Publications by authors named "Jérémy Cigna"

12 Publications

  • Page 1 of 1

European Population of : Genomic Diversity, Tuber Maceration Capacity and a Detection Tool for This Rarely Occurring Potato Pathogen.

Microorganisms 2021 Apr 8;9(4). Epub 2021 Apr 8.

French Federation of Seed Potato Growers (FN3PT-inov3PT), 43-45 Rue de Naples, 75008 Paris, France.

Enterobacteria belonging to the and genera are responsible for soft rot and blackleg diseases occurring in many crops around the world. Since 2016, the number of described species has more than doubled. However, some new species, such as , are often poorly characterized, and little is known about their genomic and phenotypic variation. Here, we explored several European culture collections and identified seven strains of All were collected from potato blackleg symptoms, sometimes from a long time ago, i.e., the IFB5596 strain isolated almost 25 years ago. We showed that this species remains rare, with less than 0.24% of strains identified among pectinolytic bacteria present in the surveyed collections. The analysis of the genomic diversity revealed the non-clonal character of species. Furthermore, the strains showed aggressiveness differences. Finally, a qPCR Taqman assay was developed for rapid and specific strain characterization and for use in diagnostic programs.
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http://dx.doi.org/10.3390/microorganisms9040781DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8068253PMC
April 2021

Pattern and causes of the establishment of the invasive bacterial potato pathogen Dickeya solani and of the maintenance of the resident pathogen D. dianthicola.

Mol Ecol 2021 01 4;30(2):608-624. Epub 2020 Dec 4.

Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Paris-Saclay University, Gif-sur-Yvette, France.

Invasive pathogens can be a threat when they affect human health, food production or ecosystem services, by displacing resident species, and we need to understand the cause of their establishment. We studied the patterns and causes of the establishment of the pathogen Dickeya solani that recently invaded potato agrosystems in Europe by assessing its invasion dynamics and its competitive ability against the closely related resident D. dianthicola species. Epidemiological records over one decade in France revealed the establishment of D. solani and the maintenance of the resident D. dianthicola in potato fields exhibiting blackleg symptoms. Using experimentations, we showed that D. dianthicola caused a higher symptom incidence on aerial parts of potato plants than D. solani, while D. solani was more aggressive on tubers (i.e. with more severe symptoms). In co-infection assays, D. dianthicola outcompeted D. solani in aerial parts, while the two species co-existed in tubers. A comparison of 76 D. solani genomes (56 of which have been sequenced here) revealed balanced frequencies of two previously uncharacterized alleles, VfmB and VfmB , at the vfmB virulence gene. Experimental inoculations showed that the VfmB population was more aggressive on tubers, while the VfmB population outcompeted the VfmB population in stem lesions, suggesting an important role of the vfmB virulence gene in the ecology of the pathogens. This study thus brings novel insights allowing a better understanding of the pattern and causes of the D.solani invasion into potato production agrosystems, and the reasons why the endemic D. dianthicola nevertheless persisted.
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http://dx.doi.org/10.1111/mec.15751DOI Listing
January 2021

Complete Genome Sequence of the Type Strain Pectobacterium punjabense SS95, Isolated from a Potato Plant with Blackleg Symptoms.

Microbiol Resour Announc 2020 Aug 6;9(32). Epub 2020 Aug 6.

Institute for Integrative Biology of the Cell (I2BC), CEA CNRS University Paris-Saclay, Gif-sur-Yvette, France

is a newly described species causing blackleg disease in potato plants. Therefore, by the combination of long (Oxford Nanopore Technologies, MinION) and short (Illumina MiSeq) reads, we sequenced the complete genome of SS95, which contains a circular chromosome of 4.793 Mb with a GC content of 50.7%.
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http://dx.doi.org/10.1128/MRA.00420-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7409842PMC
August 2020

Dickeya undicola sp. nov., a novel species for pectinolytic isolates from surface waters in Europe and Asia.

Int J Syst Evol Microbiol 2019 Aug 5;69(8):2440-2444. Epub 2019 Jun 5.

Institute for Integrative Biology of the Cell (I2BC), CEA CNRS Univ. Paris-Sud, University Paris-Saclay, 91 190 Gif-sur-Yvette, France.

