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(PDF) Core genome MLST for epidemiological and evolutionary analyses of phytopathogenicXanthomonas citri | Franklin Behlau - Academia.edu

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OtherX. citrisubsp. and pathovars are responsible for diseases in crops such as soy bean, common bean, mango, pomegranate and cashew. Tracing the spread ofX. citridisease has been performed using several different typing methods over the years but recent studies using genomic sequencing have been key to understanding evolutionary relationships within the species including fundamental differences between XCC pathotypes.In this study we developed a core genome multilocus typing scheme (cgMLST) forX. citribased upon 250 genomes comprising multiple examples ofX. citrisubsp.citripathotypes A, A* and Aw,X. citrisubsp.malvacearumandX. citripathovarsaurantifolii, fuscans, glycines, malvacearum, mangiferaeindicae, viticola, vigni...","author":[{"@context":"https://schema.org","@type":"Person","name":"Franklin Behlau"}],"contributor":[],"dateCreated":"2023-08-12","headline":"Core genome MLST for epidemiological and evolutionary analyses of phytopathogenicXanthomonas citri","image":"https://attachments.academia-assets.com/104947540/thumbnails/1.jpg","inLanguage":"en","keywords":["Biology","Genome","Phylogenetic Tree","Citrus Canker","Multilocus sequence typing","Xanthomonas citri"],"publisher":{"@context":"https://schema.org","@type":"Organization","name":"Cold Spring Harbor Laboratory"},"sourceOrganization":[{"@context":"https://schema.org","@type":"EducationalOrganization","name":null}],"thumbnailUrl":"https://attachments.academia-assets.com/104947540/thumbnails/1.jpg","url":"https://www.academia.edu/105513593/Core_genome_MLST_for_epidemiological_and_evolutionary_analyses_of_phytopathogenicXanthomonas_citri"}</script><link rel="stylesheet" media="all" href="//a.academia-assets.com/assets/single_work_page/loswp-102fa537001ba4d8dcd921ad9bd56c474abc201906ea4843e7e7efe9dfbf561d.css" /><link rel="stylesheet" media="all" href="//a.academia-assets.com/assets/design_system/body-8d679e925718b5e8e4b18e9a4fab37f7eaa99e43386459376559080ac8f2856a.css" /><link rel="stylesheet" media="all" href="//a.academia-assets.com/assets/design_system/button-3cea6e0ad4715ed965c49bfb15dedfc632787b32ff6d8c3a474182b231146ab7.css" 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OtherX. citrisubsp. and pathovars are responsible for diseases in crops such as soy bean, common bean, mango, pomegranate and cashew. Tracing the spread ofX. citridisease has been performed using several different typing methods over the years but recent studies using genomic sequencing have been key to understanding evolutionary relationships within the species including fundamental differences between XCC pathotypes.In this study we developed a core genome multilocus typing scheme (cgMLST) forX. citribased upon 250 genomes comprising multiple examples ofX. citrisubsp.citripathotypes A, A* and Aw,X. citrisubsp.malvacearumandX. citripathovarsaurantifolii, fuscans, glycines, malvacearum, mangiferaeindicae, viticola, vigni...","publisher":"Cold Spring Harbor Laboratory"},"document_type":"paper","pre_hit_view_count_baseline":null,"quality":"high","language":"en","title":"Core genome MLST for epidemiological and evolutionary analyses of phytopathogenicXanthomonas citri","broadcastable":false,"draft":null,"has_indexable_attachment":true,"indexable":true}}["work"]; window.loswp.workCoauthors = [64890966]; window.loswp.locale = "en"; window.loswp.countryCode = "SG"; window.loswp.cwvAbTestBucket = ""; window.loswp.designVariant = "ds_vanilla"; window.loswp.fullPageMobileSutdModalVariant = "control"; window.loswp.useOptimizedScribd4genScript = false; window.loginModal = {}; window.loginModal.appleClientId = 'edu.academia.applesignon';</script><script defer="" src="https://accounts.google.com/gsi/client"></script><div class="ds-loswp-container"><div class="ds-work-card--grid-container"><div class="ds-work-card--container js-loswp-work-card"><div class="ds-work-card--cover"><div class="ds-work-cover--wrapper"><div class="ds-work-cover--container"><button class="ds-work-cover--clickable js-swp-download-button" data-signup-modal="{&quot;location&quot;:&quot;swp-splash-paper-cover&quot;,&quot;attachmentId&quot;:104947540,&quot;attachmentType&quot;:&quot;pdf&quot;}"><img alt="First page of “Core genome MLST for epidemiological and evolutionary analyses of phytopathogenicXanthomonas