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In Vitro and In Planta Antagonistic Effect of Endophytic Bacteria on Blight Causing Xanthomonas axonopodis pv. punicae: A Destructive Pathogen of Pomegranate. Microorganisms 2022; 11:microorganisms11010005. [PMID: 36677297 PMCID: PMC9860609 DOI: 10.3390/microorganisms11010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/04/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Pomegranate bacterial blight caused by Xanthomonas axonopodis pv. punicae (Xap) is a highly destructive disease. In the absence of host resistance to the disease, we aimed to evaluate the biocontrol potential of endophytic bacteria against Xap. Thus, in this study, we isolated endophytes from pomegranate plants, identified them on the basis of 16S rDNA sequencing, tested them against Xap, and estimated the endophyte-mediated host defense response. The population of isolated endophytes ranged from 3 × 106 to 8 × 107 CFU/g tissue. Furthermore, 26 isolates were evaluated for their biocontrol activity against Xap, and all the tested isolates significantly reduced the in vitro growth of Xap (15.65% ± 1.25% to 56.35% ± 2.66%) as compared to control. These isolates could reduce fuscan, an uncharacterized factor of Xap involved in its aggressiveness. Lower blight incidence (11.6%) and severity (6.1%) were recorded in plants sprayed with endophytes 8 days ahead of Xap spray (Set-III) as compared to control plants which were not exposed to endophytes (77.33 and 50%, respectively%) during in vivo evaluation. Moreover, significantly high phenolic and chlorophyll contents were estimated in endophyte-treated plants as compared to control. The promising isolates mostly belonged to the genera Bacillus, Burkholderia, and Lysinibacillus, and they were deposited to the National Agriculturally Important Microbial Culture Collection, India.
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Patil PG, Sharma J, Nanjundappa M, Singh NV, Bohra A, Gunnaiah R, Jamma SM, Vinayaka J, Sangnure VR, Marathe RA. Identification and validation of SSR markers for Xanthomonas axonopodis pv. punicae an incitant of bacterial blight of pomegranate. 3 Biotech 2022; 12:153. [PMID: 35755801 DOI: 10.1007/s13205-022-03209-z] [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: 01/18/2022] [Accepted: 05/22/2022] [Indexed: 11/01/2022] Open
Abstract
This study reports genome wide characterization and development of first set of microsatellite markers through in silico analysis of eight sequenced Xanthomonas axonopodis pv. punicae strains available in the public database. SSR survey resulted in identification of ~ 4638 perfect SSRs, with mean marker frequency 901 SSRs/Mb and densitiy of 11,006 bp/Mb aross the eight genomes. Frequency distribution graphs revealed hexa-nucleotide repeats were more prominent fowllowed by tri-, tetra-, di- and penta-nucleotides in the analysed genomes. We desinged 2927 SSR primers that are specific to the strain LMG 859 and ePCR confirmed on seven other Xap genomes. This resulted in identification of 542 informative SSRs that are producing single amplicons, from which 66 primers were successfully validated through wet lab experiments on eight Xap isolates of pomegranate. Furthermore, utility of these SSRs were demostrated by analysing molecular diversity among 22 Xap isolates using 20 Xap_SSR primers. SSRs revealed moderate genetic diversity among Xap isolates (61%) and grouped 11 isolates that are repersenting six different states into one cluster. This proved the earlier evidence of wider spread of ST3 type Xap acoss India using Multi locus Sequence Typing (MLST) technique. In summary, Xap_SSR will serve as powerful genomics tools that would helps in monitoring of population dynamics, taxonomy, epidomology and quarantine aspects in bacterial blight pathogen through development of microsatellite based Multilocus Variable number of Tandem repeat analysis (MLVA) in future. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03209-z.
