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  1. Article: Plant disease symptom segmentation in chlorophyll fluorescence imaging with a synthetic dataset.

    Sapoukhina, Natalia / Boureau, Tristan / Rousseau, David

    Frontiers in plant science

    2022  Volume 13, Page(s) 969205

    Abstract: Despite the wide use of computer vision methods in plant health monitoring, little attention is paid to segmenting the diseased leaf area at its early stages. It can be explained by the lack of datasets of plant images with annotated disease lesions. We ... ...

    Abstract Despite the wide use of computer vision methods in plant health monitoring, little attention is paid to segmenting the diseased leaf area at its early stages. It can be explained by the lack of datasets of plant images with annotated disease lesions. We propose a novel methodology to generate fluorescent images of diseased plants with an automated lesion annotation. We demonstrate that a U-Net model aiming to segment disease lesions on fluorescent images of plant leaves can be efficiently trained purely by a synthetically generated dataset. The trained model showed 0.793% recall and 0.723% average precision against an empirical fluorescent test dataset. Creating and using such synthetic data can be a powerful technique to facilitate the application of deep learning methods in precision crop protection. Moreover, our method of generating synthetic fluorescent images is a way to improve the generalization ability of deep learning models.
    Language English
    Publishing date 2022-11-10
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2022.969205
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Improving Common Bacterial Blight Phenotyping by Using Rub Inoculation and Machine Learning: Cheaper, Better, Faster, Stronger.

    Foucher, Justine / Ruh, Mylène / Briand, Martial / Préveaux, Anne / Barbazange, Florian / Boureau, Tristan / Jacques, Marie-Agnès / Chen, Nicolas W G

    Phytopathology

    2022  Volume 112, Issue 3, Page(s) 691–699

    Abstract: Accurate assessment of plant symptoms plays a key role for measuring the impact of pathogens during plant-pathogen interaction. Common bacterial blight caused ... ...

    Abstract Accurate assessment of plant symptoms plays a key role for measuring the impact of pathogens during plant-pathogen interaction. Common bacterial blight caused by
    MeSH term(s) Bacteria ; Fabaceae ; Machine Learning ; Plant Diseases/microbiology ; Virulence
    Language English
    Publishing date 2022-03-02
    Publishing country United States
    Document type Journal Article
    ZDB-ID 208889-7
    ISSN 1943-7684 ; 0031-949X
    ISSN (online) 1943-7684
    ISSN 0031-949X
    DOI 10.1094/PHYTO-04-21-0129-R
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Improving Common Bacterial Blight Phenotyping by Using Rub Inoculation and Machine Learning: Cheaper, Better, Faster, Stronger

    Foucher, Justine / Ruh, Mylène / Briand, Martial / Préveaux, Anne / Barbazange, Florian / Boureau, Tristan / Jacques, Marie-Agnès / Chen, Nicolas W. G.

    Phytopathology. 2022 Mar., v. 112, no. 3

    2022  

    Abstract: Accurate assessment of plant symptoms plays a key role for measuring the impact of pathogens during plant−pathogen interaction. Common bacterial blight caused by Xanthomonas phaseoli pv. phaseoli and X. citri pv. fuscans is a major threat to common bean. ...

    Abstract Accurate assessment of plant symptoms plays a key role for measuring the impact of pathogens during plant−pathogen interaction. Common bacterial blight caused by Xanthomonas phaseoli pv. phaseoli and X. citri pv. fuscans is a major threat to common bean. The pathogenicity of these bacteria is variable among strains and depends mainly on a type III secretion system and associated type III effectors such as transcription activator-like effectors. Because the impact of a single gene is often small and difficult to detect, a discriminating methodology is required to distinguish the slight phenotype changes induced during the progression of the disease. Here, we compared two different inoculation and symptom assessment methods for their ability to distinguish two tal mutants from their corresponding wild-type strains. Interestingly, rub inoculation of the first leaves combined with symptom assessment by machine learning-based imaging allowed significant distinction between wild-type and mutant strains. By contrast, dip inoculation of first-trifoliate leaves combined with chlorophyll fluorescence imaging did not differentiate the strains. Furthermore, the new method developed here led to the miniaturization of pathogenicity tests and significant time savings.
    Keywords Xanthomonas campestris pv. phaseoli ; beans ; blight ; chlorophyll ; disease progression ; genes ; host-pathogen relationships ; mutants ; pathogenicity ; phenotype ; plant pathology
    Language English
    Dates of publication 2022-03
    Size p. 691-699.
    Publishing place The American Phytopathological Society
    Document type Article
    ZDB-ID 208889-7
    ISSN 1943-7684 ; 0031-949X
    ISSN (online) 1943-7684
    ISSN 0031-949X
    DOI 10.1094/PHYTO-04-21-0129-R
    Database NAL-Catalogue (AGRICOLA)