citri”" class="ds-work-cover--cover-thumbnail" src="https://0.academia-photos.com/attachment_thumbnails/104947540/mini_magick20230812-1-70pdj4.png?1691843020" /><img alt="PDF Icon" class="ds-work-cover--file-icon" src="//a.academia-assets.com/images/single_work_splash/adobe_icon.svg" /><div class="ds-work-cover--hover-container"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span><p>Download Free PDF</p></div><div class="ds-work-cover--ribbon-container">Download Free PDF</div><div class="ds-work-cover--ribbon-triangle"></div></button></div></div></div><div class="ds-work-card--work-information"><h1 class="ds-work-card--work-title">Core genome MLST for epidemiological and evolutionary analyses of phytopathogenicXanthomonas citri</h1><div class="ds-work-card--work-authors ds-work-card--detail"><a class="ds-work-card--author js-wsj-grid-card-author ds2-5-body-md ds2-5-body-link" data-author-id="64890966" href="https://independent.academia.edu/FranklinBehlau"><img alt="Profile image of Franklin Behlau" class="ds-work-card--author-avatar" src="//a.academia-assets.com/images/s65_no_pic.png" />Franklin Behlau</a></div><div class="ds-work-card--detail"><div class="ds-work-card--work-metadata"><div class="ds-work-card--work-metadata__stat"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">visibility</span><p class="ds2-5-body-sm" id="work-metadata-view-count">…</p></div><div class="ds-work-card--work-metadata__stat"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">description</span><p class="ds2-5-body-sm">19 pages</p></div><div class="ds-work-card--work-metadata__stat"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">link</span><p class="ds2-5-body-sm">1 file</p></div></div><script>(async () => { const workId = 105513593; 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if (!viewCountBody) { throw new Error('Failed to find work views element'); } viewCountBody.textContent = `${commaizedViewCount} views`; } catch (error) { // Remove the whole views element if there was some issue parsing. document.getElementById('work-metadata-view-count')?.parentNode?.remove(); throw new Error(`Failed to parse view count: ${viewCount}`, error); } }; // If the DOM is still loading, wait for it to be ready before updating the view count. if (document.readyState === "loading") { document.addEventListener('DOMContentLoaded', () => { updateViewCount(viewCount); }); // Otherwise, just update it immediately. } else { updateViewCount(viewCount); } })();</script></div><p class="ds-work-card--work-abstract ds-work-card--detail ds2-5-body-md">Xanthomonas citrisubspeciescitri(XCC) is the cause of bacterial citrus canker, responsible for major economic losses to the citrus industry that includes sweet orange, lime and grapefruit production in regions including South America, United States, China and Japan. OtherX. citrisubsp. and pathovars are responsible for diseases in crops such as soy bean, common bean, mango, pomegranate and cashew. Tracing the spread ofX. citridisease has been performed using several different typing methods over the years but recent studies using genomic sequencing have been key to understanding evolutionary relationships within the species including fundamental differences between XCC pathotypes.In this study we developed a core genome multilocus typing scheme (cgMLST) forX. citribased upon 250 genomes comprising multiple examples ofX. citrisubsp.citripathotypes A, A* and Aw,X. citrisubsp.malvacearumandX. citripathovarsaurantifolii, fuscans, glycines, malvacearum, mangiferaeindicae, viticola, vigni...</p><div class="ds-work-card--button-container"><button class="ds2-5-button js-swp-download-button" data-signup-modal="{&quot;location&quot;:&quot;continue-reading-button--work-card&quot;,&quot;attachmentId&quot;:104947540,&quot;attachmentType&quot;:&quot;pdf&quot;,&quot;workUrl&quot;:&quot;https://www.academia.edu/105513593/Core_genome_MLST_for_epidemiological_and_evolutionary_analyses_of_phytopathogenicXanthomonas_citri&quot;}">See full PDF</button><button class="ds2-5-button ds2-5-button--secondary js-swp-download-button" data-signup-modal="{&quot;location&quot;:&quot;download-pdf-button--work-card&quot;,&quot;attachmentId&quot;:104947540,&quot;attachmentType&quot;:&quot;pdf&quot;,&quot;workUrl&quot;:&quot;https://www.academia.edu/105513593/Core_genome_MLST_for_epidemiological_and_evolutionary_analyses_of_phytopathogenicXanthomonas_citri&quot;}"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span>Download PDF</button></div></div></div></div><div