12/21/2023]
Abstract
KEY MESSAGE Heterologous expression of a nematode-responsive promoter in tomato successfully driven the RNAi constructs to impart root-knot nematode resistance. The root-knot nematode Meloidogyne incognita seriously afflicts the global productivity of tomatoes. Nematode management options are extremely reliant on chemical methods, however, only a handful of nematicides are commercially available. Additionally, nematodes have developed resistance-breaking phenotypes against the commercially available Mi gene-expressing tomatoes. Nematode resistance in crop plants can be enhanced using the bio-safe RNAi technology, in which plants are genetically modified to express nematode gene-specific dsRNA/siRNA molecules. However, the majority of the RNAi crops conferring nematode tolerance have used constitutive promoters, which have many limitations. In the present study, using promoter-GUS fusion, we functionally validated two nematode-inducible root-specific promoters (pAt1g74770 and pAt2g18140, identified from Arabidopsis thaliana) in the Solanum lycopersicum-M. incognita pathosystem. pAt2g18140 was found to be nematode-responsive during 10-21 days post-inoculation (dpi) and became non-responsive during the late infection stage (28 dpi). In contrast, pAt1g74770 remained nematode-responsive for a longer duration (10-28 dpi). Next, a number of transgenic lines were developed that expressed RNAi constructs (independently targeting the M. incognita integrase and splicing factor genes) driven by the pAt1g74770 promoter. M. incognita parasitic success (measured by multiplication factor ratio) in pAt1g74770:integrase and pAt1g74770:splicing factor RNAi lines were significantly reduced by 60.83-74.93% and 69.34-75.31%, respectively, compared to the control. These data were comparable with the RNAi lines having CaMV35S as the promoter. Further, a long-term RNAi effect was evident, because females extracted from transgenic lines were of deformed shape with depleted transcripts of integrase and splicing factor genes. We conclude that pAt1g74770 can be an attractive alternative to drive localized expression of RNAi constructs rather than using a constitutive promoter. The pAt1g74770-driven gene silencing system can be expanded into different plant-nematode interaction models.
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Affiliation(s)
- Yogesh E Thorat
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
- Biological Control Centre, ICAR-Indian Institute of Sugarcane Research, Ahmednagar, Maharashtra, 413712, India
| | - Tushar K Dutta
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Pradeep K Jain
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | | | - Anil Sirohi
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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Dutta TK, Akhil VS, Dash M, Kundu A, Phani V, Sirohi A. Molecular and functional characterization of chemosensory genes from the root-knot nematode Meloidogyne graminicola. BMC Genomics 2023; 24:745. [PMID: 38057766 DOI: 10.1186/s12864-023-09864-7] [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: 08/18/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023] Open
Abstract
BACKGROUND Root-knot nematode Meloidogyne graminicola has emerged as a major threat in rice agroecosystems owing to climate change-induced changes in cultivation practices. Synthetic nematicides are continually being withdrawn from the nematode management toolbox because of their ill effects on the environment. A sustainable strategy would be to develop novel nematicides or resistant plants that would target nematode sensory perception, which is a key step in the host finding biology of plant-parasitic nematodes (PPNs). However, compared to the extensive literature on the free-living nematode Caenorhabditis elegans, negligible research has been performed on PPN chemosensory biology. RESULTS The present study characterizes the five chemosensory genes (Mg-odr-7, Mg-tax-4, Mg-tax-4.1, Mg-osm-9, and Mg-ocr-2) from M. graminicola that are putatively associated with nematode host-finding biology. All the genes were highly transcribed in the early life stages, and RNA interference (RNAi)-induced downregulation of each candidate gene perturbed the normal behavioural phenotypes of M. graminicola, as determined by examining the tracking pattern of juveniles on Pluronic gel medium, attraction to and penetration in rice root tip, and developmental progression in rice root. In addition, a detrimental effect on nematode chemotaxis towards different volatile and nonvolatile organic compounds and host root exudates was documented. CONCLUSION Our findings enrich the existing literature on PPN chemosensory biology and can supplement future research aimed at identifying a comprehensive chemosensory signal transduction pathway in PPNs.
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Affiliation(s)
- Tushar K Dutta
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Voodikala S Akhil
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Manoranjan Dash
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Artha Kundu
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Victor Phani
- Department of Agricultural Entomology, College of Agriculture, Uttar Banga Krishi Viswavidyalaya, Balurghat, Dakshin Dinajpur, West Bengal, India
| | - Anil Sirohi
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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Khan A, Chen S, Fatima S, Ahamad L, Siddiqui MA. Biotechnological Tools to Elucidate the Mechanism of Plant and Nematode Interactions. PLANTS (BASEL, SWITZERLAND) 2023; 12:2387. [PMID: 37376010 DOI: 10.3390/plants12122387] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 06/29/2023]
Abstract
Plant-parasitic nematodes (PPNs) pose a threat to global food security in both the developed and developing worlds. PPNs cause crop losses worth a total of more than USD 150 billion worldwide. The sedentary root-knot nematodes (RKNs) also cause severe damage to various agricultural crops and establish compatible relationships with a broad range of host plants. This review aims to provide a broad overview of the strategies used to identify the morpho-physiological and molecular events that occur during RKN parasitism. It describes the most current developments in the transcriptomic, proteomic, and metabolomic strategies of nematodes, which are important for understanding compatible interactions of plants and nematodes, and several strategies for enhancing plant resistance against RKNs. We will highlight recent rapid advances in molecular strategies, such as gene-silencing technologies, RNA interference (RNAi), and small interfering RNA (siRNA) effector proteins, that are leading to considerable progress in understanding the mechanism of plant-nematode interactions. We also take into account genetic engineering strategies, such as targeted genome editing techniques, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) (CRISPR/Cas-9) system, and quantitative trait loci (QTL), to enhance the resistance of plants against nematodes.
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Affiliation(s)
- Arshad Khan
- Department of Botany, Aligarh Muslim University, Aligarh 202002, India
| | - Shaohua Chen
- National Key Laboratory of Green Pesticide, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Saba Fatima
- Department of Botany, Aligarh Muslim University, Aligarh 202002, India
| | - Lukman Ahamad
- Department of Botany, Aligarh Muslim University, Aligarh 202002, India
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Nguyê˜n PV, Biện TLT, Tôn LB, Lê ÐÐ, Wright MK, Mantelin S, Petitot AS, Fernandez D, Bellafiore S. Meloidogyne-SP4 effector gene silencing reduces reproduction of root-knot nematodes in rice (Oryza sativa). NEMATOLOGY 2022. [DOI: 10.1163/15685411-bja10152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Summary
The root-knot nematodes (RKN) Meloidogyne graminicola and M. incognita are responsible for rice yield losses worldwide, particularly in Asia and Africa. Previous studies demonstrated that nematode-secreted proteins are crucial for root invasion and establishment in the host. We present some characteristics of a pioneer effector, M. incognita-secreted protein 4 (Mi-SP4), which is conserved in RKN and required for infection in compatible rice-RKN interactions. In situ hybridisation assays revealed Mi-SP4 expression in the dorsal pharyngeal gland of M. incognita second-stage juveniles (J2). Meloidogyne-SP4 transcripts strongly accumulated in pre-parasitic J2 and decreased in later parasitic stages of M. incognita and M. graminicola. Transient expression of the nematode effector gene in Nicotiana benthamiana leaves and onion cells indicated that GFP-tagged Mi-SP4 was present in the cytoplasm and accumulated in the nucleus of the plant cells. In vitro RNA interference (RNAi) gene silencing, obtained by soaking J2 with small-interfering (si)RNA si4-1, decreased Mi -SP4 expression in J2 by 35% and significantly reduced M. incognita reproduction in rice by at least 30%. Similarly, host-mediated gene silencing of the nematode SP4 effector candidate gene in transgenic rice plants significantly reduced M. graminicola reproduction by 26% to 47%. The data obtained demonstrate that Mi -SP4 is a pioneer virulence effector, which plays an essential role in both M. incognita and M. graminicola pathogenicity on rice.
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Affiliation(s)
- Phong V. Nguyê˜n
- Faculty of Biological Sciences, Nông Lâm University, Hô` Chí Minh City, Vietnam
| | - Thanh LT. Biện
- Faculty of Biological Sciences, Nông Lâm University, Hô` Chí Minh City, Vietnam
| | - Linh B. Tôn
- Faculty of Biological Sciences, Nông Lâm University, Hô` Chí Minh City, Vietnam
| | - Ðôn Ð. Lê
- Faculty of Biological Sciences, Nông Lâm University, Hô` Chí Minh City, Vietnam
| | | | - Sophie Mantelin
- INRAE UMR 1355 Institute Sophia Agrobiotech, 400 route des Chappes, BP 167, 06903 Sophia Antipolis-Cedex, France
| | - Anne-Sophie Petitot
- PHIM Plant Health Institute, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Diana Fernandez
- PHIM Plant Health Institute, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Stéphane Bellafiore
- PHIM Plant Health Institute, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
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Function of lipid binding proteins of parasitic helminths: still a long road. Parasitol Res 2022; 121:1117-1129. [PMID: 35169885 DOI: 10.1007/s00436-022-07463-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 02/07/2022] [Indexed: 10/19/2022]
Abstract
Infections with parasitic helminths cause severe debilitating and sometimes lethal diseases in humans and domestic animals on a global scale. Unable to synthesize de novo their own fatty acids and sterols, helminth parasites (nematodes, trematodes, cestodes) rely on their hosts for their supply. These organisms produce and secrete a wide range of lipid binding proteins that are, in most cases, structurally different from the ones found in their hosts, placing them as possible novel therapeutic targets. In this sense, a lot of effort has been made towards the structure determination of these proteins, but their precise function is still unknown. In this review, we aim to present the current knowledge on the functions of LBPs present in parasitic helminths as well as novel members of this highly heterogeneous group of proteins.
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Hada A, Singh D, Papolu PK, Banakar P, Raj A, Rao U. Host-mediated RNAi for simultaneous silencing of different functional groups of genes in Meloidogyne incognita using fusion cassettes in Nicotiana tabacum. PLANT CELL REPORTS 2021; 40:2287-2302. [PMID: 34387737 DOI: 10.1007/s00299-021-02767-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/05/2021] [Indexed: 05/27/2023]
Abstract
KEY MESSAGE This study establishes possibility of combinatorial silencing of more than one functional gene for their efficacy against root-knot nematode, M. incognita. Root-knot nematodes (RKN) of the genus Meloidogyne are the key important plant parasitic nematodes (PPNs) in agricultural and horticultural crops worldwide. Among RKNs, M. incognita is the most notorious that demand exploration of novel strategies for their management. Due to its sustainable and target-specific nature, RNA interference (RNAi) has gained unprecedented importance to combat RKNs. However, based on the available genomic information and interaction studies, it can be presumed that RKNs are dynamic and not dependent on single genes for accomplishing a particular function. Therefore, it becomes extremely important to consider silencing of more than one gene to establish any synergistic or additive effect on nematode parasitism. In this direction, we have combined three effectors specific to subventral gland cells of M. incognita, Mi-msp1, Mi-msp16, Mi-msp20 as fusion cassettes-1 and two FMRFamide-like peptides, Mi-flp14, Mi-flp18, and Mi-msp20 as fusion cassettes-2 to establish their possible utility for M. incognita management. In vitro RNAi assay in tomato and adzuki bean using these two fusion gene negatively altered nematode behavior in terms of reduced attraction, invasion, development, and reproduction. Subsequently, Nicotiana tabacum plants were transformed with these two fusion gene hairpin RNA-expressing vectors (hpRNA), and characterized via PCR, qRT-PCR, and Southern blot hybridization. Production of siRNAs specific to Mi-flp18 and Mi-msp1 was also confirmed by Northern hybridization. Further, transgenic events expressing single copy insertions of hpRNA constructs of fusion 1 and fusion-2 conferred up to 85% reduction in M. incognita multiplication. Besides, expression quantification revealed a significant reduction in mRNA abundance of target genes (up to 1.8-fold) in M. incognita females extracted from transgenic plants, and provided additional evidence for successful gene silencing.
