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

Additional files

Additional file 1:

Distribution of CDSs exclusively shared by Xanthomonas fuscans subsp. fuscans strain 4834-R (Xff 4834-R) and only one of the 15 strains used in comparative genomics. The strains, Xff 4834-R, X. fuscans subsp. aurantifolii strain ICPB10535 (Xfa ICPB10535), X. citri pv. citri strain 306 (Xac 306), X. axonopodis subsp. citrumelonis strain F1 (Xacm F1), X. euvesicatoria strain 85–10 (Xcv 85–10), X. campestris pv. musacearum strain NCPPB4381 (Xcm NCPPB4381), X. oryzae pv. oryzae strain PXO99A (Xoo PXO99A), X. oryzae pv. oryzicola strain BLS256 (Xoc BLS256), X. gardneri strain ATCC19865 (Xg ATCC19865), X. vesicatoria strain ATCC35937 (Xv ATCC35937), X. campestris pv. campestris strain ATCC33913 (Xcc ATCC33913), X. campestris pv. raphani strain 756C (Xcr 756C), Xylella fastidiosa strain Temecula1 (Xf Temecula1), Stenotrophomonas maltophilia strain R551-3 (Sm R551-3), and X. albilineans strain GPE PC73 (Xal GPE PC73), are organized according to their phylogeny represented by the Maximum Likelihood phylogenetic tree based on six housekeeping gene sequences (atpD, dnaK, efP, glnA, gyrB, rpoD). Bold line indicates that bootstrap value (1000 replicates) is 100, if not, bootstrap value of the branch is indicated on the tree. Branch length for Xf Temecula1 is 0.6 substitution per site.

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Open Data

Additional file 2:

List of the 240 unique CDSs of Xff 4834-R genome based on comparisons with the genomes of 12 other Xanthomonas spp. and two closely related organisms.

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Additional file 3:

List of putative pseudogenes and gene fragments in the genome of Xff 4834R.

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Additional file 4:

Occurrences of PIP box motifs in the genome of Xff 4834R.

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Additional file 5:

Insertion of extrachromosomal elements in Xff 4834R genome and related enzymes.

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Additional file 6:

Primers for amplification of selected flagellum genes.

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Additional file 7:

Comparative maps of the integron regions in Xcc ATCC33913 and Xff 4834-R. Are represented the integrase gene fragment intI (blue cassette), the integron-associated recombination site (attI, shown as a diamond), the pigH gene fragment (yellow cassette), several hypothetical protein encoding genes (grey cassettes), 59-base elements (be) (small square) and several insertion sequences (red cassettes). The attI and 59-be sites are white filled if their recombination site does not conform to the consensus sequence 5-GTTRRRY. Colored cassettes indicate orthologs.

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Additional file 8:

Examples of phylogenetic trees (Neighbor-joining) obtained for gene families having a putative pseudogene in Xff 4834-R: (a) XFF4834R_chr05500 is a frameshifted gene for which two overlapping peptides could be predicted and phylogenetic tree has a topology similar to that of housekeeping genes, (b) XFF4834R_25070-25100 is disrupted by ISXax1insertion (c) XFF4834R_chr25180 is a degenerated fragment of pigH, probably related to an integron insertion acquired from Xcc and (d) XFF4834R_chr33800 is a frameshifted gene for which two peptides could still be predicted.

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Additional file 9:

Primers for verification of frameshifts of selected CDSs.

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