data-auto_select="false" data-client_id="331998490334-rsn3chp12mbkiqhl6e7lu2q0mlbu0f1b" data-doc_id="104947540" data-landing_url="https://www.academia.edu/105513593/Core_genome_MLST_for_epidemiological_and_evolutionary_analyses_of_phytopathogenicXanthomonas_citri" data-login_uri="https://www.academia.edu/registrations/google_one_tap" data-moment_callback="onGoogleOneTapEvent" id="g_id_onload"></div><div class="ds-top-related-works--grid-container"><div class="ds-related-content--container ds-top-related-works--container"><h2 class="ds-related-content--heading">Related papers</h2><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="0" data-entity-id="70358826" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/70358826/Phylogenomic_Insights_into_Diversity_and_Evolution_of_Nonpathogenic_Xanthomonas_Strains_Associated_with_Citrus">Phylogenomic Insights into Diversity and Evolution of Nonpathogenic Xanthomonas Strains Associated with Citrus</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="9635657" href="https://uni-mysore.academia.edu/sanjeetKumar">sanjeet Kumar</a></div><p class="ds-related-work--metadata ds2-5-body-xs">mSphere, 2020</p><p class="ds-related-work--abstract ds2-5-body-sm">Xanthomonas species are primarily known as a group of phytopathogens infecting diverse plants. Recent molecular studies reveal the existence of potential novel species and strains of Xanthomonas following a nonpathogenic lifestyle. In the present study, we report whole-genome sequences of four nonpathogenic strains from citrus (NPXc). Taxonogenomics revealed the surprising diversity, as each of these three isolates were found to be potential novel species that together form a citrus-associated nonpathogenic Xanthomonas species complex (NPXc complex). Interestingly, this NPXc complex is related to another nonpathogenic species, Xanthomonas sontii, from rice (NPXr). On the other hand, the fourth NPXc isolate was found to be related to nonpathogenic isolates from walnut (NPXw); altogether, they form a potential taxonomic outlier of pathogenic Xanthomonas arboricola species. Furthermore, genomic investigation of well-characterized pathogenicity clusters in NPXc isolates revealed lifestyle-specific gene content dynamics. Primarily, genes essential for virulence (i.e., type 1 secretion system [T1SS], T2SS and its effectors, T3SS and its effectors, T4SS, T6SS, adhesins, and rpf gene cluster) and adaptation (i.e., gum, iron uptake and utilization, xanthomonadin, and two-component systems) were depicted by comparative genomics of a Xanthomonas community comprising diverse lifestyles. Overall, the present analysis confers that nonpathogenic isolates of diverse hosts phylogenomically converge and are evolving in parallel with their pathogenic counterparts. Hence, there is a need to understand the world of nonpathogenic isolates from diverse and economically important hosts. Genomic knowledge and resources of nonpathogenic strains will be invaluable in both basic and applied research of the genus Xanthomonas. IMPORTANCE Xanthomonas citri is one of the top phytopathogenic bacteria and is the causal agent of citrus canker. Interestingly, Xanthomonas is also reported to be associated with healthy citrus plants. The advent of the genomic era enabled us to carry out a detailed evolutionary study of a Xanthomonas community associated with citrus and other plants. Our genome-based investigations have revealed hidden and extreme interstrain diversity of nonpathogenic Xanthomonas strains from citrus plants, warranting further large-scale studies. This indicates an unexplored world of Xanthomonas from healthy citrus plant species that may be coevolving as a species complex with the host, unlike the variant pathogenic species. The knowledge and genomic resources will be valuable in evolutionary studies exploring its hidden potential and management of pathogenic species.