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Affiliation(s)
- Alkesh Hada
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Divya Singh
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Pradeep K Papolu
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Prakash Banakar
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Ankita Raj
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Uma Rao
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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Hernández-Soto A, Chacón-Cerdas R. RNAi Crop Protection Advances. Int J Mol Sci 2021; 22:12148. [PMID: 34830030 PMCID: PMC8625170 DOI: 10.3390/ijms222212148] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 12/11/2022] Open
Abstract
RNAi technology is a versatile, effective, safe, and eco-friendly alternative for crop protection. There is plenty of evidence of its use through host-induced gene silencing (HIGS) and emerging evidence that spray-induced gene silencing (SIGS) techniques can work as well to control viruses, bacteria, fungi, insects, and nematodes. For SIGS, its most significant challenge is achieving stability and avoiding premature degradation of RNAi in the environment or during its absorption by the target organism. One alternative is encapsulation in liposomes, virus-like particles, polyplex nanoparticles, and bioclay, which can be obtained through the recombinant production of RNAi in vectors, transgenesis, and micro/nanoencapsulation. The materials must be safe, biodegradable, and stable in multiple chemical environments, favoring the controlled release of RNAi. Most of the current research on encapsulated RNAi focuses primarily on oral delivery to control insects by silencing essential genes. The regulation of RNAi technology focuses on risk assessment using different approaches; however, this technology has positive economic, environmental, and human health implications for its use in agriculture. The emergence of alternatives combining RNAi gene silencing with the induction of resistance in crops by elicitation and metabolic control is expected, as well as multiple silencing and biotechnological optimization of its large-scale production.
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Affiliation(s)
- Alejandro Hernández-Soto
- Doctorado en Ciencia Naturales para el Desarrollo (DOCINADE), Instituto Tecnológico de Costa Rica, Universidad Nacional, Universidad Estatal a Distancia, Cartago P.O. Box 159-7050, Costa Rica
- Costa Rica Institute of Technology, Biology School, Biotechnology Research Center, Cartago P.O. Box 159-7050, Costa Rica;
| | - Randall Chacón-Cerdas
- Costa Rica Institute of Technology, Biology School, Biotechnology Research Center, Cartago P.O. Box 159-7050, Costa Rica;
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Campos TL, Korhonen PK, Hofmann A, Gasser RB, Young ND. Harnessing model organism genomics to underpin the machine learning-based prediction of essential genes in eukaryotes - Biotechnological implications. Biotechnol Adv 2021; 54:107822. [PMID: 34461202 DOI: 10.1016/j.biotechadv.2021.107822] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 08/17/2021] [Accepted: 08/24/2021] [Indexed: 12/17/2022]
Abstract
The availability of high-quality genomes and advances in functional genomics have enabled large-scale studies of essential genes in model eukaryotes, including the 'elegant worm' (Caenorhabditis elegans; Nematoda) and the 'vinegar fly' (Drosophila melanogaster; Arthropoda). However, this is not the case for other, much less-studied organisms, such as socioeconomically important parasites, for which functional genomic platforms usually do not exist. Thus, there is a need to develop innovative techniques or approaches for the prediction, identification and investigation of essential genes. A key approach that could enable the prediction of such genes is machine learning (ML). Here, we undertake an historical review of experimental and computational approaches employed for the characterisation of essential genes in eukaryotes, with a particular focus on model ecdysozoans (C. elegans and D. melanogaster), and discuss the possible applicability of ML-approaches to organisms such as socioeconomically important parasites. We highlight some recent results showing that high-performance ML, combined with feature engineering, allows a reliable prediction of essential genes from extensive, publicly available 'omic data sets, with major potential to prioritise such genes (with statistical confidence) for subsequent functional genomic validation. These findings could 'open the door' to fundamental and applied research areas. Evidence of some commonality in the essential gene-complement between these two organisms indicates that an ML-engineering approach could find broader applicability to ecdysozoans such as parasitic nematodes or arthropods, provided that suitably large and informative data sets become/are available for proper feature engineering, and for the robust training and validation of algorithms. This area warrants detailed exploration to, for example, facilitate the identification and characterisation of essential molecules as novel targets for drugs and vaccines against parasitic diseases. This focus is particularly important, given the substantial impact that such diseases have worldwide, and the current challenges associated with their prevention and control and with drug resistance in parasite populations.
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Affiliation(s)
- Tulio L Campos
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia; Bioinformatics Core Facility, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz (IAM-Fiocruz), Recife, Pernambuco, Brazil
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andreas Hofmann
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
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Genome Expression Dynamics Reveal the Parasitism Regulatory Landscape of the Root-Knot Nematode Meloidogyne incognita and a Promoter Motif Associated with Effector Genes. Genes (Basel) 2021; 12:genes12050771. [PMID: 34070210 PMCID: PMC8158474 DOI: 10.3390/genes12050771] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/04/2021] [Accepted: 05/10/2021] [Indexed: 12/21/2022] Open
Abstract
Root-knot nematodes (genus Meloidogyne) are the major contributor to crop losses caused by nematodes. These nematodes secrete effector proteins into the plant, derived from two sets of pharyngeal gland cells, to manipulate host physiology and immunity. Successful completion of the life cycle, involving successive molts from egg to adult, covers morphologically and functionally distinct stages and will require precise control of gene expression, including effector genes. The details of how root-knot nematodes regulate transcription remain sparse. Here, we report a life stage-specific transcriptome of Meloidogyne incognita. Combined with an available annotated genome, we explore the spatio-temporal regulation of gene expression. We reveal gene expression clusters and predicted functions that accompany the major developmental transitions. Focusing on effectors, we identify a putative cis-regulatory motif associated with expression in the dorsal glands, providing an insight into effector regulation. We combine the presence of this motif with several other criteria to predict a novel set of putative dorsal gland effectors. Finally, we show this motif, and thereby its utility, is broadly conserved across the Meloidogyne genus, and we name it Mel-DOG. Taken together, we provide the first genome-wide analysis of spatio-temporal gene expression in a root-knot nematode and identify a new set of candidate effector genes that will guide future functional analyses.
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15
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Iqbal A, Khan RS, Khan MA, Gul K, Jalil F, Shah DA, Rahman H, Ahmed T. Genetic Engineering Approaches for Enhanced Insect Pest Resistance in Sugarcane. Mol Biotechnol 2021; 63:557-568. [PMID: 33893996 DOI: 10.1007/s12033-021-00328-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/19/2021] [Indexed: 10/21/2022]
Abstract
Sugarcane (Saccharum officinarum), a sugar crop commonly grown for sugar production all over the world, is susceptible to several insect pests attack in addition to bacterial, fungal and viral infections leading to substantial reductions in its yield. The complex genetic makeup and lack of resistant genes in genome of sugarcane have made the conventional breeding a difficult and challenging task for breeders. Using pesticides for control of the attacking insects can harm beneficial insects, human and other animals and the environment as well. As alternative and effective strategy for control of insect pests, genetic engineering has been applied for overexpression of cry proteins, vegetative insecticidal proteins (vip), lectins and proteinase inhibitors (PI). In addition, the latest biotechnological tools such as host-induced gene silencing (HIGS) and CRISPR/Cas9 can be employed for sustainable control of insect pests in sugarcane. In this review overexpression of the cry, vip, lectins and PI genes in transgenic sugarcane and their disease resistance potential is described.
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Affiliation(s)
- Aneela Iqbal
- Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan
| | - Raham Sher Khan
- Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan.
| | - Mubarak Ali Khan
- Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan
| | - Karim Gul
- Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan
| | - Fazal Jalil
- Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan
| | - Daud Ali Shah
- Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan
| | - Hazir Rahman
- Department of Microbiology, Abdul Wali Khan University, Mardan, Pakistan
| | - Talaat Ahmed
- Department of Biological and Environmental Sciences, College of Arts and Science, Qatar University, Doha, Qatar
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Dutta TK, Papolu PK, Singh D, Sreevathsa R, Rao U. Expression interference of a number of Heterodera avenae conserved genes perturbs nematode parasitic success in Triticum aestivum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 301:110670. [PMID: 33218636 DOI: 10.1016/j.plantsci.2020.110670] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/01/2020] [Accepted: 09/06/2020] [Indexed: 05/26/2023]
Abstract
The cereal cyst nematode, Heterodera avenae is distributed worldwide and causes substantial damage in bread wheat, Triticum aestivum. This nematode is extremely difficult to manage because of its prolonged persistence as unhatched eggs encased in cysts. Due to its sustainable and target-specific nature, RNA interference (RNAi)-based strategy has gained unprecedented importance for pest control. To date, RNAi strategy has not been exploited to manage H. avenae in wheat. In the present study, 40 H. avenae target genes with different molecular function were rationally selected for in vitro soaking analysis in order to assess their susceptibility to RNAi. In contrast to target-specific downregulation of 18 genes, 7 genes were upregulated and 15 genes showed unaltered expression (although combinatorial soaking showed some of these genes are RNAi susceptible), suggesting that a few of the target genes were refractory or recalcitrant to RNAi. However, RNAi of 37 of these genes negatively altered nematode behavior in terms of reduced penetration, development and reproduction in wheat. Subsequently, wheat plants were transformed with seven H. avenae target genes (that showed greatest abrogation of nematode parasitic success) for host-induced gene silencing (HIGS) analysis. Transformed plants were molecularly characterized by PCR, RT-qPCR and Southern hybridization. Production of target gene-specific double- and single-stranded RNA (dsRNA/siRNA) was detected in transformed plants. Transgenic expression of galectin, cathepsin L, vap1, serpin, flp12, RanBPM and chitinase genes conferred 33.24-72.4 % reduction in H. avenae multiplication in T1 events with single copy ones exhibiting greatest reduction. A similar degree of resistance observed in T2 plants indicated the consistent HIGS effect in the subsequent generations. Intriguingly, cysts isolated from RNAi plants were of smaller size with translucent cuticle compared to normal size, dark brown control cysts, suggesting H. avenae developmental retardation due to HIGS. Our study reinforces the potential of HIGS to manage nematode problems in crop plant.
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Affiliation(s)
- Tushar K Dutta
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Pradeep K Papolu
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Divya Singh
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Rohini Sreevathsa
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India.
| | - Uma Rao
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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17
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Philbrick AN, Adhikari TB, Louws FJ, Gorny AM. Meloidogyne enterolobii, a Major Threat to Tomato Production: Current Status and Future Prospects for Its Management. FRONTIERS IN PLANT SCIENCE 2020; 11:606395. [PMID: 33304376 PMCID: PMC7701057 DOI: 10.3389/fpls.2020.606395] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 10/22/2020] [Indexed: 05/07/2023]
Abstract
The guava root-knot nematode, Meloidogyne enterolobii (Syn. M. mayaguensis), is an emerging pathogen to many crops in the world. This nematode can cause chlorosis, stunting, and reduce yields associated with the induction of many root galls on host plants. Recently, this pathogen has been considered as a global threat for tomato (Solanum lycopersicum L.) production due to the lack of known resistance in commercially accepted varieties and the aggressiveness of M. enterolobii. Both conventional morphological and molecular approaches have been used to identify M. enterolobii, an important first step in an integrated management. To combat root-knot nematodes, integrated disease management strategies such as crop rotation, field sanitation, biocontrol agents, fumigants, and resistant cultivars have been developed and successfully used in the past. However, the resistance in tomato varieties mediated by known Mi-genes does not control M. enterolobii. Here, we review the current knowledge on geographic distribution, host range, population biology, control measures, and proposed future strategies to improve M. enterolobii control in tomato.