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Affiliation(s)
- Prakash G Patil
- Biotechnology and Plant Pathology, ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 India
| | - Jyotsana Sharma
- Biotechnology and Plant Pathology, ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 India
| | - Manjunatha Nanjundappa
- Biotechnology and Plant Pathology, ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 India
| | - N V Singh
- Biotechnology and Plant Pathology, ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 India
| | - Abhishek Bohra
- State Agriculture Biotechnology, Centre, Centre for Crop & Food Innovation, Murdoch University, Perth, Western Australia
| | - Raghavendra Gunnaiah
- Department of Biotechnology and Crop Improvement, University of Horticultural Sciences (UHS), Bagalkot, 587104 India
| | - Shivani M Jamma
- Biotechnology and Plant Pathology, ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 India
| | - Jeer Vinayaka
- Biotechnology and Plant Pathology, ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 India
| | - Vipul R Sangnure
- Biotechnology and Plant Pathology, ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 India
| | - R A Marathe
- Biotechnology and Plant Pathology, ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 India
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Genetic Diversity and Streptomycin Sensitivity in Xanthomonas axonopodis pv. punicae Causing Oily Spot Disease in Pomegranates. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8050441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Xanthomonas axonopodis pv. punicae (Xap) causes bacterial blight disease in pomegranates, often leading to 60–80% economic loss. In absence of a suitable Xap-resistant variety, the near-monoculture of the susceptible variety, Bhagwa, has aggravated the problem further. In recent times, Xap has spread to different geographical regions, indicating the wide adaptability of the pathogen. Moreover, lower sensitivity of Xap towards streptocycline containing streptomycin sulphate and tetracycline sulphate (9:1) under field conditions is frequently reported. Therefore, the current study was undertaken to assess the genetic variability of Xap isolates using SSR markers, their in vitro sensitivity towards streptomycin was evaluated, and the probable molecular basis of acquired resistance was studied. Two highly diverse isolates showed extreme differences in their pathogenicity, indicating the highly evolving nature of the pathogen. Moreover, all the isolates showed less than 50% growth inhibition on media containing 1500 µg/mL streptomycin, indicating a lower level of antibiotic sensitivity. On the molecular level, 90% of the isolates showed the presence of strA-strB genes involved in streptomycin metabolism. Additionally, G to A transitions were observed in the rpsL gene in some of the isolates. The molecular data suggest that horizontal gene transfer (strAB) and/or spontaneous gene mutation (in rpsL) could be responsible for the observed lower sensitivity of Xap towards streptomycin.
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Sivaraman S, Krishnamoorthy D, Arvind K, Grace T, Sharma J, Antony G. TAL effectors and the predicted host targets of pomegranate bacterial blight pathogen Xanthomonas citri pv. punicae. Curr Genet 2022; 68:361-373. [PMID: 35275250 DOI: 10.1007/s00294-022-01232-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/24/2022] [Accepted: 02/08/2022] [Indexed: 11/29/2022]
Abstract
The molecular mechanism of pomegranate susceptibility to bacterial blight, a serious threat to pomegranate production in India, is largely unknown. In the current study, we have used PacBio and Illumina sequencing of Xanthomonas citri pv. punicae (Xcp) strain 119 genome to identify tal genes and RNA-Seq analysis to identify putative host targets in the susceptible pomegranate variety Bhagwa challenged with Xcp119. Xcp119 genome encodes seven transcription activator-like effectors (TALEs), three of which are harbored by a plasmid. RVD-based phylogenetic analysis of TALEs of Xanthomonas citri pathovars indicate the TALEs of Xcp as evolutionarily and functionally close to Xanthomonas citri pv. malvacearum and Xanthomonas citri pv. glycines. Comparative RNA-Seq of Xcp and mock-inoculated leaf tissues revealed Xcp-induced pomegranate transcription modulation. The prediction of TALE binding elements (EBEs) in the promoters of up-regulated genes identified a set of TALE-targeted candidate genes in pomegranate-Xcp interaction. The predicted candidate susceptibility genes include two oxoglutarate-dependent dioxygenase gene, ethylene-responsive transcription factor and flavanone 3-hydroxylase-like gene, and the further characterization of these would enable blight resistance engineering in pomegranate.