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{&quot;location&quot;:&quot;wsj-grid-card-download-pdf-modal&quot;,&quot;work_title&quot;:&quot;Phylogenomic Insights into Diversity and Evolution of Nonpathogenic Xanthomonas Strains Associated with Citrus&quot;,&quot;attachmentId&quot;:80146480,&quot;attachmentType&quot;:&quot;pdf&quot;,&quot;work_url&quot;:&quot;https://www.academia.edu/70358826/Phylogenomic_Insights_into_Diversity_and_Evolution_of_Nonpathogenic_Xanthomonas_Strains_Associated_with_Citrus&quot;,&quot;alternativeTracking&quot;:true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/70358826/Phylogenomic_Insights_into_Diversity_and_Evolution_of_Nonpathogenic_Xanthomonas_Strains_Associated_with_Citrus"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="1" data-entity-id="18075079" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/18075079/A_MLVA_Genotyping_Scheme_for_Global_Surveillance_of_the_Citrus_Pathogen_Xanthomonas_citri_pv_citri_Suggests_a_Worldwide_Geographical_Expansion_of_a_Single_Genetic_Lineage">A MLVA Genotyping Scheme for Global Surveillance of the Citrus Pathogen Xanthomonas citri pv. citri Suggests a Worldwide Geographical Expansion of a Single Genetic Lineage</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="7670143" href="https://ird.academia.edu/RalfKOEBNIK">Ralf KOEBNIK</a></div><p class="ds-related-work--metadata ds2-5-body-xs">PLoS ONE, 2014</p><p class="ds-related-work--abstract ds2-5-body-sm">MultiLocus Variable number of tandem repeat Analysis (MLVA) has been extensively used to examine epidemiological and evolutionary issues on monomorphic human pathogenic bacteria, but not on bacterial plant pathogens of agricultural importance albeit such tools would improve our understanding of their epidemiology, as well as of the history of epidemics on a global scale. Xanthomonas citri pv. citri is a quarantine organism in several countries and a major threat for the citrus industry worldwide. We screened the genomes of Xanthomonas citri pv. citri strain IAPAR 306 and of phylogenetically related xanthomonads for tandem repeats. From these in silico data, an optimized MLVA scheme was developed to assess the global diversity of this monomorphic bacterium. Thirty-one minisatellite loci (MLVA-31) were selected to assess the genetic structure of 129 strains representative of the worldwide pathological and genetic diversity of X. citri pv. citri. Based on Discriminant Analysis of Principal Components (DAPC), four pathotype-specific clusters were defined. DAPC cluster 1 comprised strains that were implicated in the major geographical expansion of X. citri pv. citri during the 20th century. A subset of 12 loci (MLVA-12) resolved 89% of the total diversity and matched the genetic structure revealed by MLVA-31. MLVA-12 is proposed for routine epidemiological identification of X. citri pv. citri, whereas MLVA-31 is proposed for phylogenetic and population genetics studies. MLVA-31 represents an opportunity for international X. citri pv. citri genotyping and data sharing. The MLVA-31 data generated in this study was deposited in the Xanthomonas citri genotyping database (http://www.biopred.net/MLVA/).</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{&quot;location&quot;:&quot;wsj-grid-card-download-pdf-modal&quot;,&quot;work_title&quot;:&quot;A MLVA Genotyping Scheme for Global Surveillance of the Citrus Pathogen Xanthomonas citri pv. citri Suggests a Worldwide Geographical Expansion of a Single Genetic Lineage&quot;,&quot;attachmentId&quot;:39862479,&quot;attachmentType&quot;:&quot;pdf&quot;,&quot;work_url&quot;:&quot;https://www.academia.edu/18075079/A_MLVA_Genotyping_Scheme_for_Global_Surveillance_of_the_Citrus_Pathogen_Xanthomonas_citri_pv_citri_Suggests_a_Worldwide_Geographical_Expansion_of_a_Single_Genetic_Lineage&quot;,&quot;alternativeTracking&quot;:true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/18075079/A_MLVA_Genotyping_Scheme_for_Global_Surveillance_of_the_Citrus_Pathogen_Xanthomonas_citri_pv_citri_Suggests_a_Worldwide_Geographical_Expansion_of_a_Single_Genetic_Lineage"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="2" data-entity-id="7556382" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/7556382/Novel_insights_into_the_genomic_basis_of_citrus_canker_based_on_the_genome_sequences_of_two_strains_of_Xanthomonas_fuscans_subsp_aurantifolii">Novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of Xanthomonas fuscans subsp. aurantifolii</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="13574656" href="https://usp-br.academia.edu/AlinedaSilva">Aline da Silva</a></div><p class="ds-related-work--metadata ds2-5-body-xs">BMC Genomics, 2010</p><p class="ds-related-work--abstract ds2-5-body-sm">Background: Citrus canker is a disease that has severe economic impact on the citrus industry worldwide. There are three types of canker, called A, B, and C. The three types have different phenotypes and affect different citrus species. The causative agent for type A is Xanthomonas citri subsp. citri, whose genome sequence was made available in 2002. Xanthomonas fuscans subsp. aurantifolii strain B causes canker B and Xanthomonas fuscans subsp. aurantifolii strain C causes canker C.