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Affiliation(s)
- Ashley N. Philbrick
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Tika B. Adhikari
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Frank J. Louws
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, United States
| | - Adrienne M. Gorny
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
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18
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Multi-copy alpha-amylase genes are crucial for Ditylenchus destructor to parasitize the plant host. PLoS One 2020; 15:e0240805. [PMID: 33104741 PMCID: PMC7588122 DOI: 10.1371/journal.pone.0240805] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 10/05/2020] [Indexed: 11/19/2022] Open
Abstract
Ditylenchus destructor is a migratory plant-parasitic nematode that causes huge damage to global root and tuber production annually. The main plant hosts of D. destructor contain plenty of starch, which makes the parasitic environment of D. destructor to be different from those of most other plant-parasitic nematodes. It is speculated that D. destructor may harbor some unique pathogenesis-related genes to parasitize the starch-rich hosts. Herein, we focused on the multi-copy alpha-amylase genes in D. destructor, which encode a key starch-catalyzing enzyme. Our previously published D. destructor genome showed that it has three alpha-amylase encoding genes, Dd_02440, Dd_11154, and Dd_13225. Comparative analysis of alpha-amylases from different species demonstrated that the other plant-parasitic nematodes, even Ditylenchus dipsaci in the same genus, harbor only one or no alpha-amylase gene, and the three genes from D. destructor were closely clustered in the phylogenetic tree, indicating that there was a unique expansion of the alpha-amylase gene in D. destructor. The enzymatic activity of the three alpha-amylase proteins was verified by an enzyme assay. Quantitative real-time PCR assay showed that the expression of the three alpha-amylase genes in the post-hatching stage of D. destructor was found to be significantly higher than that in eggs. In the in situ hybridization assay, the expression of the genes was localized to the intestine, implying the association of these genes with nematode digestion. An infection assay in sweet potato demonstrated that RNA interference of any one alpha-amylase gene had no influence on the infectivity of D. destructor. Using the multi-target dsRNA cocktail method, it was found that silencing of two of the three genes inhibited nematode infection, and the infectivity of worms treated with three dsRNA simultaneously changed the most, which decreased by 76.6%. Thus, the multi-copy alpha-amylase genes in D. destructor are compensatory and crucial for nematodes to parasitize the plant host.
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Zhang K, Wei J, Huff Hartz KE, Lydy MJ, Moon TS, Sander M, Parker KM. Analysis of RNA Interference (RNAi) Biopesticides: Double-Stranded RNA (dsRNA) Extraction from Agricultural Soils and Quantification by RT-qPCR. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:4893-4902. [PMID: 32212649 DOI: 10.1021/acs.est.9b07781] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Double-stranded RNA (dsRNA) molecules are used as a novel class of biopesticides. To enable assessments of the ecological risk associated with their release to receiving environments, we developed an approach to quantify dsRNA in agricultural soils using quantitative reverse transcription-polymerase chain reaction (RT-qPCR). To allow quantification of dsRNA adsorbed to particles, we also developed a protocol to transfer dsRNA from particles to the extraction buffer by changing particle surface charge and adding constituents to compete with dsRNA for adsorption sites. Our approach could quantify dsRNA amounts as low as 0.003 ngdsRNA/gsoil. This approach is the first available field-applicable approach able to quantify dsRNA biopesticides down to environmentally relevant concentrations. We applied this approach to investigate dsRNA dissipation (including dilution, degradation, and adsorption) in two agricultural soils. When we applied a low amount of dsRNA (1 ngdsRNA/gsoil) to the soils, we observed that a greater fraction of dsRNA was adsorbed to and extractable from soil particles in a silty clay loam soil than in a fine sandy loam soil. In both soils, dsRNA dissipated on the timescale of hours. Overall, these results demonstrate that our approach can be applied to assess the environmental fate of dsRNA biopesticides at concentrations relevant to their release to soils.
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Affiliation(s)
- Ke Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Jingmiao Wei
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kara E Huff Hartz
- Center for Fisheries, Aquaculture, and Aquatic Sciences, Department of Zoology, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Michael J Lydy
- Center for Fisheries, Aquaculture, and Aquatic Sciences, Department of Zoology, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Tae Seok Moon
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Michael Sander
- Department of Environmental Systems Science (DUSYS), ETH Zurich, 8092 Zurich, Switzerland
| | - Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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Iqbal S, Fosu-Nyarko J, Jones MGK. Attempt to Silence Genes of the RNAi Pathways of the Root-Knot Nematode, Meloidogyne incognita Results in Diverse Responses Including Increase and No Change in Expression of Some Genes. FRONTIERS IN PLANT SCIENCE 2020; 11:328. [PMID: 32265973 PMCID: PMC7105803 DOI: 10.3389/fpls.2020.00328] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 03/05/2020] [Indexed: 05/07/2023]
Abstract
Control of plant-parasitic nematodes (PPNs) via host-induced gene silencing (HIGS) involves rational selection of genes and detailed assessment of effects of a possible knockdown on the nematode. Some genes by nature may be very important for the survival of the nematode that knockdown may be resisted. Possible silencing and effects of 20 such genes involved in the RNA interference (RNAi) pathways of Meloidogyne incognita were investigated in this study using long double-stranded RNAs (dsRNAs) as triggers. Two of the genes, ego-1 and mes-2, could not be knocked down. Expression of six genes (xpo-1, pash-1, xpo-2, rha-1, ekl-4, and csr-1) were significantly upregulated after RNAi treatment whereas for 12 of the genes, significant knockdown was achieved and with the exception of mes-2 and mes-6, RNAi was accompanied by defective phenotypes in treated nematodes including various degrees of paralysis and abnormal behaviors and movement such as curling, extreme wavy movements, and twitching. These abnormalities resulted in up to 75% reduction in infectivity of a tomato host, the most affected being the J2s previously treated with dsRNA of the gfl-1 gene. For 10 of the genes, effects of silencing in the J2s persisted as the adult females isolated from galls were under-developed, elongated, and transparent compared to the normal saccate, white adult females. Following RNAi of ego-1, smg-2, smg-6, and eri-1, reduced expression and/or the immediate visible effects on the J2s were not permanent as the nematodes infected and developed normally in tomato hosts. Equally intriguing was the results of RNAi of the mes-2 gene where the insignificant change in gene expression and behavior of treated J2s did not mean the nematodes were not affected as they were less effective in infecting host plants. Attempt to silence drsh-1, mut-7, drh-3, rha-1, pash-1, and vig-1 through HIGS led to reduction in nematode infestation by up to 89%. Our results show that genes may respond to RNAi knockdown differently so an exhaustive assessment of target genes as targets for nematode control via RNAi is imperative.
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Affiliation(s)
| | - John Fosu-Nyarko
- Plant Biotechnology Research Group, College of Science, Health, Engineering and Education, WA State Agricultural Biotechnology Centre, Murdoch University, Perth, WA, Australia
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Castelletto ML, Gang SS, Hallem EA. Recent advances in functional genomics for parasitic nematodes of mammals. ACTA ACUST UNITED AC 2020; 223:223/Suppl_1/jeb206482. [PMID: 32034038 DOI: 10.1242/jeb.206482] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Human-parasitic nematodes infect over a quarter of the world's population and are a major cause of morbidity in low-resource settings. Currently available treatments have not been sufficient to eliminate infections in endemic areas, and drug resistance is an increasing concern, making new treatment options a priority. The development of new treatments requires an improved understanding of the basic biology of these nematodes. Specifically, a better understanding of parasitic nematode development, reproduction and behavior may yield novel drug targets or new opportunities for intervention such as repellents or traps. Until recently, our ability to study parasitic nematode biology was limited because few tools were available for their genetic manipulation. This is now changing as a result of recent advances in the large-scale sequencing of nematode genomes and the development of new techniques for their genetic manipulation. Notably, skin-penetrating gastrointestinal nematodes in the genus Strongyloides are now amenable to transgenesis, RNAi and CRISPR/Cas9-mediated targeted mutagenesis, positioning the Strongyloides species as model parasitic nematode systems. A number of other mammalian-parasitic nematodes, including the giant roundworm Ascaris suum and the tissue-dwelling filarial nematode Brugia malayi, are also now amenable to transgenesis and/or RNAi in some contexts. Using these tools, recent studies of Strongyloides species have already provided insight into the molecular pathways that control the developmental decision to form infective larvae and that drive the host-seeking behaviors of infective larvae. Ultimately, a mechanistic understanding of these processes could lead to the development of new avenues for nematode control.
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Affiliation(s)
- Michelle L Castelletto
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Spencer S Gang
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92161, USA
| | - Elissa A Hallem
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
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Li Y, Dong C, Hu M, Bai Z, Tong C, Zuo R, Liu Y, Cheng X, Cheng M, Huang J, Liu S. Identification of Flower-Specific Promoters through Comparative Transcriptome Analysis in Brassica napus. Int J Mol Sci 2019; 20:ijms20235949. [PMID: 31779216 PMCID: PMC6928827 DOI: 10.3390/ijms20235949] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/20/2019] [Accepted: 11/25/2019] [Indexed: 01/24/2023] Open
Abstract
Brassica napus (oilseed rape) is an economically important oil crop worldwide. Sclerotinia stem rot (SSR) caused by Sclerotinia sclerotiorum is a threat to oilseed rape production. Because the flower petals play pivotal roles in the SSR disease cycle, it is useful to express the resistance-related genes specifically in flowers to hinder further infection with S. sclerotiorum. To screen flower-specific promoters, we first analyzed the transcriptome data from 12 different tissues of the B. napus line ZS11. In total, 249 flower-specific candidate genes with high expression in petals were identified, and the expression patterns of 30 candidate genes were verified by quantitative real-time transcription-PCR (qRT-PCR) analysis. Furthermore, two novel flower-specific promoters (FSP046 and FSP061 promoter) were identified, and the tissue specificity and continuous expression in petals were determined in transgenic Arabidopsis thaliana with fusing the promoters to β-glucuronidase (GUS)-reporter gene. GUS staining, transcript expression pattern, and GUS activity analysis indicated that FSP046 and FSP061 promoter were strictly flower-specific promoters, and FSP046 promoter had a stronger activity. The two promoters were further confirmed to be able to direct GUS expression in B. napus flowers using transient expression system. The transcriptome data and the flower-specific promoters screened in the present study will benefit fundamental research for improving the agronomic traits as well as disease and pest control in a tissue-specific manner.
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Morozov SY, Solovyev AG, Kalinina NO, Taliansky ME. Double-Stranded RNAs in Plant Protection Against Pathogenic Organisms and Viruses in Agriculture. Acta Naturae 2019; 11:13-21. [PMID: 31993231 PMCID: PMC6977960 DOI: 10.32607/20758251-2019-11-4-13-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 11/29/2019] [Indexed: 11/24/2022] Open
Abstract
Recent studies have shown that plants are able to express the artificial genes responsible for the synthesis of double-stranded RNAs (dsRNAs) and hairpin double-stranded RNAs (hpRNAs), as well as uptake and process exogenous dsRNAs and hpRNAs to suppress the gene expression of plant pathogenic viruses, fungi, or insects. Both endogenous and exogenous dsRNAs are processed into small interfering RNAs (siRNAs) that can spread locally and systemically through the plant, enter pathogenic microorganisms, and induce RNA interference-mediated pathogen resistance in plants. There are numerous examples of the development of new biotechnological approaches to plant protection using transgenic plants and exogenous dsRNAs. This review summarizes new data on the use of transgenes and exogenous dsRNAs for the suppression of fungal and insect virulence genes, as well as viruses to increase the resistance of plants to these pathogens. We also analyzed the current ideas about the mechanisms of dsRNA processing and transport in plants.
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Affiliation(s)
- S. Y. Morozov
- International Laboratory «Resistom», The Skolkovo Innovation Center, Moscow, 143026 Russia**
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992 Russia
| | - A. G. Solovyev
- International Laboratory «Resistom», The Skolkovo Innovation Center, Moscow, 143026 Russia**
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992 Russia
| | - N. O. Kalinina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992 Russia
| | - M. E. Taliansky
- International Laboratory «Resistom», The Skolkovo Innovation Center, Moscow, 143026 Russia**
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, 117997 Russia
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Catch Me If You Can! RNA Silencing-Based Improvement of Antiviral Plant Immunity. Viruses 2019; 11:v11070673. [PMID: 31340474 PMCID: PMC6669615 DOI: 10.3390/v11070673] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/11/2019] [Accepted: 07/17/2019] [Indexed: 12/27/2022] Open
Abstract
Viruses are obligate parasites which cause a range of severe plant diseases that affect farm productivity around the world, resulting in immense annual losses of yield. Therefore, control of viral pathogens continues to be an agronomic and scientific challenge requiring innovative and ground-breaking strategies to meet the demands of a growing world population. Over the last decade, RNA silencing has been employed to develop plants with an improved resistance to biotic stresses based on their function to provide protection from invasion by foreign nucleic acids, such as viruses. This natural phenomenon can be exploited to control agronomically relevant plant diseases. Recent evidence argues that this biotechnological method, called host-induced gene silencing, is effective against sucking insects, nematodes, and pathogenic fungi, as well as bacteria and viruses on their plant hosts. Here, we review recent studies which reveal the enormous potential that RNA-silencing strategies hold for providing an environmentally friendly mechanism to protect crop plants from viral diseases.
