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12. Genome and transcriptome analysis to reveal adaptation to new environments and hosts

Author

Gagnevin, L., Roux, B., Bolot, S., Carrere, S., Charbit, E., Cunnac, S., Jacques, M. A., Noel, L. D., Arlat, M., Ralf Koebnik, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), UMR - Interactions Plantes Microorganismes Environnement (UMR IPME), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud]), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), and Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)

Subjects
[SDV]Life Sciences [q-bio], H20 - Maladies des plantes
Abstract

Pathovars of Xanthomonas are interesting working models for the analysis of mechanisms of adaptation and specialization to hosts, plant tissues, niches and environments. The understanding of such mechanisms is important on practical and academic points of view since they can help explain how emergence of new diseases or of diseases in new situations may occur. Four research groups belonging to the French Network on Xanthomonas (FNX) have recently focused on genome and transcriptome sequencing of several pathovars of Xanthomonas chosen for their adaptation particularities, in a project called “Xanthomix”. Xanthomonas strains attacking Anacardiaceae, citrus, crucifers, legumes or rice were selected to help understand adaptation processes: genetic structure revealing either convergence or divergence for causing a specific disease on a specific host ; host tissue specialization (xylem vs. mesophyll) ; virulence variation (broad vs. narrow host range); contrasted epidemic situation (endemic vs. epidemic). RNAseq experiments were performed on a large set of strains to determine the extent and the diversity of the hrp regulon. In addition, the RNAseq dataset is also being used to improve Xanthomonas genome annotation and gene prediction. Analysis of transcripts allowed us to scan for unknown specific and non-specific effectors as well as small non-coding RNAs and hypothesize new mechanisms that could be involved in adaptation to host and environment. (Texte intégral)

Published
2013

13. CRISPR systems in plant pathogens : a new tool for epidemiological surveillance

Author

Jeong, K., Bodnar, A. Munoz, Poulin, L., Rojas, N. Arias, Rodriguez-R, L. M., Gagnevin, L., Pruvost, O., and Ralf Koebnik

Subjects
C30 - Documentation et information, food and beverages, H20 - Maladies des plantes
Abstract

Rapidly evolving genetic loci, such as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), are of special interest to develop new molecular typing tools. The widely distributed CRISPR loci consist of highly conserved DNA repeats that are interspersed by unique, similarly sized spacers which originate from previous attacks by viruses and/or plasmids. For efficient management of plant diseases, knowledge about the pathogen's population structure and tools for epidemiological surveillance are prerequisite. We wish to exploit CRISPR loci as a molecular typing tool of plant pathogens, as exemplified by Xanthomonas, an important clade of Gramnegative bacteria infecting a plethora of plants, including rice, cereals, cassava, banana and citrus fruits. CRISPR loci of 56 X. citri subsp. citri strains of world-wide origin were sequenced, revealing a repertoire of 37 unique spacers. A dendrogram based on the presence and absence of spacers was largely congruent with previous typing using AFLP. Our results demonstrate that CRISPR-based spoligotyping can be used as an efficient and robust method to study the phylogenetic relationships among isolates of plantpathogenic xanthomonads, such as the citrus cancer pathogen X. citri subsp. citri. Implementation of Xanthomonas spoligotyping will serve phytosanitary measures by assisting the epidemiological surveillance of outbreaks of citrus canker and other diseases. (Texte intégral)

Published
2013

14. Phylogeography of the green turtle, Chelonia mydas, in the Southwest Indian Ocean

Author

Bourjea, Jerome, Lapegue, Sylvie, Gagnevin, L, Broderick, D, Mortimer, J.a., Ciccione, S, Roos, David, Taquet, Coralie, and Grizel, Henri

Subjects
Phylogeography, Control region, Chelonia mydas, Mozambique Channel, Indian Ocean, geographic locations, Mitochondrial DNA
Abstract