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  4. Article: A Computation Method Based on the Combination of Chlorophyll Fluorescence Parameters to Improve the Discrimination of Visually Similar Phenotypes Induced by Bacterial Virulence Factors.

    Méline, Valérian / Brin, Chrystelle / Lebreton, Guillaume / Ledroit, Lydie / Sochard, Daniel / Hunault, Gilles / Boureau, Tristan / Belin, Etienne

    Frontiers in plant science

    2020  Volume 11, Page(s) 213

    Abstract: Phenotyping biotic stresses in plant-pathogen interactions studies is often hindered by phenotypes that can hardly be discriminated by visual assessment. Particularly, single gene mutants in virulence factors could lack visible phenotypes. Chlorophyll ... ...

    Abstract Phenotyping biotic stresses in plant-pathogen interactions studies is often hindered by phenotypes that can hardly be discriminated by visual assessment. Particularly, single gene mutants in virulence factors could lack visible phenotypes. Chlorophyll fluorescence (CF) imaging is a valuable tool to monitor plant-pathogen interactions. However, while numerous CF parameters can be measured, studies on plant-pathogen interactions often focus on a restricted number of parameters. It could result in limited abilities to discriminate visually similar phenotypes. In this study, we assess the ability of the combination of multiple CF parameters to improve the discrimination of such phenotypes. Such an approach could be of interest for screening and discriminating the impact of bacterial virulence factors without prior knowledge. A computation method was developed, based on the combination of multiple CF parameters, without any parameter selection. It involves histogram Bhattacharyya distance calculations and hierarchical clustering, with a normalization approach to take into account the inter-leaves and intra-phenotypes heterogeneities. To assess the efficiency of the method, two datasets were analyzed the same way. The first dataset featured single gene mutants of a
    Language English
    Publishing date 2020-02-26
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2020.00213
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: The AvrE superfamily: ancestral type III effectors involved in suppression of pathogen-associated molecular pattern-triggered immunity.

    Degrave, Alexandre / Siamer, Sabrina / Boureau, Tristan / Barny, Marie-Anne

    Molecular plant pathology

    2015  Volume 16, Issue 8, Page(s) 899–905

    Abstract: The AvrE superfamily of type III effectors (T3Es) is widespread among type III-dependent phytobacteria and plays a crucial role during bacterial pathogenesis. Members of the AvrE superfamily are vertically inherited core effectors, indicating an ... ...

    Abstract The AvrE superfamily of type III effectors (T3Es) is widespread among type III-dependent phytobacteria and plays a crucial role during bacterial pathogenesis. Members of the AvrE superfamily are vertically inherited core effectors, indicating an ancestral acquisition of these effectors in bacterial plant pathogens. AvrE-T3Es contribute significantly to virulence by suppressing pathogen-associated molecular pattern (PAMP)-triggered immunity. They inhibit salicylic acid-mediated plant defences, interfere with vesicular trafficking and promote bacterial growth in planta. AvrE-T3Es elicit cell death in both host and non-host plants independent of any known plant resistance protein, suggesting an original interaction with the plant immune system. Recent studies in yeast have indicated that they activate protein phosphatase 2A and inhibit serine palmitoyl transferase, the first enzyme of the sphingolipid biosynthesis pathway. In this review, we describe the current picture that has emerged from studies of the different members of this fascinating large family.
    MeSH term(s) Bacterial Proteins/physiology ; Host-Pathogen Interactions ; Virulence
    Chemical Substances Bacterial Proteins
    Language English
    Publishing date 2015-02-27
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2020755-4
    ISSN 1364-3703 ; 1464-6722
    ISSN (online) 1364-3703
    ISSN 1464-6722
    DOI 10.1111/mpp.12237
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: The AvrE superfamily: ancestral type III effectors involved in suppression of pathogen‐associated molecular pattern‐triggered immunity

    Degrave, Alexandre / Siamer, Sabrina / Boureau, Tristan / Barny, Marie‐Anne

    Molecular plant pathology. 2015 Oct., v. 16, no. 8

    2015  

    Abstract: The AvrE superfamily of type III effectors (T3Es) is widespread among type III‐dependent phytobacteria and plays a crucial role during bacterial pathogenesis. Members of the AvrE superfamily are vertically inherited core effectors, indicating an ... ...