Strains 2B12, FVG1-MFV-O17 and FVG10-MFV-A16 were isolated from fresh water samples collected in Asia and Europe. The nucleotide sequences of the gapA barcodes revealed that all three strains belonged to the same cluster within the genus Dickeya. Using 13 housekeeping genes (fusA, rpoD, rpoS, glyA, purA, groEL, gapA, rplB, leuS, recA, gyrB, infB and secY), multilocus sequence analysis confirmed the existence of a new clade. When the genome sequences of these three isolates and other Dickeya species were compared, the in silico DNA-DNA hybridization and average nucleotide identity values were found to be no more than 45.50 and 91.22 %, respectively. The closest relative species was Dickeya fangzhongdai. Genome comparisons also highlighted genetic traits differentiating the new strains from D. fangzhongdai strains DSM 101947 (=CFBP 8607) and B16. Phenotypical tests were performed to distinguish the three strains from D. fangzhongdai and other Dickeya species. The name Dickeya undicola sp. nov. is proposed with strain 2B12 (=CFBP 8650=LMG 30903) as the type strain.
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http://dx.doi.org/10.1099/ijsem.0.003497DOI Listing
August 2019

Transfer of the waterfall source isolate Pectobacterium carotovorum M022 to Pectobacterium fontis sp. nov., a deep-branching species within the genus Pectobacterium.

Int J Syst Evol Microbiol 2019 Feb 2;69(2):470-475. Epub 2019 Jan 2.

1​Institute for Integrative Biology of the Cell (I2BC), CEA CNRS Univ. Paris-Sud, University Paris-Saclay, 91198 Gif-sur-Yvette, France.

Pectobacterium carotovorum M022 has been isolated from a waterfall source in Selangor district (Malaysia). Using genomic and phenotypic tests, we re-examined the taxonomical position of this strain. Based on 14 concatenated housekeeping genes (fusA, rpoD, rpoS, acnA, purA, gyrB, recA, mdh, mtlD, groEL, secY, glyA, gapA and rplB), multi-locus sequence analysis revealed that strain M022 falls into a novel clade separated from the other Pectobacterium species. The in silico DNA-DNA hybridization and average nucleotide identity values were lower than the 70 and 95 % threshold values, respectively. In addition, by combining genomic and phenotypic tests, strain M022 may be distinguished from the other Pectobacterium isolates by its incapacity to grow on d(+)-xylose, l-rhamnose, cellobiose and lactose. Strain M022 (=CFBP 8629=LMG 30744) is proposed as the type strain of the Pectobacteriumfontis sp. nov.
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http://dx.doi.org/10.1099/ijsem.0.003180DOI Listing
February 2019

Pectobacterium punjabense sp. nov., isolated from blackleg symptoms of potato plants in Pakistan.

Int J Syst Evol Microbiol 2018 Nov 21;68(11):3551-3556. Epub 2018 Sep 21.

2​Institute for Integrative Biology of the Cell (I2BC), CEA CNRS Univ. Paris-Sud, University Paris-Saclay, 91198 Gif-sur-Yvette, France.

Pectobacterium isolates SS95, SS54 and SS56 were collected from a potato field in the Chiniot district in the plains of the Punjab province, Pakistan. Sequencing of the gapA barcode revealed that these strains belong to a novel phylogenetic group separated from P.ectobacterium wasabiae and Pectobacterium parmentieri species. Furthermore, multilocus sequence analyses of 13 housekeeping genes (fusA, rpoD, acnA, purA, gyrB, recA, mdh, mtlD, groEL, secY, glyA, gapA and rplB) clearly distinguished the type strain, SS95, from its closest relatives, i.e. P. parmentieri RNS 08-42-1A and P. wasabiae CFBP3304, as well as from all the other known Pectobacteriumspecies. In silico DNA-DNA hybridization (<44.1 %) and average nucleotide identity (<90.75 %) values of strain SS95 compared with other Pectobacterium type strains supported the delineation of a new species. Genomic and phenotypic comparisons permitted the identification of additional traits that distinguished the Pakistani isolates from all other known Pectobacterium type strains. The name Pectobacterium punjabense sp. nov. is proposed for this taxon with the type strain SS95 (=CFBP 8604=LMG 30622).
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http://dx.doi.org/10.1099/ijsem.0.003029DOI Listing
November 2018

A gapA PCR-sequencing Assay for Identifying the Dickeya and Pectobacterium Potato Pathogens.

Plant Dis 2017 Jul 3;101(7):1278-1282. Epub 2017 May 3.

