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Siddique F, Mingxiu Y, Xiaofeng X, Zhe N, Younis H, Lili P, Junhua Z. Comparative Genomic Analysis and Rapid Molecular Detection of Xanthomonas euvesicatoria Using Unique ATP-Dependent DNA Helicase recQ, hrpB1, and hrpB2 Genes Isolated from Physalis pubescens in China. THE PLANT PATHOLOGY JOURNAL 2023; 39:191-206. [PMID: 37019829 PMCID: PMC10102564 DOI: 10.5423/ppj.oa.08.2022.0119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 01/04/2023] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
Ground cherry (Physalis pubescens) is the most prominent species in the Solanaceae family due to its nutritional content, and prospective health advantages. It is grown all over the world, but notably in northern China. In 2019 firstly bacterial leaf spot (BLS) disease was identified on P. pubescens in China that caused by both BLS pathogens Xanthomonas euvesicatoria pv. euvesicatoria resulted in substantial monetary losses. Here, we compared whole genome sequences of X. euvesicatoria to other Xanthomonas species that caused BLS diseases for high similarities and dissimilarities in genomic sequences through average nucleotide identity (ANI) and BLAST comparison. Molecular techniques and phylogenetic trees were adopted to detect X. euvesicatoria on P. pubescens using recQ, hrpB1, and hrpB2 genes for efficient and precise identification. For rapid molecular detection of X. euvesicatoria, loop-mediated isothermal amplification, polymerase chain reaction (PCR), and real-time PCR techniques were used. Whole genome comparison results showed that the genome of X. euvesicatoria was more closely relative to X. perforans than X. vesicatoria, and X. gardneri with 98%, 84%, and 86% ANI, respectively. All infected leaves of P. pubescens found positive amplification, and negative controls did not show amplification. The findings of evolutionary history revealed that isolated strains XeC10RQ, XeH9RQ, XeA10RQ, and XeB10RQ that originated from China were closely relative and highly homologous to the X. euvesicatoria. This research provides information to researchers on genomic variation in BLS pathogens, and further molecular evolution and identification of X. euvesicatoria using the unique target recQ gene through advance molecular approaches.
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Affiliation(s)
| | | | | | | | | | | | - Zhang Junhua
- Corresponding author. Phone) +86-18646561068, FAX) +86-0451-55190447, E-mail) ,
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Cardoso JLS, Souza AA, Vieira MLC. Molecular basis for host responses to Xanthomonas infection. PLANTA 2022; 256:84. [PMID: 36114308 DOI: 10.1007/s00425-022-03994-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
This review highlights the most relevant and recent updated information available on the defense responses of selected hosts against Xanthomonas spp. Xanthomonas is one of the most important genera of Gram-negative phytopathogenic bacteria, severely affecting the productivity of economically important crops worldwide, colonizing either the vascular system or the mesophyll tissue of the host. Due to its rapid propagation, Xanthomonas poses an enormous challenge to farmers, because it is usually controlled using huge quantities of copper-based chemicals, adversely impacting the environment. Thus, developing new ways of preventing colonization by these bacteria has become essential. Advances in genomic and transcriptomic technologies have significantly elucidated at molecular level interactions between various crops and Xanthomonas species. Understanding how these hosts respond to the infection is crucial if we are to exploit potential approaches for improving crop breeding and cutting productivity losses. This review focuses on our current knowledge of the defense response mechanisms in agricultural crops after Xanthomonas infection. We describe the molecular basis of host-bacterium interactions over a broad spectrum with the aim of improving our fundamental understanding of which genes are involved and how they work in this interaction, providing information that can help to speed up plant breeding programs, namely using gene editing approaches.
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Affiliation(s)
- Jéssica L S Cardoso
- Genetics Department, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Alessandra A Souza
- Citrus Research Center "Sylvio Moreira", Agronomic Institute (IAC), Cordeirópolis, SP, 13490-000, Brazil
| | - Maria Lucia C Vieira
- Genetics Department, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.
