Cristofer Motoche-Monar, Diego Andrade, Washington D Pijal, Francisco Hidrobo, Rolando Armas, Emily Sánchez-Real, Gabriela Rocha-Chauca, José A Castillo
{"title":"CRISPRals：用于评估 Ralstonia solanacearum 复合菌种的 CRISPR 防御系统以避免噬菌体抗性的网络数据库。","authors":"Cristofer Motoche-Monar, Diego Andrade, Washington D Pijal, Francisco Hidrobo, Rolando Armas, Emily Sánchez-Real, Gabriela Rocha-Chauca, José A Castillo","doi":"10.1094/PHYTO-01-24-0010-SC","DOIUrl":null,"url":null,"abstract":"<p><p>Clustered regularly interspaced short palindromic repeats (CRISPR) has been widely characterized as a defense system against phages and other invading elements in bacteria and archaea. A low percentage of <i>Ralstonia solanacearum</i> species complex (RSSC) strains possess the CRISPR array and the CRISPR-associated proteins (Cas) that would confer immunity against various phages. To provide a wide-range screen of the CRISPR presence in the RSSC, we analyzed 378 genomes of RSSC strains to find the CRISPR locus. We found that 20.1, 14.3, and 54.5% of the <i>R. solanacearum</i>, <i>R. pseudosolanacearum</i>, and <i>R. syzygii</i> strains, respectively, possess the CRISPR locus. In addition, we performed further analysis to identify the respective phages that are restricted by the CRISPR arrays. We found 252 different phages infecting different strains of the RSSC, by means of the identification of similarities between the protospacers in phages and spacers in bacteria. We compiled this information in a database with web access called CRISPRals (https://crisprals.yachaytech.edu.ec/). Additionally, we made available a number of tools to detect and identify CRISPR array and Cas genes in genomic sequences that could be uploaded by users. Finally, a matching tool to relate bacteria spacer with phage protospacer sequences is available. CRISPRals is a valuable resource for the scientific community that contributes to the study of bacteria-phage interaction and a starting point that will help to design efficient phage therapy strategies.</p>","PeriodicalId":20410,"journal":{"name":"Phytopathology","volume":null,"pages":null},"PeriodicalIF":2.6000,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"CRISPRals: A Web Database for Assessing the CRISPR Defense System in the <i>Ralstonia solanacearum</i> Species Complex to Avoid Phage Resistance.\",\"authors\":\"Cristofer Motoche-Monar, Diego Andrade, Washington D Pijal, Francisco Hidrobo, Rolando Armas, Emily Sánchez-Real, Gabriela Rocha-Chauca, José A Castillo\",\"doi\":\"10.1094/PHYTO-01-24-0010-SC\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Clustered regularly interspaced short palindromic repeats (CRISPR) has been widely characterized as a defense system against phages and other invading elements in bacteria and archaea. A low percentage of <i>Ralstonia solanacearum</i> species complex (RSSC) strains possess the CRISPR array and the CRISPR-associated proteins (Cas) that would confer immunity against various phages. To provide a wide-range screen of the CRISPR presence in the RSSC, we analyzed 378 genomes of RSSC strains to find the CRISPR locus. We found that 20.1, 14.3, and 54.5% of the <i>R. solanacearum</i>, <i>R. pseudosolanacearum</i>, and <i>R. syzygii</i> strains, respectively, possess the CRISPR locus. In addition, we performed further analysis to identify the respective phages that are restricted by the CRISPR arrays. We found 252 different phages infecting different strains of the RSSC, by means of the identification of similarities between the protospacers in phages and spacers in bacteria. We compiled this information in a database with web access called CRISPRals (https://crisprals.yachaytech.edu.ec/). Additionally, we made available a number of tools to detect and identify CRISPR array and Cas genes in genomic sequences that could be uploaded by users. Finally, a matching tool to relate bacteria spacer with phage protospacer sequences is available. CRISPRals is a valuable resource for the scientific community that contributes to the study of bacteria-phage interaction and a starting point that will help to design efficient phage therapy strategies.</p>\",\"PeriodicalId\":20410,\"journal\":{\"name\":\"Phytopathology\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":2.6000,\"publicationDate\":\"2024-07-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Phytopathology\",\"FirstCategoryId\":\"97\",\"ListUrlMain\":\"https://doi.org/10.1094/PHYTO-01-24-0010-SC\",\"RegionNum\":2,\"RegionCategory\":\"农林科学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/6/29 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q2\",\"JCRName\":\"PLANT SCIENCES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Phytopathology","FirstCategoryId":"97","ListUrlMain":"https://doi.org/10.1094/PHYTO-01-24-0010-SC","RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/6/29 0:00:00","PubModel":"Epub","JCR":"Q2","JCRName":"PLANT SCIENCES","Score":null,"Total":0}
CRISPRals: A Web Database for Assessing the CRISPR Defense System in the Ralstonia solanacearum Species Complex to Avoid Phage Resistance.
Clustered regularly interspaced short palindromic repeats (CRISPR) has been widely characterized as a defense system against phages and other invading elements in bacteria and archaea. A low percentage of Ralstonia solanacearum species complex (RSSC) strains possess the CRISPR array and the CRISPR-associated proteins (Cas) that would confer immunity against various phages. To provide a wide-range screen of the CRISPR presence in the RSSC, we analyzed 378 genomes of RSSC strains to find the CRISPR locus. We found that 20.1, 14.3, and 54.5% of the R. solanacearum, R. pseudosolanacearum, and R. syzygii strains, respectively, possess the CRISPR locus. In addition, we performed further analysis to identify the respective phages that are restricted by the CRISPR arrays. We found 252 different phages infecting different strains of the RSSC, by means of the identification of similarities between the protospacers in phages and spacers in bacteria. We compiled this information in a database with web access called CRISPRals (https://crisprals.yachaytech.edu.ec/). Additionally, we made available a number of tools to detect and identify CRISPR array and Cas genes in genomic sequences that could be uploaded by users. Finally, a matching tool to relate bacteria spacer with phage protospacer sequences is available. CRISPRals is a valuable resource for the scientific community that contributes to the study of bacteria-phage interaction and a starting point that will help to design efficient phage therapy strategies.
期刊介绍：
Phytopathology publishes articles on fundamental research that advances understanding of the nature of plant diseases, the agents that cause them, their spread, the losses they cause, and measures that can be used to control them. Phytopathology considers manuscripts covering all aspects of plant diseases including bacteriology, host-parasite biochemistry and cell biology, biological control, disease control and pest management, description of new pathogen species description of new pathogen species, ecology and population biology, epidemiology, disease etiology, host genetics and resistance, mycology, nematology, plant stress and abiotic disorders, postharvest pathology and mycotoxins, and virology. Papers dealing mainly with taxonomy, such as descriptions of new plant pathogen taxa are acceptable if they include plant disease research results such as pathogenicity, host range, etc. Taxonomic papers that focus on classification, identification, and nomenclature below the subspecies level may also be submitted to Phytopathology.
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