Institute for Integrative Biology of the Cell, CNRS CEA Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France.

Several pectinolytic Pectobacterium and Dickeya species and subspecies are causative agents of blackleg and soft rot diseases on potato plants and tubers. Rapid and accurate identification of these taxa is a crucial issue for the production and international trade of potato seed-tubers. Here, we developed a PCR-sequencing tool to easily characterize the different Pectobacterium and Dickeya taxa. The gapA gene sequences from 53 published genomes were aligned and a phylogeny tree was constructed. A set of 35 signature nucleotides was discovered to distinguish the Pectobacterium and Dickeya genera, species, and subspecies. Then, a PCR-primer couple was designed for amplifying the gapA gene in pectinolytic enterobacteria. The primers were tested on 22 isolates recovered from blackleg symptoms in several potato fields. Amplicons were sequenced and signature-nucleotides were analyzed. A phylogeny that includes gapA sequence specimens confirmed the taxonomical identification of these environmental isolates.
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http://dx.doi.org/10.1094/PDIS-12-16-1810-REDOI Listing
July 2017

Transfer of the potato plant isolates of Pectobacterium wasabiae to Pectobacterium parmentieri sp. nov.

Int J Syst Evol Microbiol 2016 Dec 26;66(12):5379-5383. Epub 2016 Sep 26.

Institute of Integrative Biology of the Cell (I2BC), CEA CNRS Univ. Paris-Sud, University Paris-Saclay, 91198 Gif-sur-Yvette, France.

Pectobacterium wasabiae was originally isolated from Japanese horseradish (Eutrema wasabi), but recently some Pectobacterium isolates collected from potato plants and tubers displaying blackleg and soft rot symptoms were also assigned to P. wasabiae. Here, combining genomic and phenotypical data, we re-evaluated their taxonomic position. PacBio and Illumina technologies were used to complete the genome sequences of P. wasabiae CFBP 3304T and RNS 08-42-1A. Multi-locus sequence analysis showed that the P. wasabiae strains RNS 08-42-1A, SCC3193, CFIA1002 and WPP163, which were collected from potato plant environment, constituted a separate clade from the original Japanese horseradish P. wasabiae. The taxonomic position of these strains was also supported by calculation of the in-silico DNA-DNA hybridization, genome average nucleotide indentity, alignment fraction and average nucleotide indentity values. In addition, they were phenotypically distinguished from P. wasabiae strains by producing acids from (+)-raffinose, α-d(+)-α-lactose, d(+)-galactose and (+)-melibiose but not from methyl α-d-glycopyranoside, (+)-maltose or malonic acid. The name Pectobacterium parmentieri sp. nov. is proposed for this taxon; the type strain is RNS 08-42-1AT (=CFBP 8475T=LMG 29774T).
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http://dx.doi.org/10.1099/ijsem.0.001524DOI Listing
December 2016

Biocontrol of the Potato Blackleg and Soft Rot Diseases Caused by Dickeya dianthicola.

Appl Environ Microbiol 2016 01 23;82(1):268-78. Epub 2015 Oct 23.

Institute for Integrative Biology of the Cell, CNRS CEA Université Paris-Sud, Université Paris-Saclay, Saclay Plant Sciences, Gif-sur-Yvette, France

Development of protection tools targeting Dickeya species is an important issue in the potato production. Here, we present the identification and the characterization of novel biocontrol agents. Successive screenings of 10,000 bacterial isolates led us to retain 58 strains that exhibited growth inhibition properties against several Dickeya sp. and/or Pectobacterium sp. pathogens. Most of them belonged to the Pseudomonas and Bacillus genera. In vitro assays revealed a fitness decrease of the tested Dickeya sp. and Pectobacterium sp. pathogens in the presence of the biocontrol agents. In addition, four independent greenhouse assays performed to evaluate the biocontrol bacteria effect on potato plants artificially contaminated with Dickeya dianthicola revealed that a mix of three biocontrol agents, namely, Pseudomonas putida PA14H7 and Pseudomonas fluorescens PA3G8 and PA4C2, repeatedly decreased the severity of blackleg symptoms as well as the transmission of D. dianthicola to the tuber progeny. This work highlights the use of a combination of biocontrol strains as a potential strategy to limit the soft rot and blackleg diseases caused by D. dianthicola on potato plants and tubers.
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http://dx.doi.org/10.1128/AEM.02525-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702623PMC
January 2016

Draft Genome Sequences of Pseudomonas fluorescens Strains PA4C2 and PA3G8 and Pseudomonas putida PA14H7, Three Biocontrol Bacteria against Dickeya Phytopathogens.