    Abstract The AvrE superfamily of type III effectors (T3Es) is widespread among type III‐dependent phytobacteria and plays a crucial role during bacterial pathogenesis. Members of the AvrE superfamily are vertically inherited core effectors, indicating an ancestral acquisition of these effectors in bacterial plant pathogens. AvrE‐T3Es contribute significantly to virulence by suppressing pathogen‐associated molecular pattern (PAMP)‐triggered immunity. They inhibit salicylic acid‐mediated plant defences, interfere with vesicular trafficking and promote bacterial growth in planta. AvrE‐T3Es elicit cell death in both host and non‐host plants independent of any known plant resistance protein, suggesting an original interaction with the plant immune system. Recent studies in yeast have indicated that they activate protein phosphatase 2A and inhibit serine palmitoyl transferase, the first enzyme of the sphingolipid biosynthesis pathway. In this review, we describe the current picture that has emerged from studies of the different members of this fascinating large family.
    Keywords biosynthesis ; cell death ; immunity ; microbial growth ; pathogenesis ; plant pathogenic bacteria ; sphingolipids ; virulence ; yeasts
    Language English
    Dates of publication 2015-10
    Size p. 899-905.
    Publishing place Blackwell Science in collaboration with the British Society of Plant Pathology
    Document type Article
    ZDB-ID 2020755-4
    ISSN 1364-3703 ; 1464-6722
    ISSN (online) 1364-3703
    ISSN 1464-6722
    DOI 10.1111/mpp.12237
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  7. Article: Role of the acquisition of a type 3 secretion system in the emergence of novel pathogenic strains of Xanthomonas

    Meline, Valérian / Delage, Wesley / Brin, Chrystelle / Li‐Marchetti, Camille / Sochard, Daniel / Arlat, Matthieu / Rousseau, Céline / Darrasse, Armelle / Briand, Martial / Lebreton, Guillaume / Portier, Perrine / Fischer‐Le Saux, Marion / Durand, Karine / Jacques, Marie‐Agnès / Belin, Etienne / Boureau, Tristan

    Molecular plant pathology. 2019 Jan., v. 20, no. 1

    2019  

    Abstract: Cases of emergence of novel plant‐pathogenic strains are regularly reported that reduce the yields of crops and trees. However, the molecular mechanisms underlying such emergence are still poorly understood. The acquisition by environmental non‐ ... ...

    Abstract Cases of emergence of novel plant‐pathogenic strains are regularly reported that reduce the yields of crops and trees. However, the molecular mechanisms underlying such emergence are still poorly understood. The acquisition by environmental non‐pathogenic strains of novel virulence genes by horizontal gene transfer has been suggested as a driver for the emergence of novel pathogenic strains. In this study, we tested such an hypothesis by transferring a plasmid encoding the type 3 secretion system (T3SS) and four associated type 3 secreted proteins (T3SPs) to the non‐pathogenic strains of Xanthomonas CFBP 7698 and CFBP 7700, which lack genes encoding T3SS and any previously known T3SPs. The resulting strains were phenotyped on Nicotiana benthamiana using chlorophyll fluorescence imaging and image analysis. Wild‐type, non‐pathogenic strains induced a hypersensitive response (HR)‐like necrosis, whereas strains complemented with T3SS and T3SPs suppressed this response. Such suppression depends on a functional T3SS. Amongst the T3SPs encoded on the plasmid, Hpa2, Hpa1 and, to a lesser extent, XopF1 collectively participate in suppression. Monitoring of the population sizes in planta showed that the sole acquisition of a functional T3SS by non‐pathogenic strains impairs growth inside leaf tissues. These results provide functional evidence that the acquisition via horizontal gene transfer of a T3SS and four T3SPs by environmental non‐pathogenic strains is not sufficient to make strains pathogenic. In the absence of a canonical effector, the sole acquisition of a T3SS seems to be counter‐selective, and further acquisition of type 3 effectors is probably needed to allow the emergence of novel pathogenic strains.
    Keywords Nicotiana benthamiana ; Xanthomonas ; avirulent strains ; chlorophyll ; crop yield ; genes ; horizontal gene transfer ; hypersensitive response ; image analysis ; leaves ; monitoring ; necrosis ; plasmids ; protein secretion ; tissues ; trees ; type III secretion system ; virulence ; virulent strains
    Language English
    Dates of publication 2019-01
    Size p. 33-50.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note JOURNAL ARTICLE
    ZDB-ID 2020755-4
    ISSN 1364-3703 ; 1464-6722
    ISSN (online) 1364-3703
    ISSN 1464-6722
    DOI 10.1111/mpp.12737
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  8. Article ; Online: Mutational analysis of a predicted double β-propeller domain of the DspA/E effector of Erwinia amylovora.

