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For: Sallet E, Gouzy J, Schiex T. EuGene-PP: a next-generation automated annotation pipeline for prokaryotic genomes. Bioinformatics 2014;30:2659-61. [PMID: 24880686 DOI: 10.1093/bioinformatics/btu366] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
Number Cited by Other Article(s)
1
Coluzzi C, Piscon B, Dérozier S, Chiapello H, Gal-Mor O. Comparative genomics of Salmonella enterica serovars Paratyphi A, Typhi and Typhimurium reveals distinct profiles of their pangenome, mobile genetic elements, antimicrobial resistance and defense systems repertoire. Virulence 2025;16:2504658. [PMID: 40394957 PMCID: PMC12101602 DOI: 10.1080/21505594.2025.2504658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 03/05/2025] [Accepted: 05/06/2025] [Indexed: 05/22/2025]  Open
2
Lugli GA, Fontana F, Tarracchini C, Milani C, Mancabelli L, Turroni F, Ventura M. MEGAnnotator2: a pipeline for the assembly and annotation of microbial genomes. MICROBIOME RESEARCH REPORTS 2023;2:15. [PMID: 38058405 PMCID: PMC10696586 DOI: 10.20517/mrr.2022.21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/06/2023] [Accepted: 04/17/2023] [Indexed: 12/08/2023]
3
Cohen H, Hoede C, Scharte F, Coluzzi C, Cohen E, Shomer I, Mallet L, Holbert S, Serre RF, Schiex T, Virlogeux-Payant I, Grassl GA, Hensel M, Chiapello H, Gal-Mor O. Intracellular Salmonella Paratyphi A is motile and differs in the expression of flagella-chemotaxis, SPI-1 and carbon utilization pathways in comparison to intracellular S. Typhimurium. PLoS Pathog 2022;18:e1010425. [PMID: 35381053 PMCID: PMC9012535 DOI: 10.1371/journal.ppat.1010425] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 04/15/2022] [Accepted: 03/09/2022] [Indexed: 12/21/2022]  Open
4
Pichot C, Djari A, Tran J, Verdenaud M, Marande W, Huneau C, Gautier V, Latrasse D, Arribat S, Sommard V, Troadec C, Poncet C, Bendahmane M, Szecsi J, Dogimont C, Salse J, Benhamed M, Zouine M, Boualem A, Bendahmane A. Cantaloupe melon genome reveals 3D chromatin features and structural relationship with the ancestral cucurbitaceae karyotype. iScience 2022;25:103696. [PMID: 35059606 PMCID: PMC8760558 DOI: 10.1016/j.isci.2021.103696] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/01/2021] [Accepted: 12/20/2021] [Indexed: 11/21/2022]  Open
5
Hufnagel B, Soriano A, Taylor J, Divol F, Kroc M, Sanders H, Yeheyis L, Nelson M, Péret B. Pangenome of white lupin provides insights into the diversity of the species. PLANT BIOTECHNOLOGY JOURNAL 2021;19:2532-2543. [PMID: 34346542 PMCID: PMC8633493 DOI: 10.1111/pbi.13678] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/07/2021] [Accepted: 07/22/2021] [Indexed: 05/21/2023]
6
Kimbrel JA, Jeffrey BM, Ward CS. Prokaryotic Genome Annotation. Methods Mol Biol 2021;2349:193-214. [PMID: 34718997 DOI: 10.1007/978-1-0716-1585-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
7
Boivin S, Mahé F, Debellé F, Pervent M, Tancelin M, Tauzin M, Wielbo J, Mazurier S, Young P, Lepetit M. Genetic Variation in Host-Specific Competitiveness of the Symbiont Rhizobium leguminosarum Symbiovar viciae. FRONTIERS IN PLANT SCIENCE 2021;12:719987. [PMID: 34567032 PMCID: PMC8457355 DOI: 10.3389/fpls.2021.719987] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 07/29/2021] [Indexed: 05/25/2023]
8