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{&quot;location&quot;:&quot;wsj-grid-card-download-pdf-modal&quot;,&quot;work_title&quot;:&quot;Novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of Xanthomonas fuscans subsp. aurantifolii&quot;,&quot;attachmentId&quot;:34117310,&quot;attachmentType&quot;:&quot;pdf&quot;,&quot;work_url&quot;:&quot;https://www.academia.edu/7556382/Novel_insights_into_the_genomic_basis_of_citrus_canker_based_on_the_genome_sequences_of_two_strains_of_Xanthomonas_fuscans_subsp_aurantifolii&quot;,&quot;alternativeTracking&quot;:true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/7556382/Novel_insights_into_the_genomic_basis_of_citrus_canker_based_on_the_genome_sequences_of_two_strains_of_Xanthomonas_fuscans_subsp_aurantifolii"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="3" data-entity-id="53698822" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/53698822/Comparative_genomic_and_transcriptome_analyses_of_pathotypes_of_Xanthomonas_citri_subsp_citri_provide_insights_into_mechanisms_of_bacterial_virulence_and_host_range">Comparative genomic and transcriptome analyses of pathotypes of Xanthomonas citri subsp. citri provide insights into mechanisms of bacterial virulence and host range</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="43534230" href="https://independent.academia.edu/MaxuelAndrade">Maxuel Andrade</a></div><p class="ds-related-work--metadata ds2-5-body-xs">BMC Genomics, 2013</p><p class="ds-related-work--abstract ds2-5-body-sm">Background Citrus bacterial canker is a disease that has severe economic impact on citrus industries worldwide and is caused by a few species and pathotypes of Xanthomonas. X. citri subsp. citri strain 306 (XccA306) is a type A (Asiatic) strain with a wide host range, whereas its variant X. citri subsp. citri strain Aw12879 (Xcaw12879, Wellington strain) is restricted to Mexican lime. Results To characterize the mechanism for the differences in host range of XccA and Xcaw, the genome of Xcaw12879 that was completed recently was compared with XccA306 genome. Effectors xopAF and avrGf1 are present in Xcaw12879, but were absent in XccA306. AvrGf1 was shown previously for Xcaw to cause hypersensitive response in Duncan grapefruit. Mutation analysis of xopAF indicates that the gene contributes to Xcaw growth in Mexican lime but does not contribute to the limited host range of Xcaw. RNA-Seq analysis was conducted to compare the expression profiles of Xcaw12879 and XccA306 in Nutrient Brot...</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{&quot;location&quot;:&quot;wsj-grid-card-download-pdf-modal&quot;,&quot;work_title&quot;:&quot;Comparative genomic and transcriptome analyses of pathotypes of Xanthomonas citri subsp. citri provide insights into mechanisms of bacterial virulence and host range&quot;,&quot;attachmentId&quot;:70420539,&quot;attachmentType&quot;:&quot;pdf&quot;,&quot;work_url&quot;:&quot;https://www.academia.edu/53698822/Comparative_genomic_and_transcriptome_analyses_of_pathotypes_of_Xanthomonas_citri_subsp_citri_provide_insights_into_mechanisms_of_bacterial_virulence_and_host_range&quot;,&quot;alternativeTracking&quot;:true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/53698822/Comparative_genomic_and_transcriptome_analyses_of_pathotypes_of_Xanthomonas_citri_subsp_citri_provide_insights_into_mechanisms_of_bacterial_virulence_and_host_range"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="4" data-entity-id="73857536" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/73857536/tale_Based_Genetic_Diversity_of_Chinese_Isolates_of_the_Citrus_Canker_Pathogen_Xanthomonas_citri_subsp_citri">tale -Based Genetic Diversity of Chinese Isolates of the Citrus Canker Pathogen Xanthomonas citri subsp. citri</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="26180" href="https://sjtu.academia.edu/MuhammadZakria">Muhammad Zakria</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Plant Disease, 2013</p><p class="ds-related-work--abstract ds2-5-body-sm">Pathotype A of Xanthomonas citri subsp. citri, the cause of citrus bacterial canker (CBC), is assumed to have originated in southern China. PthA, a type III secreted transcriptional activator-like effector (TALE), is a major pathogenicity determinant in X. citri subsp. citri. To investigate the diversity of X. citri subsp. citri in China, genomic and plasmid DNA of 105 X. citri subsp. citri isolates, collected from nine citrus-growing provinces of China, were digested by BamHI and hybridized with an internal repeat region of pthA. Strains were classified into 14 different genotypes (designated A to N) based on the number and size of pthA homologues. Genotypes B and G represented 19 and 62% of the isolate collection, respectively. Genotypes J and L lacked pthA or a pthA-hybridizing fragment and were less virulent on grapefruit (C. paradisi) and sweet orange (C. sinensis) compared with strains containing pthA or a pthA homologue. The virulence of genotypes J and L was increased when t...