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Affiliation(s)
- Sruthi Sivaraman
- Department of Plant Science, Central University of Kerala, Periye, 671320, Kerala, India
| | | | - Kumar Arvind
- Department of Genomic Science, Central University of Kerala, Periye, 671320, Kerala, India
| | - Tony Grace
- Department of Genomic Science, Central University of Kerala, Periye, 671320, Kerala, India
| | - Jyotsana Sharma
- ICAR-National Research Centre On Pomegranate, Kegaon, Solapur, 413255, Maharashtra, India
| | - Ginny Antony
- Department of Plant Science, Central University of Kerala, Periye, 671320, Kerala, India.
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Kumar P, Lokesh V, Doddaraju P, Kumari A, Singh P, Meti BS, Sharma J, Gupta KJ, Manjunatha G. Greenhouse and field experiments revealed that clove oil can effectively reduce bacterial blight and increase yield in pomegranate. Food Energy Secur 2021. [DOI: 10.1002/fes3.305] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
- Pavan Kumar
- Biocontrol laboratory University of Horticultural Sciences Bagalkot India
- Department of Biotechnology Basaveshwar Engineering College (Autonomous) Bagalkot India
| | - Veeresh Lokesh
- Biocontrol laboratory University of Horticultural Sciences Bagalkot India
| | - Pushpa Doddaraju
- Biocontrol laboratory University of Horticultural Sciences Bagalkot India
| | - Aprajita Kumari
- National Institute for Plant Genome Research New Delhi India
| | - Pooja Singh
- National Institute for Plant Genome Research New Delhi India
| | - Bharati S. Meti
- Department of Biotechnology Basaveshwar Engineering College (Autonomous) Bagalkot India
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Radhika DH, Gunnaiah R, Lamani A, Peerjade D, Jagadeesha RC. Long-Read Genome Sequence Resources of Xanthomonas citri pv. punicae Strain Bagalkot Causing Pomegranate Bacterial Blight. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:874-877. [PMID: 33709768 DOI: 10.1094/mpmi-01-21-0001-a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Xanthomonas citri pv. punicae causing bacterial blight is a devastating disease of pomegranate in India and Pakistan. Most xanthomonads use the type III secretion system to inject transcription activator-like effector (TALE) proteins into the host cell. TALEs bind to the effector-binding elements in the promoter of host susceptibility genes, triggering disease development. PacBio single-molecule real-time long-read sequencing technology was used to identify the TALE-encoding genes, which is otherwise not possible using next-generation short-read sequencers. In all, 1.74 Gb of raw data containing 368,980 subreads, with an average read length of 4,724 bp and longest read length of 77,471, were generated. Subreads were assembled into 15 scaffolds generating approximately 5.4 Mb (348×) of genome. X. citri pv. punicae exhibited close lineage with X. citri pv. citri with 98.78% average nucleotide identity. Of the 4,263 protein-coding genes, 11 non-TALE type III effectors and 2 TALE-encoding genes were identified.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Dattatraya Hegde Radhika
- Department of Biotechnology and Crop Improvement, College of Horticulture, Bagalkot, University of Horticultural Sciences, Bagalkot, India
| | - Raghavendra Gunnaiah
- Department of Biotechnology and Crop Improvement, College of Horticulture, Bagalkot, University of Horticultural Sciences, Bagalkot, India
| | - Ashwini Lamani
- Department of Biotechnology and Crop Improvement, College of Horticulture, Bagalkot, University of Horticultural Sciences, Bagalkot, India
| | - Dadapeer Peerjade
- Directorate of Research, University of Horticultural Sciences, Bagalkot, India
| | - Rudrappa Chandrashekhar Jagadeesha
- Department of Biotechnology and Crop Improvement, College of Horticulture, Bagalkot, University of Horticultural Sciences, Bagalkot, India
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Differential gene responses in different varieties of pomegranate during the pathogenesis of Xanthomonas axonopodis pv. punicae. 3 Biotech 2021; 11:180. [PMID: 33927971 DOI: 10.1007/s13205-021-02721-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/05/2021] [Indexed: 01/15/2023] Open
Abstract