Bradyrhizobium diazoefficiens USDA110 Nodulation of Aeschynomene afraspera Is Associated with Atypical Terminal Bacteroid Differentiation and Suboptimal Symbiotic Efficiency. mSystems 2021;6:6/3/e01237-20. [PMID: 33975972 PMCID: PMC8125078 DOI: 10.1128/msystems.01237-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]  Open
9
Boivin S, Ait Lahmidi N, Sherlock D, Bonhomme M, Dijon D, Heulin‐Gotty K, Le‐Queré A, Pervent M, Tauzin M, Carlsson G, Jensen E, Journet E, Lopez‐Bellido R, Seidenglanz M, Marinkovic J, Colella S, Brunel B, Young P, Lepetit M. Host-specific competitiveness to form nodules in Rhizobium leguminosarum symbiovar viciae. THE NEW PHYTOLOGIST 2020;226:555-568. [PMID: 31873949 PMCID: PMC7687279 DOI: 10.1111/nph.16392] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 12/09/2019] [Indexed: 05/07/2023]
10
Lacault C, Briand M, Jacques MA, Darrasse A. Zucchini Vein Clearing Disease Is Caused by Several Lineages Within Pseudomonas syringae Species Complex. PHYTOPATHOLOGY 2020;110:744-757. [PMID: 31909688 DOI: 10.1094/phyto-07-19-0266-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
11
Ferreira MASV, Bonneau S, Briand M, Cesbron S, Portier P, Darrasse A, Gama MAS, Barbosa MAG, Mariano RDLR, Souza EB, Jacques MA. Xanthomonas citri pv. viticola Affecting Grapevine in Brazil: Emergence of a Successful Monomorphic Pathogen. FRONTIERS IN PLANT SCIENCE 2019;10:489. [PMID: 31057588 PMCID: PMC6482255 DOI: 10.3389/fpls.2019.00489] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/29/2019] [Indexed: 06/09/2023]
12
Denancé N, Briand M, Gaborieau R, Gaillard S, Jacques MA. Identification of genetic relationships and subspecies signatures in Xylella fastidiosa. BMC Genomics 2019;20:239. [PMID: 30909861 PMCID: PMC6434890 DOI: 10.1186/s12864-019-5565-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 02/25/2019] [Indexed: 12/12/2022]  Open
13
EuGene: An Automated Integrative Gene Finder for Eukaryotes and Prokaryotes. Methods Mol Biol 2019;1962:97-120. [PMID: 31020556 DOI: 10.1007/978-1-4939-9173-0_6] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
14
Yu SH, Vogel J, Förstner KU. ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes. Gigascience 2018;7:5087959. [PMID: 30169674 PMCID: PMC6123526 DOI: 10.1093/gigascience/giy096] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 08/23/2018] [Indexed: 11/13/2022]  Open
15
Chen NWG, Serres-Giardi L, Ruh M, Briand M, Bonneau S, Darrasse A, Barbe V, Gagnevin L, Koebnik R, Jacques MA. Horizontal gene transfer plays a major role in the pathological convergence of Xanthomonas lineages on common bean. BMC Genomics 2018;19:606. [PMID: 30103675 PMCID: PMC6090828 DOI: 10.1186/s12864-018-4975-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 07/31/2018] [Indexed: 12/18/2022]  Open
16
López MM, Lopez-Soriano P, Garita-Cambronero J, Beltrán C, Taghouti G, Portier P, Cubero J, Fischer-Le Saux M, Marco-Noales E. Xanthomonas prunicola sp. nov., a novel pathogen that affects nectarine (Prunus persica var. nectarina) trees. Int J Syst Evol Microbiol 2018;68:1857-1866. [PMID: 29741474 DOI: 10.1099/ijsem.0.002743] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]  Open
17
Merda D, Briand M, Bosis E, Rousseau C, Portier P, Barret M, Jacques MA, Fischer-Le Saux M. Ancestral acquisitions, gene flow and multiple evolutionary trajectories of the type three secretion system and effectors in Xanthomonas plant pathogens. Mol Ecol 2017;26:5939-5952. [PMID: 28869687 PMCID: PMC7168496 DOI: 10.1111/mec.14343] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 08/03/2017] [Accepted: 08/05/2017] [Indexed: 12/13/2022]
18