</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{&quot;location&quot;:&quot;wsj-grid-card-download-pdf-modal&quot;,&quot;work_title&quot;:&quot;tale -Based Genetic Diversity of Chinese Isolates of the Citrus Canker Pathogen Xanthomonas citri subsp. citri&quot;,&quot;attachmentId&quot;:83828251,&quot;attachmentType&quot;:&quot;pdf&quot;,&quot;work_url&quot;:&quot;https://www.academia.edu/73857536/tale_Based_Genetic_Diversity_of_Chinese_Isolates_of_the_Citrus_Canker_Pathogen_Xanthomonas_citri_subsp_citri&quot;,&quot;alternativeTracking&quot;:true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/73857536/tale_Based_Genetic_Diversity_of_Chinese_Isolates_of_the_Citrus_Canker_Pathogen_Xanthomonas_citri_subsp_citri"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="5" data-entity-id="60825231" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/60825231/Genomics_of_Xanthomonas_citri_and_Related_Species">Genomics of Xanthomonas citri and Related Species</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="17121767" href="https://independent.academia.edu/JalanN">Neha Jalan</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Genomics of Plant-Associated Bacteria, 2014</p><p class="ds-related-work--abstract ds2-5-body-sm">However, the citrus industry has been threatened 17 by impending problems including pests, dis-18 eases, and climatic problems that have limited 19 expansion of the industry and affected the 20 quality and quantity of citrus production. Citrus 21 bacterial canker is one of the most devastating 22 citrus diseases (Graham et al. 2004). Citrus 23 canker affects most commercially important 24 citrus species and cultivars in many citrus-25 growing areas worldwide and severe infection À due to the disease causes extensive damage to À citrus harvest. There are no effective disease À suppression strategies against citrus canker for À the susceptible cultivars of citrus grown in wet, À tropical, and subtropical areas (Schubert et al. À</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{&quot;location&quot;:&quot;wsj-grid-card-download-pdf-modal&quot;,&quot;work_title&quot;:&quot;Genomics of Xanthomonas citri and Related Species&quot;,&quot;attachmentId&quot;:74098478,&quot;attachmentType&quot;:&quot;pdf&quot;,&quot;work_url&quot;:&quot;https://www.academia.edu/60825231/Genomics_of_Xanthomonas_citri_and_Related_Species&quot;,&quot;alternativeTracking&quot;:true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/60825231/Genomics_of_Xanthomonas_citri_and_Related_Species"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="6" data-entity-id="96723288" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/96723288/Origin_and_diversification_of_Xanthomonas_citri_subsp_citri_pathotypes_revealed_by_inclusive_phylogenomic_dating_and_biogeographic_analyses">Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="31995577" href="https://usp-br1.academia.edu/LucianoDigiampietri">Luciano A Digiampietri</a></div><p class="ds-related-work--metadata ds2-5-body-xs">BMC Genomics, 2019</p><p class="ds-related-work--abstract ds2-5-body-sm">Background Xanthomonas citri subsp. citri pathotypes cause bacterial citrus canker, being responsible for severe agricultural losses worldwide. The A pathotype has a broad host spectrum, while A* and Aw are more restricted both in hosts and in geography. Two previous phylogenomic studies led to contrasting well-supported clades for sequenced genomes of these pathotypes. No extensive biogeographical or divergence dating analytic approaches have been so far applied to available genomes. Results Based on a larger sampling of genomes than in previous studies (including six new genomes sequenced by our group, adding to a total of 95 genomes), phylogenomic analyses resulted in different resolutions, though overall indicating that A + AW is the most likely true clade. Our results suggest the high degree of recombination at some branches and the fast diversification of lineages are probable causes for this phylogenetic blurring effect. One of the genomes analyzed, X. campestris pv. durantae...