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Shivakumara TN, Dutta TK, Chaudhary S, von Reuss SH, Williamson VM, Rao U. Homologs of Caenorhabditis elegans Chemosensory Genes Have Roles in Behavior and Chemotaxis in the Root-Knot Nematode Meloidogyne incognita. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:876-887. [PMID: 30759351 DOI: 10.1094/mpmi-08-18-0226-r] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Nematode chemosensation is a vital component of their host-seeking behavior. The globally important phytonematode Meloidogyne incognita perceives and responds (via sensory organs such as amphids and phasmids) differentially to various chemical cues emanating from the rhizosphere during the course of host finding. However, compared with the free-living worm Caenorhabditis elegans, the molecular intricacies behind the plant nematode chemotaxis are a yet-unexploited territory. In the present study, four putative chemosensory genes of M. incognita, namely, Mi-odr-1, Mi-odr-3, Mi-tax-2, and Mi-tax-4 were molecularly characterized. Mi-odr-1 mRNA was found to be expressed in the cell bodies of amphidial neurons and phasmids of M. incognita. Mi-odr-1, Mi-odr-3, Mi-tax-2, and Mi-tax-4 transcripts were highly expressed in early life stages of M. incognita, consistent with a role of these genes in host recognition. Functional characterization of Mi-odr-1, Mi-odr-3, Mi-tax-2, and Mi-tax-4 via RNA interference revealed behavioral defects in M. incognita and perturbed attraction to host roots in Pluronic gel medium. Knockdown of Mi-odr-1, Mi-odr-3, Mi-tax-2, and Mi-tax-4 resulted in defective chemotaxis of M. incognita to various volatile compounds (alcohol, ketone, aromatic compound, ester, thiazole, pyrazine), nonvolatiles of plant origin (carbohydrate, phytohormone, organic acid, amino acid, phenolic), and host root exudates in an agar-Pluronic gel-based assay plate. In addition, ascaroside-mediated signaling was impeded by downregulation of chemosensory genes. This new information that behavioral response in M. incognita is modulated by specific olfactory genes can be extended to understand chemotaxis in other nematodes.
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Affiliation(s)
| | - Tushar K Dutta
- 1 Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Sonam Chaudhary
- 1 Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Stephan H von Reuss
- 2 Institute of Chemistry, University of Neuchâtel, Neuchâtel, Avenue de Bellevaux 51, Switzerland
| | - Valerie M Williamson
- 3 Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
| | - Uma Rao
- 1 Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
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Blyuss KB, Fatehi F, Tsygankova VA, Biliavska LO, Iutynska GO, Yemets AI, Blume YB. RNAi-Based Biocontrol of Wheat Nematodes Using Natural Poly-Component Biostimulants. FRONTIERS IN PLANT SCIENCE 2019; 10:483. [PMID: 31057585 PMCID: PMC6479188 DOI: 10.3389/fpls.2019.00483] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 03/28/2019] [Indexed: 06/09/2023]
Abstract
With the growing global demands on sustainable food production, one of the biggest challenges to agriculture is associated with crop losses due to parasitic nematodes. While chemical pesticides have been quite successful in crop protection and mitigation of damage from parasites, their potential harm to humans and environment, as well as the emergence of nematode resistance, have necessitated the development of viable alternatives to chemical pesticides. One of the most promising and targeted approaches to biocontrol of parasitic nematodes in crops is that of RNA interference (RNAi). In this study we explore the possibility of using biostimulants obtained from metabolites of soil streptomycetes to protect wheat (Triticum aestivum L.) against the cereal cyst nematode Heterodera avenae by means of inducing RNAi in wheat plants. Theoretical models of uptake of organic compounds by plants, and within-plant RNAi dynamics, have provided us with useful insights regarding the choice of routes for delivery of RNAi-inducing biostimulants into plants. We then conducted in planta experiments with several streptomycete-derived biostimulants, which have demonstrated the efficiency of these biostimulants at improving plant growth and development, as well as in providing resistance against the cereal cyst nematode. Using dot blot hybridization we demonstrate that biostimulants trigger a significant increase of the production in plant cells of si/miRNA complementary with plant and nematode mRNA. Wheat germ cell-free experiments show that these si/miRNAs are indeed very effective at silencing the translation of nematode mRNA having complementary sequences, thus reducing the level of nematode infestation and improving plant resistance to nematodes. Thus, we conclude that natural biostimulants produced from metabolites of soil streptomycetes provide an effective tool for biocontrol of wheat nematode.
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Affiliation(s)
| | - Farzad Fatehi
- Department of Mathematics, University of Sussex, Brighton, United Kingdom
| | - Victoria A. Tsygankova
- Department of Chemistry of Bioactive Nitrogen-Containing Heterocyclic Compounds, Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Liudmyla O. Biliavska
- Department of General and Soil Microbiology, Zabolotny Institute of Microbiology and Virology, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Galyna O. Iutynska
- Department of General and Soil Microbiology, Zabolotny Institute of Microbiology and Virology, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Alla I. Yemets
- Department of Cell Biology and Biotechnology, Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Yaroslav B. Blume
- Department of Genomics and Molecular Biotechnology, Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
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27
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Chaudhary S, Dutta TK, Tyagi N, Shivakumara TN, Papolu PK, Chobhe KA, Rao U. Host-induced silencing of Mi-msp-1 confers resistance to root-knot nematode Meloidogyne incognita in eggplant. Transgenic Res 2019; 28:327-340. [PMID: 30955133 DOI: 10.1007/s11248-019-00126-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/02/2019] [Indexed: 11/28/2022]
Abstract
RNA interference (RNAi)-based host-induced gene silencing (HIGS) is emerging as a novel, efficient and target-specific tool to combat phytonematode infection in crop plants. Mi-msp-1, an effector gene expressed in the subventral pharyngeal gland cells of Meloidogyne incognita plays an important role in the parasitic process. Mi-msp-1 effector is conserved in few of the species of root-knot nematodes (RKNs) and does not share considerable homology with the other phytonematodes, thereby making it a suitable target for HIGS with minimal off-target effects. Six putative eggplant transformants harbouring a single copy RNAi transgene of Mi-msp-1 was generated. Stable expression of the transgene was detected in T1, T2 and T3 transgenic lines for which a detrimental effect on RKN penetration, development and reproduction was documented upon challenge infection with nematode juveniles. The post-parasitic nematode stages extracted from the transgenic plants showed long-term RNAi effect in terms of targeted downregulation of Mi-msp-1. These findings suggest that HIGS of Mi-msp-1 enhances nematode resistance in eggplant and protect the plant against RKN parasitism at very early stage.
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Affiliation(s)
- Sonam Chaudhary
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.,School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, 751024, India
| | - Tushar K Dutta
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Nidhi Tyagi
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | | | - Pradeep K Papolu
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Kapil A Chobhe
- Division of Soil Science and Agricultural Chemistry, New Delhi, 110012, India
| | - Uma Rao
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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Worrall EA, Hayward AC, Fletcher SJ, Mitter N. Molecular characterization and analysis of conserved potyviral motifs in bean common mosaic virus (BCMV) for RNAi-mediated protection. Arch Virol 2018; 164:181-194. [DOI: 10.1007/s00705-018-4065-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 09/21/2018] [Indexed: 01/01/2023]
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Gahoi S, Singh S, Gautam B. Genome-wide identification and comprehensive analysis of Excretory/Secretory proteins in nematodes provide potential drug targets for parasite control. Genomics 2018. [PMID: 29522800 DOI: 10.1016/j.ygeno.2018.03.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Nematodes are responsible for causing severe diseases in plants, humans and other animals. Infection is associated with the release of Excretory/Secretory (ES) proteins into host cytoplasm and interference with the host immune system which make them attractive targets for therapeutic use. The identification of ES proteins through bioinformatics approaches is cost- and time-effective and could be used for screening of potential targets for parasitic diseases for further experimental studies. Here, we identified and functionally annotated 93,949 ES proteins, in the genome of 73 nematodes using integration of various bioinformatics tools. 30.6% of ES proteins were found to be supported at RNA level. The predicted ES proteins, annotated by Gene Ontology terms, domains, metabolic pathways, proteases and enzyme class analysis were enriched in molecular functions of proteases, protease inhibitors, c-type lectin and hydrolases which are strongly associated with typical functions of ES proteins. We identified a total of 452 ES proteins from human and plant parasitic nematodes, homologues to DrugBank-approved targets and C. elegans RNA interference phenotype genes which could represent potential targets for parasite control and provide valuable resource for further experimental studies to understand host-pathogen interactions.
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Affiliation(s)
- Shachi Gahoi
- Department of Computational Biology and Bioinformatics, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad 211007, India.
| | - Satendra Singh
- Department of Computational Biology and Bioinformatics, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad 211007, India.
| | - Budhayash Gautam
- Department of Computational Biology and Bioinformatics, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad 211007, India.
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30
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Roderick H, Urwin PE, Atkinson HJ. Rational design of biosafe crop resistance to a range of nematodes using RNA interference. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:520-529. [PMID: 28703405 PMCID: PMC5787825 DOI: 10.1111/pbi.12792] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 07/05/2017] [Accepted: 07/05/2017] [Indexed: 05/31/2023]
Abstract
Double-stranded RNA (dsRNA) molecules targeting two genes have been identified that suppress economically important parasitic nematode species of banana. Proteasomal alpha subunit 4 (pas-4) and Actin-4 (act-4) were identified from a survey of sequence databases and cloned sequences for genes conserved across four pests of banana, Radopholus similis, Pratylenchus coffeae, Meloidogyne incognita and Helicotylenchus multicinctus. These four species were targeted with dsRNAs containing exact 21 nucleotide matches to the conserved regions. Potential off-target effects were limited by comparison with Caenorhabditis, Drosophila, rat, rice and Arabidopsis genomes. In vitro act-4 dsRNA treatment of R. similis suppressed target gene expression by 2.3-fold, nematode locomotion by 66 ± 4% and nematode multiplication on carrot discs by 49 ± 5%. The best transgenic carrot hairy root lines expressing act-4 or pas-4 dsRNA reduced transcript message abundance of target genes in R. similis by 7.9-fold and fourfold and nematode multiplication by 94 ± 2% and 69 ± 3%, respectively. The same act-4 and pas-4 lines reduced P. coffeae target transcripts by 1.7- and twofold and multiplication by 50 ± 6% and 73 ± 8%. Multiplication of M. incognita on the pas-4 lines was reduced by 97 ± 1% and 99 ± 1% while target transcript abundance was suppressed 4.9- and 5.6-fold. There was no detectable RNAi effect on nontarget nematodes exposed to dsRNAs targeting parasitic nematodes. This work defines a framework for development of a range of nonprotein defences to provide broad resistance to pests and pathogens of crops.