Patterns of mitochondrial DNA (mtDNA) variation were used to analyse the population genetic structure of southwestern Indian Ocean green turtle (Chelonia mydas) populations. Analysis of sequence variation over 396 bp of the mtDNA control region revealed seven haplotypes among 288 individuals from 10 nesting sites in the Southwest Indian Ocean. This is the first time that Atlantic Ocean haplotypes have been recorded among any Indo-Pacific nesting populations. Previous studies indicated that the Cape of Good Hope was a major biogeographical barrier between the Atlantic and Indian Oceans because evidence for gene flow in the last 1.5 million years has yet to emerge. This study, by sampling localities adjacent to this barrier, demonstrates that recent gene flow has occurred from the Atlantic Ocean into the Indian Ocean via the Cape of Good Hope. We also found compelling genetic evidence that green turtles nesting at the rookeries of the South Mozambique Channel (SMC) and those nesting in the North Mozambique Channel (NMC) belong to separate genetic stocks. Furthermore, the SMC could be subdivided in two different genetic stocks, one in Europa and the other one in Juan de Nova. We suggest that this particular genetic pattern along the Mozambique Channel is attributable to a recent colonization from the Atlantic Ocean and is maintained by oceanic conditions in the northern and southern Mozambique Channel that influence early stages in the green turtle life cycle.

Published
2007

15. New Multilocus Variable-Number Tandem-Repeat Analysis Tool for Surveillance and Local Epidemiology of Bacterial Leaf Blight and Bacterial Leaf Streak of Rice Caused by Xanthomonas oryzae

Author

Poulin, L., primary, Grygiel, P., additional, Magne, M., additional, Gagnevin, L., additional, Rodriguez-R, L. M., additional, Forero Serna, N., additional, Zhao, S., additional, El Rafii, M., additional, Dao, S., additional, Tekete, C., additional, Wonni, I., additional, Koita, O., additional, Pruvost, O., additional, Verdier, V., additional, Vernière, C., additional, and Koebnik, R., additional

Published
2015
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22. High-Quality Draft Genome Sequences of Xanthomonas axonopodis pv. glycines Strains CFBP 2526 and CFBP 7119

Author

Darrasse, A., primary, Bolot, S., additional, Serres-Giardi, L., additional, Charbit, E., additional, Boureau, T., additional, Fisher-Le Saux, M., additional, Briand, M., additional, Arlat, M., additional, Gagnevin, L., additional, Koebnik, R., additional, Noël, L. D., additional, Carrère, S., additional, and Jacques, M. A., additional

Published
2013
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23. Phylogeography of the green turtle, Chelonia mydas, in the Southwest Indian Ocean

Author

Bourjea, J., Lapegue, S., Gagnevin, L., Broderick, D., Mortimer, J.A., Ciccione, S., Roos, D., Taquet, C., Bourjea, J., Lapegue, S., Gagnevin, L., Broderick, D., Mortimer, J.A., Ciccione, S., Roos, D., and Taquet, C.

Abstract

Patterns of mitochondrial DNA (mtDNA) variation were used to analyse the population genetic structure of southwestern Indian Ocean green turtle (Chelonia mydas) populations. Analysis of sequence variation over 396 bp of the mtDNA control region revealed seven haplotypes among 288 individuals from 10 nesting sites in the Southwest Indian Ocean. This is the first time that Atlantic Ocean haplotypes have been recorded among any Indo-Pacific nesting populations. Previous studies indicated that the Cape of Good Hope was a major biogeographical barrier between the Atlantic and Indian Oceans because evidence for gene flow in the last 1.5 million years has yet to emerge. This study, by sampling localities adjacent to this barrier, demonstrates that recent gene flow has occurred from the Atlantic Ocean into the Indian Ocean via the Cape of Good Hope. We also found compelling genetic evidence that green turtles nesting at the rookeries of the South Mozambique Channel (SMC) and those nesting in the North Mozambique Channel (NMC) belong to separate genetic stocks. Furthermore, the SMC could be subdivided in two different genetic stocks, one in Europa and the other one in Juan de Nova. We suggest that this particular genetic pattern along the Mozambique Channel is attributable to a recent colonization from the Atlantic Ocean and is maintained by oceanic conditions in the northern and southern Mozambique Channel that influence early stages in the green turtle life cycle.

Published
2007

29. Pseudomonas aeruginosa Outbreak Linked to Mineral Water Bottles in a Neonatal Intensive Care Unit: Fast Typing by Use of High-Resolution Melting Analysis of a Variable-Number Tandem-Repeat Locus

Author

Naze, F., primary, Jouen, E., additional, Randriamahazo, R. T., additional, Simac, C., additional, Laurent, P., additional, Blériot, A., additional, Chiroleu, F., additional, Gagnevin, L., additional, Pruvost, O., additional, and Michault, A., additional

Published
2010
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46. Pseudomonas aeruginosaOutbreak Linked to Mineral Water Bottles in a Neonatal Intensive Care Unit: Fast Typing by Use of High-Resolution Melting Analysis of a Variable-Number Tandem-Repeat Locus

Author

Naze, F., Jouen, E., Randriamahazo, R. T., Simac, C., Laurent, P., Ble´riot, A., Chiroleu, F., Gagnevin, L., Pruvost, O., and Michault, A.