</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{&quot;location&quot;:&quot;wsj-grid-card-download-pdf-modal&quot;,&quot;work_title&quot;:&quot;Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses&quot;,&quot;attachmentId&quot;:98542839,&quot;attachmentType&quot;:&quot;pdf&quot;,&quot;work_url&quot;:&quot;https://www.academia.edu/96723288/Origin_and_diversification_of_Xanthomonas_citri_subsp_citri_pathotypes_revealed_by_inclusive_phylogenomic_dating_and_biogeographic_analyses&quot;,&quot;alternativeTracking&quot;:true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/96723288/Origin_and_diversification_of_Xanthomonas_citri_subsp_citri_pathotypes_revealed_by_inclusive_phylogenomic_dating_and_biogeographic_analyses"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="7" data-entity-id="74490853" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/74490853/Molecular_Diversity_among_the_Isolates_of_Xanthomonas_axonopodis_pv_citri_Causing_Bacterial_Canker_in_Citrus">Molecular Diversity among the Isolates of Xanthomonas axonopodis pv. citri Causing Bacterial Canker in Citrus</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="16669659" href="https://mkuniversity.academia.edu/rutujakharde">rutuja kharde</a></div><p class="ds-related-work--metadata ds2-5-body-xs">International Journal of Current Microbiology and Applied Sciences</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{&quot;location&quot;:&quot;wsj-grid-card-download-pdf-modal&quot;,&quot;work_title&quot;:&quot;Molecular Diversity among the Isolates of Xanthomonas axonopodis pv. citri Causing Bacterial Canker in Citrus&quot;,&quot;attachmentId&quot;:82624965,&quot;attachmentType&quot;:&quot;pdf&quot;,&quot;work_url&quot;:&quot;https://www.academia.edu/74490853/Molecular_Diversity_among_the_Isolates_of_Xanthomonas_axonopodis_pv_citri_Causing_Bacterial_Canker_in_Citrus&quot;,&quot;alternativeTracking&quot;:true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/74490853/Molecular_Diversity_among_the_Isolates_of_Xanthomonas_axonopodis_pv_citri_Causing_Bacterial_Canker_in_Citrus"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="8" data-entity-id="70879808" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/70879808/CitrusKB_A_Comprehensive_Knowledge_Base_for_Transcriptome_and_Interactome_of_Citrus_spp_Infected_by_Xanthomonas_citri_subsp_citri_at_Different_Infection_Stages">CitrusKB: A Comprehensive Knowledge Base for Transcriptome and Interactome of Citrus spp. Infected by Xanthomonas citri subsp. citri at Different Infection Stages</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="1012795" href="https://unesp.academia.edu/TeresaCofre">Teresa Cofre</a></div><p class="ds-related-work--abstract ds2-5-body-sm">Citrus canker type A is a serious disease caused by Xanthomonas citri subsp. citri (X. citri), which is responsible for severe losses to growers and to the citrus industry worldwide. To date, no canker-resistant citrus genotypes are available, and there is limited information regarding the molecular and genetic mechanisms involved in the early stages of the citrus canker development. Here, we present the knowledge base for transcriptome of in vivo citrus interactome, the CitrusKB. This is the first in vivo interactome database for different citrus cultivars, and it was produced to provide a valuable source of information on citrus and their interaction with the citrus canker bacterium X. citri. The database provides tools for a user-friendly web interface to search and analyze a large amount of information regarding eight citrus cultivars with distinct levels of susceptibility to the disease and their interaction, at different stages of infection, with the citrus canker bacterium X. citri. Currently, CitrusKB comprises a reference citrus genome and its transcriptome, expressed transcripts, pseudogenes and predicted genomic variations (SNPs and SSRs). The updating process will continue by incorporating annotations and analysis tools. We expect that CitrusKB may substantially contribute to the area of citrus genomics. CitrusKB is accessible at http://bioinfo.deinfo.uepg.br/citrus. Users can download all the generated raw sequences and generated datasets by this study from the CitrusKB website.