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31
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Knight AL, Light DM, Judd GJR, Witzgall P. Pear Ester – From Discovery to Delivery for Improved Codling Moth Management. ACS SYMPOSIUM SERIES 2018. [DOI: 10.1021/bk-2018-1294.ch008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Alan L. Knight
- Temperate Tree Fruit and Vegetable Research, Agricultural Research Service, U.S. Department of Agriculture, 5230 Konnowac Pass Road, Wapato, Washington 98951, United States
| | - Douglas M. Light
- Foodborne Toxin Detection and Prevention Research Unit, Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 800 Buchanan Street, Albany California 94710, United States
| | - Gary J. R. Judd
- Agriculture and Agri-Food Canada, Summerland Research and Development Centre, 4200 Highway 97, Summerland, British Columbia, Canada
| | - Peter Witzgall
- Division of Chemical Ecology, Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
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32
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Tool-Driven Advances in Neuropeptide Research from a Nematode Parasite Perspective. Trends Parasitol 2017; 33:986-1002. [DOI: 10.1016/j.pt.2017.08.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/10/2017] [Accepted: 08/21/2017] [Indexed: 01/21/2023]
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33
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Raman P, Zaghab SM, Traver EC, Jose AM. The double-stranded RNA binding protein RDE-4 can act cell autonomously during feeding RNAi in C. elegans. Nucleic Acids Res 2017; 45:8463-8473. [PMID: 28541563 PMCID: PMC5737277 DOI: 10.1093/nar/gkx484] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 05/17/2017] [Indexed: 02/07/2023] Open
Abstract
Long double-stranded RNA (dsRNA) can silence genes of matching sequence upon ingestion in many invertebrates and is therefore being developed as a pesticide. Such feeding RNA interference (RNAi) is best understood in the worm Caenorhabditis elegans, where the dsRNA-binding protein RDE-4 initiates silencing by recruiting an endonuclease to process long dsRNA into short dsRNA. These short dsRNAs are thought to move between cells because muscle-specific rescue of rde-4 using repetitive transgenes enables silencing in other tissues. Here, we extend this observation using additional promoters, report an inhibitory effect of repetitive transgenes, and discover conditions for cell-autonomous silencing in animals with tissue-specific rescue of rde-4. While expression of rde-4(+) in intestine, hypodermis, or neurons using a repetitive transgene can enable silencing also in unrescued tissues, silencing can be inhibited wihin tissues that express a repetitive transgene. Single-copy transgenes that express rde-4(+) in body-wall muscles or hypodermis, however, enable silencing selectively in the rescued tissue but not in other tissues. These results suggest that silencing by the movement of short dsRNA between cells is not an obligatory feature of feeding RNAi in C. elegans. We speculate that similar control of dsRNA movement could modulate tissue-specific silencing by feeding RNAi in other invertebrates.
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Affiliation(s)
- Pravrutha Raman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Soriayah M Zaghab
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Edward C Traver
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Antony M Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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Ali MA, Azeem F, Abbas A, Joyia FA, Li H, Dababat AA. Transgenic Strategies for Enhancement of Nematode Resistance in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:750. [PMID: 28536595 PMCID: PMC5422515 DOI: 10.3389/fpls.2017.00750] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/21/2017] [Indexed: 05/19/2023]
Abstract
Plant parasitic nematodes (PPNs) are obligate biotrophic parasites causing serious damage and reduction in crop yields. Several economically important genera parasitize various crop plants. The root-knot, root lesion, and cyst nematodes are the three most economically damaging genera of PPNs on crops within the family Heteroderidae. It is very important to devise various management strategies against PPNs in economically important crop plants. Genetic engineering has proven a promising tool for the development of biotic and abiotic stress tolerance in crop plants. Additionally, the genetic engineering leading to transgenic plants harboring nematode resistance genes has demonstrated its significance in the field of plant nematology. Here, we have discussed the use of genetic engineering for the development of nematode resistance in plants. This review article also provides a detailed account of transgenic strategies for the resistance against PPNs. The strategies include natural resistance genes, cloning of proteinase inhibitor coding genes, anti-nematodal proteins and use of RNA interference to suppress nematode effectors. Furthermore, the manipulation of expression levels of genes induced and suppressed by nematodes has also been suggested as an innovative approach for inducing nematode resistance in plants. The information in this article will provide an array of possibilities to engineer resistance against PPNs in different crop plants.
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Affiliation(s)
- Muhammad A. Ali
- Department of Plant Pathology, University of AgricultureFaisalabad, Pakistan
- Centre of Agricultural Biochemistry and Biotechnology, University of AgricultureFaisalabad, Pakistan
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College UniversityFaisalabad, Pakistan
| | - Amjad Abbas
- Department of Plant Pathology, University of AgricultureFaisalabad, Pakistan
| | - Faiz A. Joyia
- Centre of Agricultural Biochemistry and Biotechnology, University of AgricultureFaisalabad, Pakistan
| | - Hongjie Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
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Abstract
Biological processes such as defense mechanisms and microbial offense strategies are regulated through RNA induced interference in eukaryotes. Genetic mutations are modulated through biogenesis of small RNAs which directly impacts upon host development. Plant defense mechanisms are regulated and supported by a diversified group of small RNAs which are involved in streamlining several RNA interference pathways leading toward the initiation of pathogen gene silencing mechanisms. In the similar context, pathogens also utilize the support of small RNAs to launch their offensive attacks. Also there are strong evidences about the active involvement of these RNAs in symbiotic associations. Interestingly, small RNAs are not limited to the individuals in whom they are produced; they also show cross kingdom influences through variable interactions with other species thus leading toward the inter-organismic gene silencing. The phenomenon is understandable in the microbes which utilize these mechanisms to overcome host defense line. Understanding the mechanism of triggering host defense strategies can be a valuable step toward the generation of disease resistant host plants. We think that the cross kingdom trafficking of small RNA is an interesting insight that is needed to be explored for its vitality.
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Affiliation(s)
- Waqar Islam
- a College of Plant Protection , Fujian Agriculture and Forestry University , Fuzhou , Fujian , China
| | - Saif Ul Islam
- a College of Plant Protection , Fujian Agriculture and Forestry University , Fuzhou , Fujian , China
| | - Muhammad Qasim
- a College of Plant Protection , Fujian Agriculture and Forestry University , Fuzhou , Fujian , China
| | - Liande Wang
- a College of Plant Protection , Fujian Agriculture and Forestry University , Fuzhou , Fujian , China
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36
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Kumari C, Dutta TK, Chaudhary S, Banakar P, Papolu PK, Rao U. Molecular characterization of FMRFamide-like peptides in Meloidogyne graminicola and analysis of their knockdown effect on nematode infectivity. Gene 2017; 619:50-60. [PMID: 28366833 DOI: 10.1016/j.gene.2017.03.042] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 03/22/2017] [Accepted: 03/29/2017] [Indexed: 11/18/2022]
Abstract
The rice root-knot nematode, Meloidogyne graminicola, seriously impairs the growth and yield of rice which is an important staple food worldwide. The disruption of neuropeptide signalling leading to attenuation in nematode behaviour and thereby perturbed infection, offers an attractive alternative to control nematodes. In this direction, the present study was aimed at mining of putative FMRFamide-like peptides (FLPs) from the transcriptomic dataset of M. graminicola followed by characterization of those FLPs via sequencing of PCR products, qRT-PCR and Southern hybridization analysis. We have characterized nine flp genes (flp-1, flp-3, flp-6, flp-7, flp-11, flp-12, flp-14, flp-16 and flp-18) and a partial neuropeptide receptor gene (flp-18 GPCR) from M. graminicola in the present study. In addition, in situ localization revealed the expression of flp-1 and flp-7 in neurons posterior to the circumpharyngeal nerve ring of M. graminicola. In vitro silencing of nine flp genes and flp-18 GPCR in M. graminicola J2 and their subsequent infection in rice and wheat roots demonstrated the reduced penetration ability of FLP silenced worms which underscores the potential of the FLPergic system as a broad-spectrum target to manage the root-knot nematode problem in rice-wheat cropping system.
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Affiliation(s)
- Chanchal Kumari
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Tushar K Dutta
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Sonam Chaudhary
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Prakash Banakar
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Pradeep K Papolu
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Uma Rao
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India.
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Shivakumara TN, Chaudhary S, Kamaraju D, Dutta TK, Papolu PK, Banakar P, Sreevathsa R, Singh B, Manjaiah KM, Rao U. Host-Induced Silencing of Two Pharyngeal Gland Genes Conferred Transcriptional Alteration of Cell Wall-Modifying Enzymes of Meloidogyne incognita vis-à-vis Perturbed Nematode Infectivity in Eggplant. FRONTIERS IN PLANT SCIENCE 2017; 8:473. [PMID: 28424727 PMCID: PMC5371666 DOI: 10.3389/fpls.2017.00473] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 03/17/2017] [Indexed: 05/19/2023]
Abstract
The complex parasitic strategy of Meloidogyne incognita appears to involve simultaneous expression of its pharyngeal gland-specific effector genes in order to colonize the host plants. Research reports related to effector crosstalk in phytonematodes for successful parasitism of the host tissue is yet underexplored. In view of this, we have used in planta effector screening approach to understand the possible interaction of pioneer genes (msp-18 and msp-20, putatively involved in late and early stage of M. incognita parasitism, respectively) with other unrelated effectors such as cell-wall modifying enzymes (CWMEs) in M. incognita. Host-induced gene silencing (HIGS) strategy was used to generate the transgenic eggplants expressing msp-18 and msp-20, independently. Putative transformants were characterized via qRT-PCR and Southern hybridization assay. SiRNAs specific to msp-18 and msp-20 were also detected in the transformants via Northern hybridization assay. Transgenic expression of the RNAi constructs of msp-18 and msp-20 genes resulted in 43.64-69.68% and 41.74-67.30% reduction in M. incognita multiplication encompassing 6 and 10 events, respectively. Additionally, transcriptional oscillation of CWMEs documented in the penetrating and developing nematodes suggested the possible interaction among CWMEs and pioneer genes. The rapid assimilation of plant-derived carbon by invading nematodes was also demonstrated using 14C isotope probing approach. Our data suggests that HIGS of msp-18 and msp-20, improves nematode resistance in eggplant by affecting the steady-state transcription level of CWME genes in invading nematodes, and safeguard the plant against nematode invasion at very early stage because nematodes may become the recipient of bioactive RNA species during the process of penetration into the plant root.
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Affiliation(s)
- Tagginahalli N. Shivakumara
- Division of Nematology, Indian Council of Agricultural Research – Indian Agricultural Research InstituteNew Delhi, India
| | - Sonam Chaudhary
- Division of Nematology, Indian Council of Agricultural Research – Indian Agricultural Research InstituteNew Delhi, India
| | - Divya Kamaraju
- Division of Nematology, Indian Council of Agricultural Research – Indian Agricultural Research InstituteNew Delhi, India
| | - Tushar K. Dutta
- Division of Nematology, Indian Council of Agricultural Research – Indian Agricultural Research InstituteNew Delhi, India
| | - Pradeep K. Papolu
- Division of Nematology, Indian Council of Agricultural Research – Indian Agricultural Research InstituteNew Delhi, India
| | - Prakash Banakar
- Division of Nematology, Indian Council of Agricultural Research – Indian Agricultural Research InstituteNew Delhi, India
| | - Rohini Sreevathsa
- Indian Council of Agricultural Research – National Research Centre on Plant BiotechnologyNew Delhi, India
| | - Bhupinder Singh
- Nuclear Research Laboratory, Indian Council of Agricultural Research – Indian Agricultural Research InstituteNew Delhi, India
| | - K. M. Manjaiah
- Division of Soil Science and Agricultural Chemistry, Indian Council of Agricultural Research – Indian Agricultural Research InstituteNew Delhi, India
| | - Uma Rao
- Division of Nematology, Indian Council of Agricultural Research – Indian Agricultural Research InstituteNew Delhi, India
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Rosa BA, McNulty SN, Mitreva M, Jasmer DP. Direct experimental manipulation of intestinal cells in Ascaris suum, with minor influences on the global transcriptome. Int J Parasitol 2017; 47:271-279. [PMID: 28223178 DOI: 10.1016/j.ijpara.2016.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/16/2016] [Accepted: 12/21/2016] [Indexed: 12/24/2022]
Abstract
Ascaris suum provides a powerful model for studying parasitic nematodes, including individual tissues such as the intestine, an established target for anthelmintic treatments. Here, we add a valuable experimental component to our existing functional, proteomic, transcriptomic and phylogenomic studies of the Ascaris suum intestine, by developing a method to manipulate intestinal cell functions via direct delivery of experimental treatments (in this case, double-stranded (ds)RNA) to the apical intestinal membrane. We developed an intestinal perfusion method for direct, controlled delivery of dsRNA/heterogeneous small interfering (hsi) RNA into the intestinal lumen for experimentation. RNA-Seq (22 samples) was used to assess influences of the method on global intestinal gene expression. Successful mRNA-specific knockdown in intestinal cells of adult A. suum was accomplished with this new experimental method. Global transcriptional profiling confirmed that targeted transcripts were knocked down more significantly than any others, with only 12 (0.07% of all genes) or 238 (1.3%) off-target gene transcripts consistently differentially regulated by dsRNA treatment or the perfusion experimental design, respectively (after 24h). The system supports controlled, effective delivery of treatments (dsRNA/hsiRNA) to the apical intestinal membrane with relatively minor off-target effects, and builds on our experimental model to dissect A. suum intestinal cell functions with broad relevance to parasitic nematodes.