Ruh M, Briand M, Bonneau S, Jacques MA, Chen NWG. Xanthomonas adaptation to common bean is associated with horizontal transfers of genes encoding TAL effectors. BMC Genomics 2017;18:670. [PMID: 28854875 PMCID: PMC5577687 DOI: 10.1186/s12864-017-4087-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 08/24/2017] [Indexed: 12/25/2022]  Open
19
Volpicella M, Leoni C, Manzari C, Chiara M, Picardi E, Piancone E, Italiano F, D'Erchia A, Trotta M, Horner DS, Pesole G, Ceci LR. Transcriptomic analysis of nickel exposure in Sphingobium sp. ba1 cells using RNA-seq. Sci Rep 2017;7:8262. [PMID: 28811613 PMCID: PMC5557971 DOI: 10.1038/s41598-017-08934-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/10/2017] [Indexed: 02/06/2023]  Open
20
Kremer FS, Eslabão MR, Dellagostin OA, Pinto LDS. Genix: a new online automated pipeline for bacterial genome annotation. FEMS Microbiol Lett 2016;363:fnw263. [DOI: 10.1093/femsle/fnw263] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/30/2016] [Accepted: 11/15/2016] [Indexed: 12/23/2022]  Open
21
López-Soriano P, Boyer K, Cesbron S, Morente MC, Peñalver J, Palacio-Bielsa A, Vernière C, López MM, Pruvost O. Multilocus Variable Number of Tandem Repeat Analysis Reveals Multiple Introductions in Spain of Xanthomonas arboricola pv. pruni, the Causal Agent of Bacterial Spot Disease of Stone Fruits and Almond. PLoS One 2016;11:e0163729. [PMID: 27669415 PMCID: PMC5036818 DOI: 10.1371/journal.pone.0163729] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 09/13/2016] [Indexed: 12/05/2022]  Open
22
Ceizel Borella G, Lagares A, Valverde C. Expression of the Sinorhizobium meliloti small RNA gene mmgR is controlled by the nitrogen source. FEMS Microbiol Lett 2016;363:fnw069. [PMID: 27010014 DOI: 10.1093/femsle/fnw069] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2016] [Indexed: 01/30/2023]  Open
23
Jacques MA, Denancé N, Legendre B, Morel E, Briand M, Mississipi S, Durand K, Olivier V, Portier P, Poliakoff F, Crouzillat D. New Coffee Plant-Infecting Xylella fastidiosa Variants Derived via Homologous Recombination. Appl Environ Microbiol 2015;82:1556-68. [PMID: 26712553 PMCID: PMC4771316 DOI: 10.1128/aem.03299-15] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 12/19/2015] [Indexed: 11/20/2022]  Open
24
Cesbron S, Briand M, Essakhi S, Gironde S, Boureau T, Manceau C, Fischer-Le Saux M, Jacques MA. Comparative Genomics of Pathogenic and Nonpathogenic Strains of Xanthomonas arboricola Unveil Molecular and Evolutionary Events Linked to Pathoadaptation. FRONTIERS IN PLANT SCIENCE 2015;6:1126. [PMID: 26734033 DOI: 10.3389/fpls.2015.01126.ecollection2015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 11/27/2015] [Indexed: 05/24/2023]
25
Whole-Genome Sequencing of 10 Pseudomonas syringae Strains Representing Different Host Range Spectra. GENOME ANNOUNCEMENTS 2015;3:3/2/e00379-15. [PMID: 25931602 PMCID: PMC4417698 DOI: 10.1128/genomea.00379-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
26
Cesbron S, Briand M, Essakhi S, Gironde S, Boureau T, Manceau C, Fischer-Le Saux M, Jacques MA. Comparative Genomics of Pathogenic and Nonpathogenic Strains of Xanthomonas arboricola Unveil Molecular and Evolutionary Events Linked to Pathoadaptation. FRONTIERS IN PLANT SCIENCE 2015;6:1126. [PMID: 26734033 PMCID: PMC4686621 DOI: 10.3389/fpls.2015.01126] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 11/27/2015] [Indexed: 05/03/2023]
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