CRISPR elements provide a new framework for the genealogy of the citrus canker pathogen Xanthomonas citri pv. citri
Background: Xanthomonads are an important clade of Gram-negative bacteria infecting a plethora of economically important host plants, including citrus. Knowledge about the pathogen's diversity and population structure are prerequisite for epidemiological surveillance and efficient disease management. Rapidly evolving genetic loci, such as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), are of special interest to develop new molecular typing tools. Results: We analyzed CRISPR loci of 56 Xanthomonas citri pv. citri strains of world-wide origin, a regulated pathogen causing Asiatic citrus canker in several regions of the world. With one exception, 23 unique sequences built up the repertoire of spacers, suggesting that this set of strains originated from a common ancestor that already harbored these 23 spacers. One isolate originating from Pakistan contained a string of 14 additional, probably more recently acquired spacers indicating that this genetic lineage has or had until recently the capacity to acquire new spacers. Comparison of CRISPR arrays with previously obtained molecular typing data, such as amplified fragment length polymorphisms (AFLP), variable-number of tandem-repeats (VNTR) and genome-wide single-nucleotide polymorphisms (SNP), demonstrated that these methods reveal similar evolutionary trajectories. Notably, genome analyses allowed to generate a model for CRISPR array evolution in X. citri pv. citri, which provides a new framework for the genealogy of the citrus canker pathogen. Conclusions: CRISPR-based typing will further improve the accuracy of the genetic identification of X. citri pv. citri outbreak strains in molecular epidemiology analyses, especially when used concomitantly with another genotyping method.
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Subjects: | H20 - Maladies des plantes, F30 - Génétique et amélioration des plantes, pathologie végétale, agent pathogène, variation génétique, surveillance épidémiologique, CRISPR, http://aims.fao.org/aos/agrovoc/c_5974, http://aims.fao.org/aos/agrovoc/c_5630, http://aims.fao.org/aos/agrovoc/c_15975, http://aims.fao.org/aos/agrovoc/c_16411, http://aims.fao.org/aos/agrovoc/c_572d9f63, |
Online Access: | http://agritrop.cirad.fr/596216/ http://agritrop.cirad.fr/596216/1/bmc19.pdf |
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dig-cirad-fr-5962162024-01-29T02:56:35Z http://agritrop.cirad.fr/596216/ http://agritrop.cirad.fr/596216/ CRISPR elements provide a new framework for the genealogy of the citrus canker pathogen Xanthomonas citri pv. citri. Jeong Kwanho, Muñoz-Bodnar Alejandra, Arias Rojas Nathalia, Poulin Lucie, Rodríguez-R Luis Miguel, Gagnevin Lionel, Vernière Christian, Pruvost Olivier, Koebnik Ralf. 2019. BMC Genomics, 20:917, 19 p.https://doi.org/10.1186/s12864-019-6267-z <https://doi.org/10.1186/s12864-019-6267-z> CRISPR elements provide a new framework for the genealogy of the citrus canker pathogen Xanthomonas citri pv. citri Jeong, Kwanho Muñoz-Bodnar, Alejandra Arias Rojas, Nathalia Poulin, Lucie Rodríguez-R, Luis Miguel Gagnevin, Lionel Vernière, Christian Pruvost, Olivier Koebnik, Ralf eng 2019 BMC Genomics H20 - Maladies des plantes F30 - Génétique et amélioration des plantes pathologie végétale agent pathogène variation génétique surveillance épidémiologique CRISPR http://aims.fao.org/aos/agrovoc/c_5974 http://aims.fao.org/aos/agrovoc/c_5630 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_16411 http://aims.fao.org/aos/agrovoc/c_572d9f63 Background: Xanthomonads are an important clade of Gram-negative bacteria infecting a plethora of economically important host plants, including citrus. Knowledge about the pathogen's diversity and population structure are prerequisite for epidemiological surveillance and efficient disease management. Rapidly evolving genetic loci, such as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), are of special interest to develop new molecular typing tools. Results: We analyzed CRISPR loci of 56 Xanthomonas citri pv. citri strains of world-wide origin, a regulated pathogen causing Asiatic citrus canker in several regions of the world. With one exception, 23 unique sequences built up the repertoire of spacers, suggesting that this set of strains originated from a common ancestor that already harbored these 23 spacers. One isolate originating from Pakistan contained a string of 14 additional, probably more recently acquired spacers indicating that this genetic lineage has or had until recently the capacity to acquire new spacers. Comparison of CRISPR arrays with previously obtained molecular typing data, such as amplified fragment length polymorphisms (AFLP), variable-number of tandem-repeats (VNTR) and genome-wide single-nucleotide polymorphisms (SNP), demonstrated that these methods reveal similar evolutionary trajectories. Notably, genome analyses allowed to generate a model for CRISPR array evolution in X. citri pv. citri, which provides a new framework for the genealogy of the citrus canker pathogen. Conclusions: CRISPR-based typing will further improve the accuracy of the genetic identification of X. citri pv. citri outbreak strains in molecular epidemiology analyses, especially when used concomitantly with another genotyping method. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/596216/1/bmc19.pdf text cc_by info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/ https://doi.org/10.1186/s12864-019-6267-z 10.1186/s12864-019-6267-z info:eu-repo/semantics/altIdentifier/doi/10.1186/s12864-019-6267-z info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1186/s12864-019-6267-z info:eu-repo/semantics/dataset/purl/https://figshare.com/articles/journal_contribution/MOESM10_of_CRISPR_elements_provide_a_new_framework_for_the_genealogy_of_the_citrus_canker_pathogen_Xanthomonas_citri_pv_citri/11308106 |