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Affiliation(s)
- Bruce A Rosa
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Samantha N McNulty
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Makedonka Mitreva
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Douglas P Jasmer
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164, USA.
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Yang D, Chen C, Liu Q, Jian H. Comparative analysis of pre- and post-parasitic transcriptomes and mining pioneer effectors of Heterodera avenae. Cell Biosci 2017; 7:11. [PMID: 28289537 PMCID: PMC5309974 DOI: 10.1186/s13578-017-0138-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 02/06/2017] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The cereal cyst nematode (CCN, Heterodera avenae) is a devastating pathogen of wheat and barley crops in many countries. We aimed to prioritize genetic and molecular targets for H. avenae control via the powerful and integrative bioinformatics platform. RESULTS Here, we sequenced mRNA isolated from Chinese H. avenae at pre-parasitic (consisting of egg, J1 and hatched-J2) stages and post-parasitic (consisting of parasitic-J2, J3, J4 and adults) stages. Total 1,066,719 reads of whole life cycle transcriptomes were assembled into 10,811 contigs with N50 length of 1754 bp and 71,401 singletons. Comparative analyses of orthologous among H. avenae and 7 other nematodes with various life-styles revealed the significance and peculiarity of neurological system for sedentary phytonematode. KEGG pathway enrichment demonstrated active crosstalk events of nervous system at pre-parasitic stages, and 6 FMRFamide-like neuropeptides were verified to display an expression peak at the hatched-J2 stage in H. avenae. Furthermore, multiple approaches were undertaken to mine putative effectors and parasitism-specific genes. Notably, H. avenae might represent the first phytonematode reported to possess the pioneer effectors with RxLR motif and potential effectors with homologies to Ant-5/Ant-34. CONCLUSION Our work provides valuable resources for in-depth understanding the parasitism and pathogenicity of H. avenae, as well as developing new targets-oriented strategies on effective managements.
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Affiliation(s)
- Dan Yang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193 China
| | - Changlong Chen
- Department of Plant Pathology, China Agricultural University, Beijing, 100193 China
- Institute of Crop Research, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Qian Liu
- Department of Plant Pathology, China Agricultural University, Beijing, 100193 China
| | - Heng Jian
- Department of Plant Pathology, China Agricultural University, Beijing, 100193 China
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Mitter N, Worrall EA, Robinson KE, Li P, Jain RG, Taochy C, Fletcher SJ, Carroll BJ, Lu GQM, Xu ZP. Clay nanosheets for topical delivery of RNAi for sustained protection against plant viruses. NATURE PLANTS 2017; 3:16207. [PMID: 28067898 DOI: 10.1038/nplants.2016.207] [Citation(s) in RCA: 413] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 11/24/2016] [Indexed: 05/19/2023]
Abstract
Topical application of pathogen-specific double-stranded RNA (dsRNA) for virus resistance in plants represents an attractive alternative to transgenic RNA interference (RNAi). However, the instability of naked dsRNA sprayed on plants has been a major challenge towards its practical application. We demonstrate that dsRNA can be loaded on designer, non-toxic, degradable, layered double hydroxide (LDH) clay nanosheets. Once loaded on LDH, the dsRNA does not wash off, shows sustained release and can be detected on sprayed leaves even 30 days after application. We provide evidence for the degradation of LDH, dsRNA uptake in plant cells and silencing of homologous RNA on topical application. Significantly, a single spray of dsRNA loaded on LDH (BioClay) afforded virus protection for at least 20 days when challenged on sprayed and newly emerged unsprayed leaves. This innovation translates nanotechnology developed for delivery of RNAi for human therapeutics to use in crop protection as an environmentally sustainable and easy to adopt topical spray.
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Affiliation(s)
- Neena Mitter
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Elizabeth A Worrall
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Karl E Robinson
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Peng Li
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Ritesh G Jain
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Christelle Taochy
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Stephen J Fletcher
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Bernard J Carroll
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - G Q Max Lu
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- University of Surrey, Guildford GU2 7XH, UK
| | - Zhi Ping Xu
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
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Britton C, Roberts B, Marks ND. Functional Genomics Tools for Haemonchus contortus and Lessons From Other Helminths. ADVANCES IN PARASITOLOGY 2016; 93:599-623. [PMID: 27238014 DOI: 10.1016/bs.apar.2016.02.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The availability of genome and transcriptome data for parasitic nematodes, including Haemonchus contortus, has highlighted the need to develop functional genomics tools. Comparative genomic analysis, particularly using data from the free-living nematode Caenorhabditis elegans, can help predict gene function. Reliable approaches to study function directly in parasitic nematodes are currently lacking. However, gene knockdown by RNA interference (RNAi) is being successfully used in schistosome and planarian species to define gene functions. Lessons from these systems may be applied to improve RNAi in H. contortus. Previous studies in H. contortus and related nematodes demonstrated reliable RNAi-mediated silencing of some genes, but not others. Current data suggest that susceptibility to RNAi in these nematodes is limited to genes expressed in sites accessible to the environment, such as the gut, amphids and excretory cell. Therefore, RNAi is functional in H. contortus, but improvements are needed to develop this system as a functional genomics platform. Here, we summarize RNAi studies on H. contortus and discuss the optimization of RNA delivery and improvements to culture methods to enhance larval development, protein turnover and the induction of phenotypic effects in vitro. The transgenic delivery of RNA or dominant-negative gene constructs and the recently developed CRISPR/Cas genome-editing technique are considered as potential alternative approaches for gene knockout. This is a key time to devote greater effort in progressing from genome to function, to improve our understanding of the biology of Haemonchus and identify novel targets for parasite control.
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Affiliation(s)
- C Britton
- University of Glasgow, Glasgow, United Kingdom
| | - B Roberts
- University of Glasgow, Glasgow, United Kingdom
| | - N D Marks
- University of Glasgow, Glasgow, United Kingdom
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Zhou B, Bailey A, Niblett CL, Qu R. Control of brown patch (Rhizoctonia solani) in tall fescue (Festuca arundinacea Schreb.) by host induced gene silencing. PLANT CELL REPORTS 2016; 35:791-802. [PMID: 26800976 DOI: 10.1007/s00299-015-1921-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/19/2015] [Accepted: 12/09/2015] [Indexed: 06/05/2023]
Abstract
Transgenic tall fescue plants expressing RNAi constructs of essential genes of Rhizoctonia solani were resistant to R. solani. Tall fescue (Festuca arundinacea Schreb.) is an important turf and forage grass species widely used for home lawns and on golf courses in North Carolina and other transition zone states in the US. The most serious and frequently occurring disease of tall fescue is brown patch, caused by a basidiomycete fungus, Rhizoctonia solani. This research demonstrates resistance to brown patch disease achieved by the application of host induced gene silencing. We transformed tall fescue with RNAi constructs of four experimentally determined "essential" genes from R. solani (including genes encoding RNA polymerase, importin beta-1 subunit, Cohesin complex subunit Psm1, and a ubiquitin E3 ligase) to suppress expression of those genes inside the fungus and thus inhibit fungal infection. Four gene constructs were tested, and 19 transgenic plants were obtained, among which 12 plants had detectable accumulation of siRNAs of the target genes. In inoculation tests, six plants displayed significantly improved resistance against R. solani. Lesion size was reduced by as much as 90 %. Plants without RNAi accumulation did not show resistance. To our knowledge, this is the first case that RNAi constructs of pathogen genes introduced into a host plant can confer resistance against a necrotrophic fungus.
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Affiliation(s)
- Binbin Zhou
- Department of Crop Science, North Carolina State University, Raleigh, NC, 27695-7287, USA
- Omicsoft Corp., Cary, NC, 27513, USA
| | - Ana Bailey
- Venganza Inc., St. Augustine, FL, 32080, USA
| | - C L Niblett
- Venganza Inc., St. Augustine, FL, 32080, USA
| | - Rongda Qu
- Department of Crop Science, North Carolina State University, Raleigh, NC, 27695-7287, USA.
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43
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Rehman S, Gupta VK, Goyal AK. Identification and functional analysis of secreted effectors from phytoparasitic nematodes. BMC Microbiol 2016; 16:48. [PMID: 27001199 PMCID: PMC4802876 DOI: 10.1186/s12866-016-0632-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 01/22/2016] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Plant parasitic nematodes develop an intimate and long-term feeding relationship with their host plants. They induce a multi-nucleate feeding site close to the vascular bundle in the roots of their host plant and remain sessile for the rest of their life. Nematode secretions, produced in the oesophageal glands and secreted through a hollow stylet into the host plant cytoplasm, are believed to play key role in pathogenesis. To combat these persistent pathogens, the identity and functional analysis of secreted effectors can serve as a key to devise durable control measures. In this review, we will recapitulate the knowledge over the identification and functional characterization of secreted nematode effector repertoire from phytoparasitic nematodes. RESEARCH Despite considerable efforts, the identity of genes encoding nematode secreted proteins has long been severely hampered because of their microscopic size, long generation time and obligate biotrophic nature. The methodologies such as bioinformatics, protein structure modeling, in situ hybridization microscopy, and protein-protein interaction have been used to identify and to attribute functions to the effectors. In addition, RNA interference (RNAi) has been instrumental to decipher the role of the genes encoding secreted effectors necessary for parasitism and genes attributed to normal development. Recent comparative and functional genomic approaches have accelerated the identification of effectors from phytoparasitic nematodes and offers opportunities to control these pathogens. CONCLUSION Plant parasitic nematodes pose a serious threat to global food security of various economically important crops. There is a wealth of genomic and transcriptomic information available on plant parasitic nematodes and comparative genomics has identified many effectors. Bioengineering crops with dsRNA of phytonematode genes can disrupt the life cycle of parasitic nematodes and therefore holds great promise to develop resistant crops against plant-parasitic nematodes.
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Affiliation(s)
- Sajid Rehman
- />International Center for Agriculture Research in the Dry Areas (ICARDA), Rabat-Instituts-Morocco, P.O.Box 6299, Rabat, Morocco
| | - Vijai K. Gupta
- />National University of Ireland Galway, Galway, Ireland
| | - Aakash K. Goyal
- />International Center for Agriculture Research in the Dry Areas (ICARDA), Rabat-Instituts-Morocco, P.O.Box 6299, Rabat, Morocco
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Ratnappan R, Vadnal J, Keaney M, Eleftherianos I, O'Halloran D, Hawdon JM. RNAi-mediated gene knockdown by microinjection in the model entomopathogenic nematode Heterorhabditis bacteriophora. Parasit Vectors 2016; 9:160. [PMID: 26993791 PMCID: PMC4797128 DOI: 10.1186/s13071-016-1442-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 03/10/2016] [Indexed: 12/21/2022] Open
Abstract
Background Parasitic nematodes threaten the health of humans and livestock and cause a major financial and socioeconomic burden to modern society. Given the widespread distribution of diseases caused by parasitic nematodes there is an urgent need to develop tools that will elucidate the genetic complexity of host-parasite interactions. Heterorhabditis bacteriophora is a parasitic nematode that allows simultaneous monitoring of nematode infection processes and host immune function, and offers potential as a tractable model for parasitic nematode infections. However, molecular tools to investigate these processes are required prior to its widespread acceptance as a robust model organism. In this paper we describe microinjection in adult H. bacteriophora as a suitable means of dsRNA delivery to knockdown gene transcripts. Methods RNA interference was used to knockdown four genes by injecting dsRNA directly into the gonad of adult hermaphrodite nematodes. RNAi phenotypes were scored in the F1 progeny on the fifth day post-injection, and knockdown of gene-specific transcripts was quantified with real-time quantitative RT-PCR (qRT-PCR). Results RNAi injection in adult hermaphrodites significantly decreased the level of target transcripts to varying degrees when compared with controls. The genes targeted by RNAi via injection included cct-2, nol-5, dpy-7, and dpy-13. In each case, RNAi knockdown was confirmed phenotypically by examining the progeny of injected animals, and also confirmed at the transcriptional level by real-time qRT-PCR. Conclusions Here we describe for the first time the successful use of microinjection to knockdown gene transcripts in H. bacteriophora. This technique can be used widely to study the molecular basis of parasitism.