Abstract

ABSTRACTPseudomonas aeruginosais an opportunistic pathogen that causes nosocomial infections in intensive care units. Determining a system of typing that is discriminatory is essential for epidemiological surveillance of P. aeruginosa. We developed a method for the typing of Pseudomonas aeruginosa, namely, multiple-locus variable-number tandem-repeat (VNTR) typing with high-resolution melting analysis (HRMA). The technology was used to genotype a collection of 43 environmental and clinical strains isolated during an outbreak in a neonatal intensive care unit (NICU) that we report. Nineteen strains isolated in other departments or outside the hospital were also tested. The genetic diversity of this collection was determined using VNTR-HRMA, with amplified fragment length polymorphism (AFLP) analysis as a reference. Twenty-five and 28 genotypes were identified, respectively, and both techniques produced congruent data. VNTR-HRMA established clonal relationships between the strains of P. aeruginosaisolated during the outbreak in the NICU and proved, for the first time, the role of mineral water as the inoculum source. VNTR typing with one primer pair in association with HRMA is highly reproducible and discriminative, easily portable among laboratories, fast, and inexpensive, and it demonstrated excellent typeability in this study. VNTR-HRMA represents a promising tool for the molecular surveillance of P. aeruginosaand perhaps for molecular epidemiologic analysis of other hospital infections.

Published
2010
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47. Development of 14 minisatellite markers for the citrus canker bacterium, Xanthomonas citri pv. citri.

Author

BUI THI NGOC, L., VERNIERE, C., VITAL, K., GUERIN, F., GAGNEVIN, L., BRISSE, S., AH-YOU, N., and PRUVOST, O.

Subjects
XANTHOMONAS, GENOMES, POLYMERASE chain reaction, GENETICS, PLANT diseases, PSEUDOMONADACEAE
Abstract

We screened the genome of Xanthomonas citri pv. citri strain 306 for tandem repeats. A multiplex polymerase chain reaction protocol was used to assess the genetic diversity of 239 strains of X. citri pv. citri from Asia. The total number of alleles per locus ranged from three to 20. Using pooled data sets, 223 different haplotypes were identified. Successful amplifications were obtained at most loci for seven other X. citri pathovars. This typing scheme is expected to be useful at different spatial scales for population studies of pathovars of X. citri, several of which cause plant diseases of economic importance. [ABSTRACT FROM AUTHOR]

Published
2009
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48. Polyphasic Characterization of Xanthomonas axonopodis pv. allii Associated with Outbreaks of Bacterial Blight on Three A ilium Species in the Mascarene Archipelago.

Author

Picard, Y., Roumagnac, P., Legrand, D., Humeau, L., Robène-Soustrade, I., Chiroleu, F., Gagnevin, L., and Pruvost, O.

Subjects
*XANTHOMONAS, *FUNCTIONAL analysis, *PLANT diseases, *POLYMORPHISM (Zoology), *DISEASED plants
Abstract

Based on the number of new reports during the last two decades, bacterial blight of onion (A ilium cepa) is considered an emerging disease. The causal agent, Xanthomonas axonopodis pv. ailii, is pathogenic to several A ilium species after inoculation, but outbreaks worldwide have been primarily reported on onion. We describe a unique epidemiological situation in Reunion Island, France, with concomitant outbreaks on three A ilium species, onion, leek (A. porrum), and garlic (A. sativum). There was no host specialization within Alhum spp. among strains associated with the three host species. Based on amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism, strains associated with these outbreaks in Reunion Island were highly related genetically to strains isolated from diseased plant samples and contaminated seed lots in the neighboring island of Mauritius, where the disease has occurred since 1984. All AFLP haplotypes were identified as X. axonopodis pv. allu based on polymerase chain reaction analysis using specific primers, biochemical tests, and/or pathogenicity tests. Two genetically related groups of strains (A and B) that can be distinguished by AFLP, differential utilization of three carbon sources, and xanthomonadin pigment production were detected initially after establishment of the pathogen. In less than 10 years after the establishment of the pathogen there was nearly an extinction of group A strains in Reunion Island, suggesting differences in fitness between strains in the two groups. [ABSTRACT FROM AUTHOR]

Published
2008
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49. New, Complete Circularized Genomes of Xanthomonas citri pv. mangiferaeindicae Produced from Short- and Long-Read Co-Assembly Shed Light on Strains that Emerged a Decade Ago on Mango and Cashew in Burkina Faso.