Bacterial blight (BB) caused by Xanthomonas axonopodis pv. punicae (Xap) is the major scourge in pomegranate cultivation leading to an extensive yield loss up to 60-80%. Hence, identifying a novel resistance source for BB is very necessary for developing a suitable management strategy. Host range analysis and cross-inoculation studies revealed that Xap is specific to pomegranate and there are no alternative hosts to the pathogen. Screening of 149 accessions recorded the varied disease resistance levels with mean disease severity of 30.67%. Accession lines IC318735, IC318724, and IC318762 exhibited maximum disease tolerance by exhibiting the lowest disease severity of 4.91, 5.66, and 6.82%, respectively. Comparative expression analysis of defence genes in IC318724 and IC318735 recorded significant upregulation of phenylalanine ammonia-lyase (PAL), callose synthase-3 (CS3), chitinase, pathogenesis-related protein-1 (PR1), and pathogenesis-related protein-10 (PR10), indicating these genes might be actively involved in conferring disease tolerance. Abiotic elicitors were tested to induce systemic resistance in agronomically superior and widely adapted variety Bhagwa for managing BB of pomegranate. Among the various elicitors tested; proline (600 ppm), gamma-aminobutyric acid (600 ppm), chitosan (600 ppm), β-aminobutyric acid (200 ppm), laminarin (600 ppm), and eugenol (200 ppm) recorded maximum disease protection in prophylactic treatment with disease protection of 89.59, 88.59, 87.15, 86.08, 81.05, and 78.72%, respectively. Similar observations were recorded when these were applied as curative treatment. The present study will broaden our understanding of host-pathogen interactions during BB infection in pomegranate, also aid in developing ideal approach for developing effective disease management. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02721-y.
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Singh NV, Parashuram S, Sharma J, Potlannagari RS, Karuppannan DB, Pal RK, Patil P, Mundewadikar DM, Sangnure VR, Parvati Sai Arun PV, Mutha NVR, Kumar B, Tripathi A, Peddamma SK, Kothandaraman H, Yellaboina S, Baghel DS, Reddy UK. Comparative transcriptome profiling of pomegranate genotypes having resistance and susceptible reaction to Xanthomonas axonopodis pv. punicae. Saudi J Biol Sci 2020; 27:3514-3528. [PMID: 33304163 PMCID: PMC7714969 DOI: 10.1016/j.sjbs.2020.07.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 07/16/2020] [Accepted: 07/18/2020] [Indexed: 01/14/2023] Open
Abstract
Pomegranate (Punica granatum L.) is an important fruit crop, rich in fiber, vitamins, antioxidants, minerals and source of different biologically active compounds. The bacterial blight caused by Xanthomonas axonopodispv. punicae is a serious threat to the crop leading to 60–80% yield loss under epiphytotic conditions. In this work, we have generated comparative transcriptome profile to mark the gene expression signatures during resistance and susceptible interactions. We analyzed leaf and fruits samples of moderately resistant genotype (IC 524207) and susceptible variety (Bhagawa) of pomegranate at three progressive infection stages upon inoculation with the pathogen. RNA-Seq with the Illumina HiSeq 2500 platform revealed 1,88,337 non-redundant (nr) transcript sequences from raw sequencing data, for a total of 34,626 unigenes with size >2 kb. Moreover, 85.3% unigenes were annotated in at least one of the seven databases examined. Comparative analysis of gene-expression signatures in resistant and susceptible varieties showed that the genes known to be involved in defense mechanism in plants were up-regulated in resistant variety. Gene Ontology (GO) analysis successfully annotated 90,485 pomegranate unigenes, of which 68,464 were assigned to biological, 78,107 unigenes molecular function and 44,414 to cellular components. Significantly enriched GO terms in DEGs were related to oxidations reduction biological process, protein binding and oxidoreductase activity. This transcriptome data on pomegranate could help in understanding resistance and susceptibility nature of cultivars and further detailed fine mapping and functional validation of identified candidate gene would provide scope for resistance breeding programme in pomegranate.