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{&quot;location&quot;:&quot;wsj-grid-card-download-pdf-modal&quot;,&quot;work_title&quot;:&quot;CitrusKB: A Comprehensive Knowledge Base for Transcriptome and Interactome of Citrus spp. Infected by Xanthomonas citri subsp. citri at Different Infection Stages&quot;,&quot;attachmentId&quot;:80444682,&quot;attachmentType&quot;:&quot;pdf&quot;,&quot;work_url&quot;:&quot;https://www.academia.edu/70879808/CitrusKB_A_Comprehensive_Knowledge_Base_for_Transcriptome_and_Interactome_of_Citrus_spp_Infected_by_Xanthomonas_citri_subsp_citri_at_Different_Infection_Stages&quot;,&quot;alternativeTracking&quot;:true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/70879808/CitrusKB_A_Comprehensive_Knowledge_Base_for_Transcriptome_and_Interactome_of_Citrus_spp_Infected_by_Xanthomonas_citri_subsp_citri_at_Different_Infection_Stages"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="9" data-entity-id="70358824" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/70358824/Ecological_and_evolutionary_insights_into_pathovar_diversity_of_Xanthomonas_citri">Ecological and evolutionary insights into pathovar diversity of Xanthomonas citri</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="9635657" href="https://uni-mysore.academia.edu/sanjeetKumar">sanjeet Kumar</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Applied and environmental microbiology, 2017</p><p class="ds-related-work--abstract ds2-5-body-sm">Citrus canker, caused by Xanthomonas citri pv. citri (Xct), is a serious disease of citrus plants worldwide. Earlier phylogenetic studies using housekeeping genes revealed that Xct is related to many other pathovars, which can be collectively referred as Xanthomonas citri pathovars (XCPs). In the present study, we report the genome sequence of eighteen XCPs compared with four XCPs available in the public domain. In a tree based on phylogenomic marker genes, all the XCPs form a monophyletic cluster suggesting their origin from a common ancestor. Phylogenomic analysis using the type strain further established that all the XCPs belong to one species. Clonal analysis of the core genome revealed the presence of two major lineages within this monophyletic cluster consisting of some clonal variants. Incidentally, majority of these XCPs were first noticed in India corroborating their clonal relationship and their common origin. Comparative analysis revealed an open pan-genome and the role o...</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{&quot;location&quot;:&quot;wsj-grid-card-download-pdf-modal&quot;,&quot;work_title&quot;:&quot;Ecological and evolutionary insights into pathovar diversity of Xanthomonas citri&quot;,&quot;attachmentId&quot;:80146481,&quot;attachmentType&quot;:&quot;pdf&quot;,&quot;work_url&quot;:&quot;https://www.academia.edu/70358824/Ecological_and_evolutionary_insights_into_pathovar_diversity_of_Xanthomonas_citri&quot;,&quot;alternativeTracking&quot;:true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/70358824/Ecological_and_evolutionary_insights_into_pathovar_diversity_of_Xanthomonas_citri"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div></div></div><div class="ds-sticky-ctas--wrapper js-loswp-sticky-ctas hidden"><div class="ds-sticky-ctas--grid-container"><div class="ds-sticky-ctas--container"><button class="ds2-5-button js-swp-download-button" data-signup-modal="{&quot;location&quot;:&quot;continue-reading-button--sticky-ctas&quot;,&quot;attachmentId&quot;:104947540,&quot;attachmentType&quot;:&quot;pdf&quot;,&quot;workUrl&quot;:null}">See full PDF</button><button class="ds2-5-button ds2-5-button--secondary js-swp-download-button" data-signup-modal="{&quot;location&quot;:&quot;download-pdf-button--sticky-ctas&quot;,&quot;attachmentId&quot;:104947540,&quot;attachmentType&quot;:&quot;pdf&quot;,&quot;workUrl&quot;:null}"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span>Download PDF</button></div></div></div><div class="ds-below-fold--grid-container"><div class="ds-work--container js-loswp-embedded-document"><div class="attachment_preview" data-attachment="Attachment_104947540" style="display: none"><div class="js-scribd-document-container"><div class="scribd--document-loading js-scribd-document-loader" style="display: block;"><img alt="Loading..." src="//a.academia-assets.com/images/loaders/paper-load.gif" /><p>Loading Preview</p></div></div><div style="text-align: center;"><div class="scribd--no-preview-alert js-preview-unavailable"><p>Sorry, preview is currently unavailable. 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