Genome Announc 2015 Jan 29;3(1). Epub 2015 Jan 29.

CNRS, Institut des Sciences du Végétal, UPR2355, Saclay Plant Sciences, Gif-sur-Yvette, France

Pseudomonas fluorescens strains PA4C2 and PA3G8 and Pseudomonas putida strain PA14H7 were isolated from potato rhizosphere and show an ability to inhibit the growth of Dickeya phytopathogens. Here, we report their draft genome sequences, which provide a basis for understanding the molecular mechanisms involved in antibiosis against Dickeya.
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http://dx.doi.org/10.1128/genomeA.01503-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4319517PMC
January 2015

Highly local environmental variability promotes intrapopulation divergence of quantitative traits: an example from tropical rain forest trees.

Ann Bot 2013 Oct 10;112(6):1169-79. Epub 2013 Sep 10.

INRA, UMR 'Ecologie des Forêts de Guyane', Campus agronomique, BP 709, 97387 Kourou cedex, French Guiana.

Background And Aims: In habitat mosaics, plant populations face environmental heterogeneity over short geographical distances. Such steep environmental gradients can induce ecological divergence. Lowland rainforests of the Guiana Shield are characterized by sharp, short-distance environmental variations related to topography and soil characteristics (from waterlogged bottomlands on hydromorphic soils to well-drained terra firme on ferralitic soils). Continuous plant populations distributed along such gradients are an interesting system to study intrapopulation divergence at highly local scales. This study tested (1) whether conspecific populations growing in different habitats diverge at functional traits, and (2) whether they diverge in the same way as congeneric species having different habitat preferences.

Methods: Phenotypic differentiation was studied within continuous populations occupying different habitats for two congeneric, sympatric, and ecologically divergent tree species (Eperua falcata and E. grandiflora, Fabaceae). Over 3000 seeds collected from three habitats were germinated and grown in a common garden experiment, and 23 morphological, biomass, resource allocation and physiological traits were measured.

Key Results: In both species, seedling populations native of different habitats displayed phenotypic divergence for several traits (including seedling growth, biomass allocation, leaf chemistry, photosynthesis and carbon isotope composition). This may occur through heritable genetic variation or other maternally inherited effects. For a sub-set of traits, the intraspecific divergence associated with environmental variation coincided with interspecific divergence.

Conclusions: The results indicate that mother trees from different habitats transmit divergent trait values to their progeny, and suggest that local environmental variation selects for different trait optima even at a very local spatial scale. Traits for which differentiation within species follows the same pattern as differentiation between species indicate that the same ecological processes underlie intra- and interspecific variation.
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http://dx.doi.org/10.1093/aob/mct176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3783240PMC
October 2013

Atlas of genetics and cytogenetics in oncology and haematology in 2013.

Nucleic Acids Res 2013 Jan 17;41(Database issue):D920-4. Epub 2012 Nov 17.

'Atlas in Poitiers Editorial Group', University and Hospital of Poitiers, INSERM U 935, 86021 Poitiers, France.

The Atlas of Genetics and Cytogenetics in Oncology and Haematology (http://AtlasGeneticsOncology.org) is a peer-reviewed internet journal/encyclopaedia/database focused on genes implicated in cancer, cytogenetics and clinical entities in cancer and cancer-prone hereditary diseases. The main goal of the Atlas is to provide review articles that describe complementary topics, namely, genes, genetic abnormalities, histopathology, clinical diagnoses and a large iconography. This description, which was historically based on karyotypic abnormalities and in situ hybridization (fluorescence in situ hybridization) techniques, now benefits from comparative genomic hybridization and massive sequencing, uncovering a tremendous amount of genetic rearrangements. As the Atlas combines different types of information (genes, genetic abnormalities, histopathology, clinical diagnoses and external links), its content is currently unique. The Atlas is a cognitive tool for fundamental and clinical research and has developed into an encyclopaedic work. In clinical practice, it contributes to the cytogenetic diagnosis and may guide treatment decision making, particularly regarding rare diseases (because they are numerous and are frequently encountered). Readers as well as the authors of the Atlas are researchers and/or clinicians.
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http://dx.doi.org/10.1093/nar/gks1082DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531131PMC
January 2013