    Siamer, Sabrina / Gaubert, Stéphane / Boureau, Tristan / Brisset, Marie-Noëlle / Barny, Marie-Anne

    FEMS microbiology letters

    2013  Volume 342, Issue 1, Page(s) 54–61

    Abstract: The bacterium Erwinia amylovora causes fire blight, an invasive disease that threatens apple trees, pear trees and other plants of the Rosaceae family. Erwinia amylovora pathogenicity relies on a type III secretion system and on a single effector DspA/E. ...

    Abstract The bacterium Erwinia amylovora causes fire blight, an invasive disease that threatens apple trees, pear trees and other plants of the Rosaceae family. Erwinia amylovora pathogenicity relies on a type III secretion system and on a single effector DspA/E. This effector belongs to the widespread AvrE family of effectors whose biological function is unknown. In this manuscript, we performed a bioinformatic analysis of DspA/E- and AvrE-related effectors. Motif search identified nuclear localization signals, peroxisome targeting signals, endoplasmic reticulum membrane retention signals and leucine zipper motifs, but none of these motifs were present in all the AvrE-related effectors analysed. Protein threading analysis, however, predicted a conserved double β-propeller domain in the N-terminal part of all the analysed effector sequences. We then performed a random pentapeptide mutagenesis of DspA/E, which led to the characterization of 13 new altered proteins with a five amino acids insertion. Eight harboured the insertion inside the predicted β-propeller domain and six of these eight insertions impaired DspA/E stability or function. Conversely, the two remaining insertions generated proteins that were functional and abundantly secreted in the supernatant suggesting that these two insertions stabilized the protein.
    MeSH term(s) Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Computational Biology ; DNA Mutational Analysis ; Erwinia amylovora/genetics ; Erwinia amylovora/pathogenicity ; Plant Diseases/microbiology ; Protein Sorting Signals ; Protein Structure, Tertiary ; Protein Transport ; Rosaceae/microbiology ; Virulence Factors/genetics ; Virulence Factors/metabolism
    Chemical Substances Bacterial Proteins ; DspA protein, Erwinia amylovora ; Protein Sorting Signals ; Virulence Factors
    Language English
    Publishing date 2013-05
    Publishing country England
    Document type Letter
    ZDB-ID 752343-9
    ISSN 1574-6968 ; 0378-1097
    ISSN (online) 1574-6968
    ISSN 0378-1097
    DOI 10.1111/1574-6968.12108
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  9. Article ; Online: Two ancestral genes shaped the Xanthomonas campestris TAL effector gene repertoire.

    Denancé, Nicolas / Szurek, Boris / Doyle, Erin L / Lauber, Emmanuelle / Fontaine-Bodin, Lisa / Carrère, Sébastien / Guy, Endrick / Hajri, Ahmed / Cerutti, Aude / Boureau, Tristan / Poussier, Stéphane / Arlat, Matthieu / Bogdanove, Adam J / Noël, Laurent D

    The New phytologist

    2018  Volume 219, Issue 1, Page(s) 391–407

    Abstract: Xanthomonas transcription activator-like effectors (TALEs) are injected inside plant cells to promote host susceptibility by enhancing transcription of host susceptibility genes. TALE-encoding (tal) genes were thought to be absent from Brassicaceae- ... ...