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Affiliation(s)
- Ramesh Ratnappan
- Department of Microbiology Immunology and Tropical Medicine, George Washington University Medical Center, Washington, DC, 20037, USA
| | - Jonathan Vadnal
- Department of Microbiology Immunology and Tropical Medicine, George Washington University Medical Center, Washington, DC, 20037, USA
| | - Melissa Keaney
- Department of Microbiology Immunology and Tropical Medicine, George Washington University Medical Center, Washington, DC, 20037, USA
| | - Ioannis Eleftherianos
- Department of Biological Sciences, George Washington University, Science and Engineering Hall, suite 6000, 800 22nd Street NW, Washington, DC, 20052, USA
| | - Damien O'Halloran
- Department of Biological Sciences, George Washington University, Science and Engineering Hall, suite 6000, 800 22nd Street NW, Washington, DC, 20052, USA.,Institute for Neuroscience, George Washington University, 636 Ross Hall, 2300 I Street NW, Washington, DC, 20052, USA
| | - John M Hawdon
- Department of Microbiology Immunology and Tropical Medicine, George Washington University Medical Center, Washington, DC, 20037, USA.
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Wang M, Wang D, Zhang X, Wang X, Liu W, Hou X, Huang X, Xie B, Cheng X. Double-stranded RNA-mediated interference of dumpy genes in Bursaphelenchus xylophilus by feeding on filamentous fungal transformants. Int J Parasitol 2016; 46:351-60. [PMID: 26953254 DOI: 10.1016/j.ijpara.2016.01.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 01/27/2016] [Accepted: 01/28/2016] [Indexed: 01/05/2023]
Abstract
RNA interference (RNAi) is a valuable tool for studying gene function in vivo and provides a functional genomics platform in a wide variety of organisms. The pinewood nematode, Bursaphelenchus xylophilus, is a prominent invasive plant-parasitic nematode and has become a serious worldwide threat to forest ecosystems. Presently, the complete genome sequence of B. xylophilus has been published, and research involving genome-wide functional analyses is likely to increase. In this study, we describe the construction of an effective silencing vector, pDH-RH, which contains a transcriptional unit for a hairpin loop structure. Utilising this vector, double-stranded (ds)RNAs with sequences homologous to the target genes can be expressed in a transformed filamentous fungus via Agrobacterium tumefaciens-mediated transformation technology, and can subsequently induce the knockdown of target gene mRNA expression in B. xylophilus by allowing the nematode to feed on the fungal transformants. Four dumpy genes (Bx-dpy-2, 4, 10 and 11) were used as targets to detect RNAi efficiency. By allowing the nematode to feed on target gene-transformed Fusarium oxysporum strains, target transcripts were knocked down 34-87% compared with those feeding on the wild-type strain as determined by real-time quantitative PCR (RT-qPCR). Morphological RNAi phenotypes were observed, displaying obviously reduced body length; weak dumpy or small (short and thin) body size; or general abnormalities. Moreover, compensatory regulation and non-specific silencing of dpy genes were found in B. xylophilus. Our results indicate that RNAi delivery by feeding in B. xylophilus is a successful technique. This platform may provide a new opportunity for undertaking RNAi-based, genome-wide gene functional studies in vitro in B. xylophilus. Moreover, as B. xylophilus feeds on endophytic fungi when a host has died, RNAi feeding technology will offer the prospect for developing a novel control strategy for the nematode. Furthermore, this platform may also be applicable to other parasitic nematodes that have a facultative, fungivorous habit.
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Affiliation(s)
- Meng Wang
- College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Diandong Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Yangtze Normal University, Chongqing 408100, China
| | - Xi Zhang
- College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Xu Wang
- College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Wencui Liu
- College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Xiaomeng Hou
- College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Xiaoyin Huang
- College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Bingyan Xie
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Xinyue Cheng
- College of Life Sciences, Beijing Normal University, Beijing 100875, China; Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Beijing 100875, China.
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Peng H, Cui J, Long H, Huang W, Kong L, Liu S, He W, Hu X, Peng D. Novel Pectate Lyase Genes of Heterodera glycines Play Key Roles in the Early Stage of Parasitism. PLoS One 2016; 11:e0149959. [PMID: 26930215 PMCID: PMC4773153 DOI: 10.1371/journal.pone.0149959] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 02/08/2016] [Indexed: 11/19/2022] Open
Abstract
Pectate lyases are known to play a key role in pectin degradation by catalyzing the random cleavage of internal polymer linkages (endo-pectinases). In this paper, four novel cDNAs, designated Hg-pel-3, Hg-pel-4, Hg-pel-6 and Hg-pel-7, that encode pectate lyases were cloned and characterized from the soybean cyst nematode, Heterodera glycines. The predicted protein sequences of HG-PEL-3, HG-PEL-4 and HG-PEL-6 differed significantly in both their amino acid sequences and their genomic structures from other pectate lyases of H. glycines (HG-PEL-1, HG-PEL-2 and HG-PEL-7). A phylogenetic study revealed that the pectate lyase proteins of H. glycines are clustered into distinct clades and have distinct numbers and positioning of introns, which suggests that the pectate lyase genes of H. glycines may have evolved from at least two ancestral genes. A Southern blot analysis revealed that multiple Hg-pel-6-like genes were present in the H. glycines genome. In situ hybridization showed that four novel pectate lyases (Hg-pel-3, Hg-pel-4, Hg-pel-6 and Hg-pel-7) were actively transcribed in the subventral esophageal gland cells. A semi-quantitative RT-PCR assay supported the finding that the expression of these genes was strong in the egg, pre-parasitic second-stage juvenile (J2) and early parasitic J2 stages and that it declined in further developmental stages of the nematode. This expression pattern suggests that these proteins play a role in the migratory phase of the nematode life cycle. Knocking down Hg-pel-6 using in vitro RNA interference resulted in a 46.9% reduction of the number of nematodes that invaded the plants and a 61.5% suppression of the development of H. glycines females within roots compared to the GFP-dsRNA control. Plant host-derived RNAi induced the silencing of the Hg-pel-6gene, which significantly reduced the nematode infection levels at 7 Days post inoculation (dpi). Similarly, this procedure reduced the number of female adults at 40 dpi, which suggests the important roles of this gene in the early stages of parasitism. Our combined data suggest that two types of pectate lyases are present in the H. glycines genome and may have different roles during infection.
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Affiliation(s)
- Huan Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiangkuan Cui
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haibo Long
- Key Laboratory of Pests Comprehensive Governance for Tropical crops, Ministry of Agriculture, P. R. China, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Science, Danzhou, China
| | - Wenkun Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lingan Kong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shiming Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenting He
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xianqi Hu
- The National Engineering Research Center of Agri-biodiversity Applied Technologies, Yunnan Agricultural University, Kunming, China
| | - Deliang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Shivakumara TN, Papolu PK, Dutta TK, Kamaraju D, Chaudhary S, Rao U. RNAi-induced silencing of an effector confers transcriptional oscillation in another group of effectors in the root-knot nematode, Meloidogyne incognita. NEMATOLOGY 2016. [DOI: 10.1163/15685411-00003003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The sophisticated parasitic tactic of sedentary endoparasitic nematodes seems to involve the simultaneous alteration of the expression of multitude of its effector genes in order to hijack the plant metabolic and developmental pathway. In concordance with this hypothesis, we have targeted some candidate effector genes of Meloidogyne incognita to understand the possible interaction among those effectors for successful infection of the host plant. In vitro RNAi strategy was used to knock down M. incognita-specific pioneer effector genes, such as msp-18, msp-20, msp-24, msp-33 and msp-16 (known to interact with plant transcription factor), to investigate their possible effect on the expression of key cell wall-degrading enzymes (CWDE) and vice versa. Supported by the phenotypic data, intriguingly our study revealed that induced suppression of these pioneer genes cause transcriptional alteration of CWDE genes in M. incognita. This remarkable finding may provide some useful links for future research on nematode effector interaction.
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Affiliation(s)
| | - Pradeep K. Papolu
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India, 110012
| | - Tushar K. Dutta
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India, 110012
| | - Divya Kamaraju
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India, 110012
| | - Sonam Chaudhary
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India, 110012
| | - Uma Rao
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India, 110012
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Zheng M, Long H, Zhao Y, Li L, Xu D, Zhang H, Liu F, Deng G, Pan Z, Yu M. RNA-Seq Based Identification of Candidate Parasitism Genes of Cereal Cyst Nematode (Heterodera avenae) during Incompatible Infection to Aegilops variabilis. PLoS One 2015; 10:e0141095. [PMID: 26517841 PMCID: PMC4627824 DOI: 10.1371/journal.pone.0141095] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 10/05/2015] [Indexed: 11/19/2022] Open
Abstract
One of the reasons for the progressive yield decline observed in cereals production is the rapid build-up of populations of the cereal cyst nematode (CCN, Heterodera avenae). These nematodes secrete so-call effectors into their host plant to suppress the plant defense responses, alter plant signaling pathways and then induce the formation of syncytium after infection. However, little is known about its molecular mechanism and parasitism during incompatible infection. To gain insight into its repertoire of parasitism genes, we investigated the transcriptome of the early parasitic second-stage (30 hours, 3 days and 9 days post infection) juveniles of the CCN as well as the CCN infected tissue of the host Aegilops variabilis by Illumina sequencing. Among all assembled unigenes, 681 putative genes of parasitic nematode were found, in which 56 putative effectors were identified, including novel pioneer genes and genes corresponding to previously reported effectors. All the 681 CCN unigenes were mapped to 229 GO terms and 200 KEGG pathways, including growth, development and several stimulus-related signaling pathways. Sixteen clusters were involved in the CCN unigene expression atlas at the early stages during infection process, and three of which were significantly gene-enriched. Besides, the protein-protein interaction network analysis revealed 35 node unigenes which may play an important role in the plant-CCN interaction. Moreover, in a comparison of differentially expressed genes between the pre-parasitic juveniles and the early parasitic juveniles, we found that hydrolase activity was up-regulated in pre J2s whereas binding activity was upregulated in infective J2s. RT-qPCR analysis on some selected genes showed detectable expression, indicating possible secretion of the proteins and putative role in infection. This study provided better insights into the incompatible interaction between H. avenae and the host plant Ae. varabilis. Moreover, RNAi targets with potential lethality were screened out and primarily validated, which provide candidates for engineering-based control of cereal cyst nematode in crops breeding.