Author

Boyer C, Lefeuvre P, Zombre C, Rieux A, Wonni I, Gagnevin L, and Pruvost O

Subjects
Burkina Faso, Plasmids genetics, Phylogeny, Virulence genetics, Xanthomonas genetics, Xanthomonas pathogenicity, Xanthomonas isolation & purification, Mangifera microbiology, Plant Diseases microbiology, Genome, Bacterial genetics, Anacardium microbiology
Abstract

We report high-quality genomes of three strains of Xanthomonas citri pv . mangiferaeindicae , the causal agent of mango bacterial canker disease, including the pathotype strain of this pathovar and two strains from Burkina Faso that emerged a decade ago. These strains hosted two to three plasmids of sizes ranging from 19 to 86 kb. Genome mining revealed the presence of several secretion systems and effectors involved in the virulence of xanthomonads with (i) a type I secretion system of the hlyDB group; (ii) xps and xcs type II secretion systems; (iii) a type III secretion system with several type III effectors, including transcription activator-like effectors; (iv) several type IV secretion systems associated with plasmid or integrative conjugative elements mobility; (v) three type V secretion system subclasses (Va, Vb, and Vc); and (vi) a single i3* type VI secretion system. The two strains isolated in Burkina Faso from mango ( Mangifera indica ) and cashew ( Anacardium occidentale ) differed by only 14 single-nucleotide polymorphisms and shared identical secretion systems and type III effector repertoires. Several transcription activator-like effectors were identified in each strain, some of which may target plant genes previously found implicated in disease development in other xanthomonad-associated pathosystems. These results support the emergence in Burkina Faso a decade ago of very closely related strains that became epidemic on mango and cashew (i.e., two distinct host genera of a same plant family). These new genomic resources will contribute to better understanding the biology and evolution of this agriculturally major crop pathogen., Competing Interests: The author(s) declare no conflict of interest.

Published
2025
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50. Evolutionary and Epidemiological Insights from Historical and Modern Genomes of Xanthomonas oryzae pv. oryzicola , the Causal Agent of Bacterial Leaf Streak of Rice.

Author

Hutin M, Carpenter S, Baruah S, Campos P, Boyer K, Andriantsimialona D, Rapanarivo SH, Pruvost O, Becker N, Gagnevin L, Koebnik R, Szurek B, Koita O, Bogdanove AJ, and Rieux A

Subjects
Phylogeny, Plant Leaves microbiology, Evolution, Molecular, Asia, Oryza microbiology, Xanthomonas genetics, Xanthomonas pathogenicity, Plant Diseases microbiology, Genome, Bacterial
Abstract

Xanthomonas oryzae pv. oryzicola ( Xoc ) causes bacterial leaf streak (BLS) of rice. This disease represents a major constraint for rice production, which is a crop feeding more than half of the world's population. Xoc was first described in 1918 in the Philippines and is prevalent in southeast Asia. Today, BLS is also omnipresent in both East- and West-Africa, where the disease was first reported in the early 1980s. The appearance of Xoc in Africa decades after its first report in Asia suggests that the disease could have been introduced from Asia to Africa. Strict conservation of five transcription activator-like (TAL) effectors in whole-genome sequences of 10 strains of Xoc including three from West-Africa and seven from Asia also support this hypothesis. East-Africa, especially Madagascar, where the disease was first described in 1985 is located at the interface between Asia and Africa, hence representing an interesting region to explore the link between strains from Asia and West-Africa. In this study, we did the following: (i) reconstructed the genome of a historical Xoc strain from a herbarium specimen of rice showing symptoms of BLS that was sampled in Madagascar in 1931, 50 years before the first description of the disease, and (ii) sequenced nine new modern strains, including five from Madagascar and East-Africa. The analysis of those new genomes along with previously published ones shed light within the evolutionary and epidemiological history of Xoc . [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license., Competing Interests: The author(s) declare no conflict of interest.

Published
2024
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