    Abstract Xanthomonas transcription activator-like effectors (TALEs) are injected inside plant cells to promote host susceptibility by enhancing transcription of host susceptibility genes. TALE-encoding (tal) genes were thought to be absent from Brassicaceae-infecting Xanthomonas campestris (Xc) genomes based on four reference genomic sequences. We discovered tal genes in 26 of 49 Xc strains isolated worldwide and used a combination of single molecule real time (SMRT) and tal amplicon sequencing to yield a near-complete description of the TALEs found in Xc (Xc TALome). The 53 sequenced tal genes encode 21 distinct DNA binding domains that sort into seven major DNA binding specificities. In silico analysis of the Brassica rapa promoterome identified a repertoire of predicted TALE targets, five of which were experimentally validated using quantitative reverse transcription polymerase chain reaction. The Xc TALome shows multiple signs of DNA rearrangements that probably drove its evolution from two ancestral tal genes. We discovered that Tal12a and Tal15a of Xcc strain Xca5 contribute together in the development of disease symptoms on susceptible B. oleracea var. botrytis cv Clovis. This large and polymorphic repertoire of TALEs opens novel perspectives for elucidating TALE-mediated susceptibility of Brassicaceae to black rot disease and for understanding the molecular processes underlying TALE evolution.
    MeSH term(s) Brassica/microbiology ; Genome, Bacterial ; Host-Pathogen Interactions/genetics ; Phylogeny ; Plant Diseases/microbiology ; Transcription Activator-Like Effectors/genetics ; Xanthomonas campestris/genetics ; Xanthomonas campestris/pathogenicity
    Chemical Substances Transcription Activator-Like Effectors
    Language English
    Publishing date 2018-04-20
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 208885-x
    ISSN 1469-8137 ; 0028-646X
    ISSN (online) 1469-8137
    ISSN 0028-646X
    DOI 10.1111/nph.15148
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  10. Article: Comparative Genomics of Pathogenic and Nonpathogenic Strains of Xanthomonas arboricola Unveil Molecular and Evolutionary Events Linked to Pathoadaptation.

    Cesbron, Sophie / Briand, Martial / Essakhi, Salwa / Gironde, Sophie / Boureau, Tristan / Manceau, Charles / Fischer-Le Saux, Marion / Jacques, Marie-Agnès

    Frontiers in plant science

    2015  Volume 6, Page(s) 1126

    Abstract: The bacterial species Xanthomonas arboricola contains plant pathogenic and nonpathogenic strains. It includes the pathogen X. arboricola pv. juglandis, causing the bacterial blight of Juglans regia. The emergence of a new bacterial disease of J. regia in ...

    Abstract The bacterial species Xanthomonas arboricola contains plant pathogenic and nonpathogenic strains. It includes the pathogen X. arboricola pv. juglandis, causing the bacterial blight of Juglans regia. The emergence of a new bacterial disease of J. regia in France called vertical oozing canker (VOC) was previously described and the causal agent was identified as a distinct genetic lineage within the pathovar juglandis. Symptoms on walnut leaves and fruits are similar to those of a bacterial blight but VOC includes also cankers on trunk and branches. In this work, we used comparative genomics and physiological tests to detect differences between four X. arboricola strains isolated from walnut tree: strain CFBP 2528 causing walnut blight (WB), strain CFBP 7179 causing VOC and two nonpathogenic strains, CFBP 7634 and CFBP 7651, isolated from healthy walnut buds. Whole genome sequence comparisons revealed that pathogenic strains possess a larger and wider range of mobile genetic elements than nonpathogenic strains. One pathogenic strain, CFBP 7179, possessed a specific integrative and conjugative element (ICE) of 95 kb encoding genes involved in copper resistance, transport and regulation. The type three effector repertoire was larger in pathogenic strains than in nonpathogenic strains. Moreover, CFBP 7634 strain lacked the type three secretion system encoding genes. The flagellar system appeared incomplete and nonfunctional in the pathogenic strain CFBP 2528. Differential sets of chemoreceptor and different repertoires of genes coding adhesins were identified between pathogenic and nonpathogenic strains. Besides these differences, some strain-specific differences were also observed. Altogether, this study provides valuable insights to highlight the mechanisms involved in ecology, environment perception, plant adhesion and interaction, leading to the emergence of new strains in a dynamic environment.
    Language English
    Publishing date 2015-12-22
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2711035-7
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2015.01126
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