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Fonseca NP, Felestrino ÉB, Caneschi WL, Sanchez AB, Cordeiro IF, Lemes CGC, Assis RAB, Carvalho FMS, Ferro JA, Varani AM, Belasque J, Setubal JC, Telles GP, Aguena DS, Almeida NF, Moreira LM. Detection and identification of Xanthomonas pathotypes associated with citrus diseases using comparative genomics and multiplex PCR. PeerJ 2019; 7:e7676. [PMID: 31592342 PMCID: PMC6777491 DOI: 10.7717/peerj.7676] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/15/2019] [Indexed: 12/25/2022] Open
Abstract
Background In Citrus cultures, three species of Xanthomonas are known to cause distinct diseases. X. citri subsp. citri patothype A, X. fuscans subsp. aurantifolii pathotypes B and C, and X. alfalfae subsp. citrumelonis, are the causative agents of cancrosis A, B, C, and citrus bacterial spots, respectively. Although these species exhibit different levels of virulence and aggressiveness, only limited alternatives are currently available for proper and early detection of these diseases in the fields. The present study aimed to develop a new molecular diagnostic method based on genomic sequences derived from the four species of Xanthomonas. Results Using comparative genomics approaches, primers were synthesized for the identification of the four causative agents of citrus diseases. These primers were validated for their specificity to their target DNA by both conventional and multiplex PCR. Upon evaluation, their sensitivity was found to be 0.02 ng/µl in vitro and 1.5 × 104 CFU ml−1 in infected leaves. Additionally, none of the primers were able to generate amplicons in 19 other genomes of Xanthomonas not associated with Citrus and one species of Xylella, the causal agent of citrus variegated chlorosis (CVC). This denotes strong specificity of the primers for the different species of Xanthomonas investigated in this study. Conclusions We demonstrated that these markers can be used as potential candidates for performing in vivo molecular diagnosis exclusively for citrus-associated Xanthomonas. The bioinformatics pipeline developed in this study to design specific genomic regions is capable of generating specific primers. It is freely available and can be utilized for any other model organism.
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Affiliation(s)
- Natasha P Fonseca
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Érica B Felestrino
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Washington L Caneschi
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Angélica B Sanchez
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Isabella F Cordeiro
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Camila G C Lemes
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Renata A B Assis
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Flávia M S Carvalho
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, Universidade Estadual Paulista-Unesp, Jaboticabal, São Paulo, Brazil
| | - Jesus A Ferro
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, Universidade Estadual Paulista-Unesp, Jaboticabal, São Paulo, Brazil
| | - Alessandro M Varani
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, Universidade Estadual Paulista-Unesp, Jaboticabal, São Paulo, Brazil
| | - José Belasque
- Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura "Luiz de Queiroz", Piracicaba, São Paulo, Brazil
| | - Joao C Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Guilherme P Telles
- Instituto de Computação, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Deiviston S Aguena
- Faculdade de Computação, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Nalvo F Almeida
- Faculdade de Computação, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Leandro M Moreira
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil.,Departamento de Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
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Purić J, Vieira G, Cavalca LB, Sette LD, Ferreira H, Vieira MLC, Sass DC. Activity of Antarctic fungi extracts against phytopathogenic bacteria. Lett Appl Microbiol 2018. [PMID: 29527704 DOI: 10.1111/lam.12875] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
This study aims to obtain secondary metabolites extracts from filamentous fungi isolated from soil and marine sediments from Antarctic ecosystems and to assess its potential antibacterial activity on Xanthomonas euvesicatoria and Xanthomonas axonopodis pv. passiflorae (phytopathogenic bacteria causing diseases in pepper and tomato and passionfruit, respectively). Among the 66 crude intracellular and extracellular extracts obtained from fungi recovered from soil and 79 obtained from marine sediment samples, 25 showed the ability to prevent the growth of X. euvesicatoria in vitro and 28 showed the ability to prevent the growth of X. axonopodis pv. passiflorae in vitro. Intracellular and extracellular extracts from soil fungi inhibited around 97% of X. euvesicatoria and 98% of X. axonopodis pv. passiflorae at 2·1 mg ml-1 . The average inhibition rates against X. euvesicatoria and X. axonopodis pv. passiflorae for intracellular and extracellular extracts from marine sediments fungi were around 96 and 97%, respectively, at 3·0 mg ml-1 . Extracts containing secondary metabolites with antimicrobial activity against X. euvesicatoria and X. axonopodis pv. passiflorae were obtained, containing possible substitutes for the products currently used to control these phytopathogens. SIGNIFICANCE AND IMPACT OF THE STUDY Micro-organisms from extreme ecosystems, such as the Antarctic ecosystem, need to survive in harsh conditions with low temperatures, low nutrients and high UV radiation. Micro-organisms adapt to these conditions evolving diverse biochemical and physiological adaptations essential for survival. All this makes these micro-organisms a rich source of novel natural products based on unique chemical scaffolds. Discovering novel bioactive compounds is essential because of the rise in antibiotic-resistant micro-organisms and the emergence of new infections. Fungi from Antarctic environments have been proven to produce bioactive secondary metabolites against various micro-organisms, but few studies have shown activity against Xanthomonas phytopathogens.