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H20 - Maladies des plantes F30 - Génétique et amélioration des plantes pathologie végétale agent pathogène variation génétique surveillance épidémiologique CRISPR http://aims.fao.org/aos/agrovoc/c_5974 http://aims.fao.org/aos/agrovoc/c_5630 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_16411 http://aims.fao.org/aos/agrovoc/c_572d9f63 H20 - Maladies des plantes F30 - Génétique et amélioration des plantes pathologie végétale agent pathogène variation génétique surveillance épidémiologique CRISPR http://aims.fao.org/aos/agrovoc/c_5974 http://aims.fao.org/aos/agrovoc/c_5630 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_16411 http://aims.fao.org/aos/agrovoc/c_572d9f63 |
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H20 - Maladies des plantes F30 - Génétique et amélioration des plantes pathologie végétale agent pathogène variation génétique surveillance épidémiologique CRISPR http://aims.fao.org/aos/agrovoc/c_5974 http://aims.fao.org/aos/agrovoc/c_5630 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_16411 http://aims.fao.org/aos/agrovoc/c_572d9f63 H20 - Maladies des plantes F30 - Génétique et amélioration des plantes pathologie végétale agent pathogène variation génétique surveillance épidémiologique CRISPR http://aims.fao.org/aos/agrovoc/c_5974 http://aims.fao.org/aos/agrovoc/c_5630 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_16411 http://aims.fao.org/aos/agrovoc/c_572d9f63 Jeong, Kwanho Muñoz-Bodnar, Alejandra Arias Rojas, Nathalia Poulin, Lucie Rodríguez-R, Luis Miguel Gagnevin, Lionel Vernière, Christian Pruvost, Olivier Koebnik, Ralf CRISPR elements provide a new framework for the genealogy of the citrus canker pathogen Xanthomonas citri pv. citri |
description |
Background: Xanthomonads are an important clade of Gram-negative bacteria infecting a plethora of economically important host plants, including citrus. Knowledge about the pathogen's diversity and population structure are prerequisite for epidemiological surveillance and efficient disease management. Rapidly evolving genetic loci, such as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), are of special interest to develop new molecular typing tools. Results: We analyzed CRISPR loci of 56 Xanthomonas citri pv. citri strains of world-wide origin, a regulated pathogen causing Asiatic citrus canker in several regions of the world. With one exception, 23 unique sequences built up the repertoire of spacers, suggesting that this set of strains originated from a common ancestor that already harbored these 23 spacers. One isolate originating from Pakistan contained a string of 14 additional, probably more recently acquired spacers indicating that this genetic lineage has or had until recently the capacity to acquire new spacers. Comparison of CRISPR arrays with previously obtained molecular typing data, such as amplified fragment length polymorphisms (AFLP), variable-number of tandem-repeats (VNTR) and genome-wide single-nucleotide polymorphisms (SNP), demonstrated that these methods reveal similar evolutionary trajectories. Notably, genome analyses allowed to generate a model for CRISPR array evolution in X. citri pv. citri, which provides a new framework for the genealogy of the citrus canker pathogen. Conclusions: CRISPR-based typing will further improve the accuracy of the genetic identification of X. citri pv. citri outbreak strains in molecular epidemiology analyses, especially when used concomitantly with another genotyping method. |
format |
article |
topic_facet |
H20 - Maladies des plantes F30 - Génétique et amélioration des plantes pathologie végétale agent pathogène variation génétique surveillance épidémiologique CRISPR http://aims.fao.org/aos/agrovoc/c_5974 http://aims.fao.org/aos/agrovoc/c_5630 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_16411 http://aims.fao.org/aos/agrovoc/c_572d9f63 |
author |
Jeong, Kwanho Muñoz-Bodnar, Alejandra Arias Rojas, Nathalia Poulin, Lucie Rodríguez-R, Luis Miguel Gagnevin, Lionel Vernière, Christian Pruvost, Olivier Koebnik, Ralf |
author_facet |
Jeong, Kwanho Muñoz-Bodnar, Alejandra Arias Rojas, Nathalia Poulin, Lucie Rodríguez-R, Luis Miguel Gagnevin, Lionel Vernière, Christian Pruvost, Olivier Koebnik, Ralf |
author_sort |
Jeong, Kwanho |
title |
CRISPR elements provide a new framework for the genealogy of the citrus canker pathogen Xanthomonas citri pv. citri |
title_short |
CRISPR elements provide a new framework for the genealogy of the citrus canker pathogen Xanthomonas citri pv. citri |
title_full |
CRISPR elements provide a new framework for the genealogy of the citrus canker pathogen Xanthomonas citri pv. citri |
title_fullStr |
CRISPR elements provide a new framework for the genealogy of the citrus canker pathogen Xanthomonas citri pv. citri |
title_full_unstemmed |
CRISPR elements provide a new framework for the genealogy of the citrus canker pathogen Xanthomonas citri pv. citri |
title_sort |
crispr elements provide a new framework for the genealogy of the citrus canker pathogen xanthomonas citri pv. citri |
url |
http://agritrop.cirad.fr/596216/ http://agritrop.cirad.fr/596216/1/bmc19.pdf |
work_keys_str_mv |
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