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Affiliation(s)
- Minghui Zheng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of the Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Hai Long
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Yun Zhao
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Lin Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Delin Xu
- Zunyi Medical University, Zunyi, China
| | - Haili Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Feng Liu
- Plant Protection College, Shandong Agriculture University, Tai’an, China
| | - Guangbing Deng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Zhifen Pan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Maoqun Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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Weiberg A, Jin H. Small RNAs--the secret agents in the plant-pathogen interactions. CURRENT OPINION IN PLANT BIOLOGY 2015; 26:87-94. [PMID: 26123395 PMCID: PMC4573252 DOI: 10.1016/j.pbi.2015.05.033] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/28/2015] [Accepted: 05/29/2015] [Indexed: 05/15/2023]
Abstract
Eukaryotic regulatory small RNAs (sRNAs) that induce RNA interference (RNAi) are involved in a plethora of biological processes, including host immunity and pathogen virulence. In plants, diverse classes of sRNAs contribute to the regulation of host innate immunity. These immune-regulatory sRNAs operate through distinct RNAi pathways that trigger transcriptional or post-transcriptional gene silencing. Similarly, many pathogen-derived sRNAs also regulate pathogen virulence. Remarkably, the influence of regulatory sRNAs is not limited to the individual organism in which they are generated. It can sometimes extend to interacting species from even different kingdoms. There they trigger gene silencing in the interacting organism, a phenomenon called cross-kingdom RNAi. This is exhibited in advanced pathogens and parasites that produce sRNAs to suppress host immunity. Conversely, in host-induced gene silencing (HIGS), diverse plants are engineered to trigger RNAi against pathogens and pests to confer host resistance. Cross-kingdom RNAi opens up a vastly unexplored area of research on mobile sRNAs in the battlefield between hosts and pathogens.
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Affiliation(s)
- Arne Weiberg
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Hailing Jin
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA.
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50
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Lourenço-Tessutti IT, Souza Junior JDA, Martins-de-Sa D, Viana AAB, Carneiro RMDG, Togawa RC, de Almeida-Engler J, Batista JAN, Silva MCM, Fragoso RR, Grossi-de-Sa MF. Knock-down of heat-shock protein 90 and isocitrate lyase gene expression reduced root-knot nematode reproduction. PHYTOPATHOLOGY 2015; 105:628-37. [PMID: 26020830 DOI: 10.1094/phyto-09-14-0237-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Crop losses caused by nematode infections are estimated to be valued at USD 157 billion per year. Meloidogyne incognita, a root-knot nematode (RKN), is considered to be one of the most important plant pathogens due to its worldwide distribution and the austere damage it can cause to a large variety of agronomically important crops. RNA interference (RNAi), a gene silencing process, has proven to be a valuable biotechnology alternative method for RKN control. In this study, the RNAi approach was applied, using fragments of M. incognita genes that encode for two essential molecules, heat-shock protein 90 (HSP90) and isocitrate lyase (ICL). Plant-mediated RNAi of these genes led to a significant level of resistance against M. incognita in the transgenic Nicotiana tabacum plants. Bioassays of plants expressing HSP90 dsRNA demonstrated a delay in gall formation and up to 46% reduction in eggs compared with wild-type plants. A reduction in the level of HSP90 transcripts was observed in recovered eggs from plants expressing dsRNA, indicating that gene silencing persisted and was passed along to first progeny. The ICL knock-down had no clear effect on gall formation but resulted in up to 77% reduction in egg oviposition compared with wild-type plants. Our data suggest that both genes may be involved in RKN development and reproduction. Thus, in this paper, we describe essential candidate genes that could be applied to generate genetically modified crops, using the RNAi strategy to control RKN parasitism.
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Affiliation(s)
- Isabela Tristan Lourenço-Tessutti
- First, second, third, fourth, fifth, sixth, eighth, ninth, and eleventh authors: Embrapa Genetic Resources and Biotechnology, Laboratory of Molecular Plant-Pest Interaction, Brasília, DF, Brazil; first, second, and third authors: University of Brasília, Department of Cell Biology, Graduate Program in Molecular Biology, Brasília, DF, Brazil; seventh author: Institut National de la Recherche Agronomique, Sophia-Antipolis, France; eighth author: Federal University of Minas Gerais, Botany Department, Belo Horizonte, MG, Brazil; tenth author: Embrapa Cerrados, Laboratory of Phytopathology, Planaltina, DF, Brazil; and eleventh author: Catholic University of Brasília, Graduate Program in Genomic Sciences and Biotechnology, Brasília, DF, Brazil
| | - José Dijair Antonino Souza Junior
- First, second, third, fourth, fifth, sixth, eighth, ninth, and eleventh authors: Embrapa Genetic Resources and Biotechnology, Laboratory of Molecular Plant-Pest Interaction, Brasília, DF, Brazil; first, second, and third authors: University of Brasília, Department of Cell Biology, Graduate Program in Molecular Biology, Brasília, DF, Brazil; seventh author: Institut National de la Recherche Agronomique, Sophia-Antipolis, France; eighth author: Federal University of Minas Gerais, Botany Department, Belo Horizonte, MG, Brazil; tenth author: Embrapa Cerrados, Laboratory of Phytopathology, Planaltina, DF, Brazil; and eleventh author: Catholic University of Brasília, Graduate Program in Genomic Sciences and Biotechnology, Brasília, DF, Brazil
| | - Diogo Martins-de-Sa
- First, second, third, fourth, fifth, sixth, eighth, ninth, and eleventh authors: Embrapa Genetic Resources and Biotechnology, Laboratory of Molecular Plant-Pest Interaction, Brasília, DF, Brazil; first, second, and third authors: University of Brasília, Department of Cell Biology, Graduate Program in Molecular Biology, Brasília, DF, Brazil; seventh author: Institut National de la Recherche Agronomique, Sophia-Antipolis, France; eighth author: Federal University of Minas Gerais, Botany Department, Belo Horizonte, MG, Brazil; tenth author: Embrapa Cerrados, Laboratory of Phytopathology, Planaltina, DF, Brazil; and eleventh author: Catholic University of Brasília, Graduate Program in Genomic Sciences and Biotechnology, Brasília, DF, Brazil
| | - Antônio Américo Barbosa Viana
- First, second, third, fourth, fifth, sixth, eighth, ninth, and eleventh authors: Embrapa Genetic Resources and Biotechnology, Laboratory of Molecular Plant-Pest Interaction, Brasília, DF, Brazil; first, second, and third authors: University of Brasília, Department of Cell Biology, Graduate Program in Molecular Biology, Brasília, DF, Brazil; seventh author: Institut National de la Recherche Agronomique, Sophia-Antipolis, France; eighth author: Federal University of Minas Gerais, Botany Department, Belo Horizonte, MG, Brazil; tenth author: Embrapa Cerrados, Laboratory of Phytopathology, Planaltina, DF, Brazil; and eleventh author: Catholic University of Brasília, Graduate Program in Genomic Sciences and Biotechnology, Brasília, DF, Brazil
| | - Regina Maria Dechechi Gomes Carneiro
- First, second, third, fourth, fifth, sixth, eighth, ninth, and eleventh authors: Embrapa Genetic Resources and Biotechnology, Laboratory of Molecular Plant-Pest Interaction, Brasília, DF, Brazil; first, second, and third authors: University of Brasília, Department of Cell Biology, Graduate Program in Molecular Biology, Brasília, DF, Brazil; seventh author: Institut National de la Recherche Agronomique, Sophia-Antipolis, France; eighth author: Federal University of Minas Gerais, Botany Department, Belo Horizonte, MG, Brazil; tenth author: Embrapa Cerrados, Laboratory of Phytopathology, Planaltina, DF, Brazil; and eleventh author: Catholic University of Brasília, Graduate Program in Genomic Sciences and Biotechnology, Brasília, DF, Brazil
| | - Roberto Coiti Togawa
- First, second, third, fourth, fifth, sixth, eighth, ninth, and eleventh authors: Embrapa Genetic Resources and Biotechnology, Laboratory of Molecular Plant-Pest Interaction, Brasília, DF, Brazil; first, second, and third authors: University of Brasília, Department of Cell Biology, Graduate Program in Molecular Biology, Brasília, DF, Brazil; seventh author: Institut National de la Recherche Agronomique, Sophia-Antipolis, France; eighth author: Federal University of Minas Gerais, Botany Department, Belo Horizonte, MG, Brazil; tenth author: Embrapa Cerrados, Laboratory of Phytopathology, Planaltina, DF, Brazil; and eleventh author: Catholic University of Brasília, Graduate Program in Genomic Sciences and Biotechnology, Brasília, DF, Brazil
| | - Janice de Almeida-Engler
- First, second, third, fourth, fifth, sixth, eighth, ninth, and eleventh authors: Embrapa Genetic Resources and Biotechnology, Laboratory of Molecular Plant-Pest Interaction, Brasília, DF, Brazil; first, second, and third authors: University of Brasília, Department of Cell Biology, Graduate Program in Molecular Biology, Brasília, DF, Brazil; seventh author: Institut National de la Recherche Agronomique, Sophia-Antipolis, France; eighth author: Federal University of Minas Gerais, Botany Department, Belo Horizonte, MG, Brazil; tenth author: Embrapa Cerrados, Laboratory of Phytopathology, Planaltina, DF, Brazil; and eleventh author: Catholic University of Brasília, Graduate Program in Genomic Sciences and Biotechnology, Brasília, DF, Brazil
| | - João Aguiar Nogueira Batista
- First, second, third, fourth, fifth, sixth, eighth, ninth, and eleventh authors: Embrapa Genetic Resources and Biotechnology, Laboratory of Molecular Plant-Pest Interaction, Brasília, DF, Brazil; first, second, and third authors: University of Brasília, Department of Cell Biology, Graduate Program in Molecular Biology, Brasília, DF, Brazil; seventh author: Institut National de la Recherche Agronomique, Sophia-Antipolis, France; eighth author: Federal University of Minas Gerais, Botany Department, Belo Horizonte, MG, Brazil; tenth author: Embrapa Cerrados, Laboratory of Phytopathology, Planaltina, DF, Brazil; and eleventh author: Catholic University of Brasília, Graduate Program in Genomic Sciences and Biotechnology, Brasília, DF, Brazil
| | - Maria Cristina Mattar Silva
- First, second, third, fourth, fifth, sixth, eighth, ninth, and eleventh authors: Embrapa Genetic Resources and Biotechnology, Laboratory of Molecular Plant-Pest Interaction, Brasília, DF, Brazil; first, second, and third authors: University of Brasília, Department of Cell Biology, Graduate Program in Molecular Biology, Brasília, DF, Brazil; seventh author: Institut National de la Recherche Agronomique, Sophia-Antipolis, France; eighth author: Federal University of Minas Gerais, Botany Department, Belo Horizonte, MG, Brazil; tenth author: Embrapa Cerrados, Laboratory of Phytopathology, Planaltina, DF, Brazil; and eleventh author: Catholic University of Brasília, Graduate Program in Genomic Sciences and Biotechnology, Brasília, DF, Brazil
| | - Rodrigo Rocha Fragoso
- First, second, third, fourth, fifth, sixth, eighth, ninth, and eleventh authors: Embrapa Genetic Resources and Biotechnology, Laboratory of Molecular Plant-Pest Interaction, Brasília, DF, Brazil; first, second, and third authors: University of Brasília, Department of Cell Biology, Graduate Program in Molecular Biology, Brasília, DF, Brazil; seventh author: Institut National de la Recherche Agronomique, Sophia-Antipolis, France; eighth author: Federal University of Minas Gerais, Botany Department, Belo Horizonte, MG, Brazil; tenth author: Embrapa Cerrados, Laboratory of Phytopathology, Planaltina, DF, Brazil; and eleventh author: Catholic University of Brasília, Graduate Program in Genomic Sciences and Biotechnology, Brasília, DF, Brazil
| | - Maria Fatima Grossi-de-Sa
- First, second, third, fourth, fifth, sixth, eighth, ninth, and eleventh authors: Embrapa Genetic Resources and Biotechnology, Laboratory of Molecular Plant-Pest Interaction, Brasília, DF, Brazil; first, second, and third authors: University of Brasília, Department of Cell Biology, Graduate Program in Molecular Biology, Brasília, DF, Brazil; seventh author: Institut National de la Recherche Agronomique, Sophia-Antipolis, France; eighth author: Federal University of Minas Gerais, Botany Department, Belo Horizonte, MG, Brazil; tenth author: Embrapa Cerrados, Laboratory of Phytopathology, Planaltina, DF, Brazil; and eleventh author: Catholic University of Brasília, Graduate Program in Genomic Sciences and Biotechnology, Brasília, DF, Brazil
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