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Affiliation(s)
- J Purić
- Department of Biochemistry and Microbiology, Institute of Biosciences, São Paulo State University (UNESP) 'Júlio de Mesquita Filho', Rio Claro, São Paulo, Brazil
| | - G Vieira
- Department of Biochemistry and Microbiology, Institute of Biosciences, São Paulo State University (UNESP) 'Júlio de Mesquita Filho', Rio Claro, São Paulo, Brazil
| | - L B Cavalca
- Department of Biochemistry and Microbiology, Institute of Biosciences, São Paulo State University (UNESP) 'Júlio de Mesquita Filho', Rio Claro, São Paulo, Brazil
| | - L D Sette
- Department of Biochemistry and Microbiology, Institute of Biosciences, São Paulo State University (UNESP) 'Júlio de Mesquita Filho', Rio Claro, São Paulo, Brazil
| | - H Ferreira
- Department of Biochemistry and Microbiology, Institute of Biosciences, São Paulo State University (UNESP) 'Júlio de Mesquita Filho', Rio Claro, São Paulo, Brazil
| | - M L C Vieira
- Escola Superior de Agricultura 'Luiz de Queiroz', Departamento de Genética, Piracicaba, Brazil
| | - D C Sass
- Department of Biochemistry and Microbiology, Institute of Biosciences, São Paulo State University (UNESP) 'Júlio de Mesquita Filho', Rio Claro, São Paulo, Brazil
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Mordukhovich G, Bahar O. Isolation of Outer Membrane Vesicles from Phytopathogenic Xanthomonas campestris pv. campestris. Bio Protoc 2017; 7:e2160. [PMID: 34458473 DOI: 10.21769/bioprotoc.2160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 12/05/2016] [Accepted: 02/03/2017] [Indexed: 11/02/2022] Open
Abstract
Gram-negative bacteria naturally release outer membrane vesicles (OMVs) to the surrounding environment. OMVs contribute to multiple processes, such as cell-cell communication, delivery of enzymes and toxins, resistance to environmental stresses and pathogenesis. Little is known about OMVs produced by plant-pathogenic bacteria, and their interactions with host plants. The protocol described below discusses the isolation process of OMVs from Xanthomonas campestris pv. campestris strain 33913, a bacterial pathogen of Crucifiers. Nevertheless, this protocol can be used and/or adapted for isolation of OMVs from other phytopathogenic bacteria to promote the study of OMVs in the context of plant-microbe interactions.
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Affiliation(s)
- Gideon Mordukhovich
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel.,Robert H. Smith Faculty of Agriculture, Food, and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Ofir Bahar
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
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Genetic Variability of Beauveria bassiana and a DNA Marker for Environmental Monitoring of a Highly Virulent Isolate Against Cosmopolites sordidus. Indian J Microbiol 2012; 52:569-74. [PMID: 24293712 DOI: 10.1007/s12088-012-0292-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 07/11/2012] [Indexed: 10/28/2022] Open
Abstract
The banana weevil Cosmopolites sordidus (Germar) is one of a number of pests that attack banana crops. The use of the entomopathogenic fungus Beauveria bassiana as a biological control agent for this pest may contribute towards reducing the application of chemical insecticides on banana crops. In this study, the genetic variability of a collection of Brazilian isolates of B. bassiana was evaluated. Samples were obtained from various geographic regions of Brazil, and from different hosts of the Curculionidae family. Based on the DNA fingerprints generated by RAPD and AFLP, we found that 92 and 88 % of the loci were polymorphic, respectively. The B. bassiana isolates were attributed to two genotypic clusters based on the RAPD data, and to three genotypic clusters, when analyzed with AFLP. The nucleotide sequences of nuclear ribosomal DNA intergenic spacers confirmed that all isolates are in fact B. bassiana. Analysis of molecular variance showed that variability among the isolates was not correlated with geographic origin or hosts. A RAPD-specific marker for isolate CG 1024, which is highly virulent to C. sordidus, was cloned and sequenced. Based on the sequences obtained, specific PCR primers BbasCG1024F (5'-TGC GGC TGA GGA GGA CT-3') and BbasCG1024R (5'-TGC GGC TGA GTG TAG AAC-3') were designed for detecting and monitoring this isolate in the field.
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