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Affiliation(s)
| | - Shilpa Parashuram
- ICAR-National Research Centre on Pomegranate, Solapur, Maharashtra 413255, India
| | - Jyotsana Sharma
- ICAR-National Research Centre on Pomegranate, Solapur, Maharashtra 413255, India
| | | | | | - Ram Krishna Pal
- ICAR-National Research Centre on Pomegranate, Solapur, Maharashtra 413255, India
| | - Prakash Patil
- ICAR-National Research Centre on Pomegranate, Solapur, Maharashtra 413255, India
| | | | - Vipul R Sangnure
- ICAR-National Research Centre on Pomegranate, Solapur, Maharashtra 413255, India
| | | | - Naresh V R Mutha
- Nucleome Informatics Private Limited., Hyderabad, Telangana State 500049, India
| | - Bipin Kumar
- Nucleome Informatics Private Limited., Hyderabad, Telangana State 500049, India
| | - Abhishek Tripathi
- Nucleome Informatics Private Limited., Hyderabad, Telangana State 500049, India
| | | | | | - Sailu Yellaboina
- Nucleome Informatics Private Limited., Hyderabad, Telangana State 500049, India
| | | | - Umesh K Reddy
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, USA
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Doddaraju P, Kumar P, Gunnaiah R, Gowda AA, Lokesh V, Pujer P, Manjunatha G. Reliable and early diagnosis of bacterial blight in pomegranate caused by Xanthomonas axonopodis pv. punicae using sensitive PCR techniques. Sci Rep 2019; 9:10097. [PMID: 31300709 PMCID: PMC6625978 DOI: 10.1038/s41598-019-46588-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 06/27/2019] [Indexed: 11/09/2022] Open
Abstract
Bacterial blight caused by Xanthomonas axonopodis pv. punicae is a major disease of pomegranate. Bacterial blight drastically reduces the yield and quality of fruits, which are critical for pomegranate production. Precise and early diagnosis of bacterial blight is crucial for active surveillance and effective management of the disease. Symptoms based disease diagnostic methods are labor-intensive, time-consuming and may not detect disease on asymptomatic plants. DNA-based disease diagnostics using polymerase chain reaction (PCR) are reliable, precise, accurate and quick. PCR coupled with agarose gel electrophoresis (PCR-AGE), PCR coupled with capillary electrophoresis (PCR-CE) and real-time PCR (qPCR) were applied for the early and accurate diagnosis of bacterial blight in pomegranate. PCR-CE and qPCR were capable of diagnosing bacterial blight 6 to 10 days before symptom appearance, with detection limits of 100 fg and 10 fg of bacterial DNA respectively. However, conventional PCR-AGE detected pathogen at the onset of disease symptoms with a detection limit of 10 pg of bacterial DNA. qPCR detected bacterial blight in orchards that did not show any disease symptoms. Our data demonstrate that qPCR is more sensitive than other PCR methods along with being reliable for early diagnosis.
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Affiliation(s)
- Pushpa Doddaraju
- Bio-control Lab, Directorate of Research, University of Horticultural Sciences, Bagalkot, Karnataka, India
| | - Pavan Kumar
- Bio-control Lab, Directorate of Research, University of Horticultural Sciences, Bagalkot, Karnataka, India
| | - Raghavendra Gunnaiah
- Department of Biotechnology and Crop Improvement, University of Horticultural Sciences, Bagalkot, Karnataka, India
| | - Abhishek A Gowda
- Bio-control Lab, Directorate of Research, University of Horticultural Sciences, Bagalkot, Karnataka, India
| | - Veeresh Lokesh
- Bio-control Lab, Directorate of Research, University of Horticultural Sciences, Bagalkot, Karnataka, India
| | - Parvati Pujer
- Department of Biotechnology and Crop Improvement, University of Horticultural Sciences, Bagalkot, Karnataka, India
| | - Girigowda Manjunatha
- Bio-control Lab, Directorate of Research, University of Horticultural Sciences, Bagalkot, Karnataka, India.
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