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Open Access Highly Accessed Research article

Genome sequence of Xanthomonas fuscans subsp. fuscans strain 4834-R reveals that flagellar motility is not a general feature of xanthomonads

Armelle Darrasse123, Sébastien Carrère45, Valérie Barbe6, Tristan Boureau123, Mario L Arrieta-Ortiz147, Sophie Bonneau123, Martial Briand123, Chrystelle Brin123, Stéphane Cociancich8, Karine Durand123, Stéphanie Fouteau6, Lionel Gagnevin109, Fabien Guérin109, Endrick Guy45, Arnaud Indiana123, Ralf Koebnik11, Emmanuelle Lauber45, Alejandra Munoz7, Laurent D Noël45, Isabelle Pieretti8, Stéphane Poussier11023, Olivier Pruvost109, Isabelle Robène-Soustrade109, Philippe Rott8, Monique Royer8, Laurana Serres-Giardi123, Boris Szurek11, Marie-Anne van Sluys12, Valérie Verdier11, Christian Vernière109, Matthieu Arlat1345, Charles Manceau11523 and Marie-Agnès Jacques123*

Author Affiliations

1 INRA, UMR1345 Institut de Recherche en Horticulture et Semences, F-49071, Beaucouzé, France

2 AGROCAMPUS OUEST, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045, Angers, France

3 Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, F-49045, Angers, France

4 INRA, LIPM UMR 441, F-31326, Castanet-Tolosan, France

5 CNRS, LIPM UMR 2594, F-31326, Castanet-Tolosan, France

6 CEA, Genoscope, Centre National de Séquençage, F-91057, Evry Cedex, France

7 Universidad de Los Andes, Laboratorio de Micología y Fitopatología Uniandes, Bogotá, Colombia

8 CIRAD, UMR BGPI, F-34398, Montpellier Cedex 5, France

9 CIRAD, UMR PVBMT, F-97410, Saint-Pierre, La Réunion, France

10 Université de la Réunion, UMR PVBMT, F-97715, Saint-Denis, La Réunion, France

11 IRD, UMR RPB, F-34394, Montpellier Cedex 5, France

12 GaTE Lab Botanica IBUSP 277 05508-900, São Paulo, SP, Brasil

13 Université de Toulouse, Université Paul Sabatier, UMR LIPM, F-31326, Castanet-Tolosan Cedex, France

14 current address: Department of Biology, Center for Genomics and Systems Biology, New York University, 10003, New York, NY, USA

15 current address: ANSES, Laboratoire de Santé des végétaux, F-49044, Angers, France

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BMC Genomics 2013, 14:761  doi:10.1186/1471-2164-14-761

Published: 6 November 2013



Xanthomonads are plant-associated bacteria responsible for diseases on economically important crops. Xanthomonas fuscans subsp. fuscans (Xff) is one of the causal agents of common bacterial blight of bean. In this study, the complete genome sequence of strain Xff 4834-R was determined and compared to other Xanthomonas genome sequences.


Comparative genomics analyses revealed core characteristics shared between Xff 4834-R and other xanthomonads including chemotaxis elements, two-component systems, TonB-dependent transporters, secretion systems (from T1SS to T6SS) and multiple effectors. For instance a repertoire of 29 Type 3 Effectors (T3Es) with two Transcription Activator-Like Effectors was predicted. Mobile elements were associated with major modifications in the genome structure and gene content in comparison to other Xanthomonas genomes. Notably, a deletion of 33 kbp affects flagellum biosynthesis in Xff 4834-R. The presence of a complete flagellar cluster was assessed in a collection of more than 300 strains representing different species and pathovars of Xanthomonas. Five percent of the tested strains presented a deletion in the flagellar cluster and were non-motile. Moreover, half of the Xff strains isolated from the same epidemic than 4834-R was non-motile and this ratio was conserved in the strains colonizing the next bean seed generations.


This work describes the first genome of a Xanthomonas strain pathogenic on bean and reports the existence of non-motile xanthomonads belonging to different species and pathovars. Isolation of such Xff variants from a natural epidemic may suggest that flagellar motility is not a key function for in planta fitness.

Seed-borne pathogen; Secretion system; Insertion sequence; Bean; Effector; Chemotaxis; Pseudogene