Open Access Research article

Genomic insights into strategies used by Xanthomonas albilineans with its reduced artillery to spread within sugarcane xylem vessels

Isabelle Pieretti1, Monique Royer1, Valérie Barbe2, Sébastien Carrere3, Ralf Koebnik4, Arnaud Couloux2, Armelle Darrasse5, Jérôme Gouzy3, Marie-Agnès Jacques5, Emmanuelle Lauber6, Charles Manceau5, Sophie Mangenot2, Stéphane Poussier7, Béatrice Segurens2, Boris Szurek4, Valérie Verdier4, Matthieu Arlat8, Dean W Gabriel9, Philippe Rott1 and Stéphane Cociancich110*

Author Affiliations

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

2 CEA/DSV/IG/Génoscope, Centre National de Séquençage, F-91057 Evry Cedex France

3 INRA, UMR LIPM, F-31326 Castanet-Tolosan Cedex France

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

5 INRA, UMR IRHS, F-49071 Beaucouzé France

6 CNRS, UMR LIPM, F-31326 Castanet-Tolosan Cedex France

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

8 Université Paul Sabatier, UMR LIPM, F-31326 Castanet-Tolosan Cedex France

9 University of Florida, Plant Pathology Department, Gainesville FL 32605 USA

10 UMR BGPI, Campus International de Baillarguet, TA A-54/K, F-34398 Montpellier Cedex 5, France

For all author emails, please log on.

BMC Genomics 2012, 13:658  doi:10.1186/1471-2164-13-658

Published: 21 November 2012

Additional files

Additional file 1:

List of proteins from X. albilineans strain GPE PC73 putatively T2SS-secreted based on SignalP 4.0 prediction [http://www.cbs.dtu.dk/services/SignalP/ webcite].

Format: XLS Size: 61KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

LPS gene cluster comparison between X. albilineans strain GPE PC73, X. campestris pv. campestris strain B100 and X. campestris pv. vasculorum strain NCPPB702. Orthologs shared by at least two species are represented by arrows with identical colours. Specific genes for each species are shown by specific and neutral colour: grey for X. campestris pv. campestris, sky blue for X. albilineans and beige for X. campestris pv. vasculorum. HP = hypothetical protein. IS = insertion sequence.

Format: PDF Size: 173KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3:

Chemotaxis gene cluster comparison between Xanthomonas species. Orthologs shared by at least two species are represented by arrows with identical colours; the length of each arrow is proportional to the length in amino acids of each ORF. Specific proteins are shown by specific colours: grey for hypothetical protein, black for IS element or transposases, all other colours except pink for Methyl-accepting proteins and pink for other chemotaxis proteins.

Format: PDF Size: 244KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4:

List of two-component signal transduction system identified in the genome of strain GPE PC73 of X. albilineans . Two-component system regulatory proteins (I), two-component system sensor proteins (II) and two-component system sensor-response regulator hybrid proteins (III) are listed.

Format: XLS Size: 34KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 5:

List of transposases found in the chromosome of the strain GPE PC73 of X. albilineans. The ORFs named “ISXal” are specific to X. albilineans. However, the recent publication of the complete genome sequence of X. oryzae pv. oryzicola revealed that XALc_2324, XALc_2365, XALc_2622 and XALc_2931, corresponding to ISXal5, ISXal7 and ISXal9 in X. albilineans strain GPE PC73, showed similarities with transposases found in the strain BLS256 of X. oryzae pv. oryzicola.

Format: XLS Size: 28KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 6:

CRISPR-1 and CRISPR-2 spacer distribution in X. albilineans strain GPE PC73. Each box represents a CRISPR spacer, with the spacer positions numbered inside each box from the trailer end spacer to the leader end spacer. Pink boxes = CRISPR-1 spacers. Green boxes = CRISPR-2 spacers. Spacers showing nucleic acid identity with sequences of strain GPE PC73 of X. albilineans are listed in three separated tables according to the origin of these sequences (a same prophage region located between XALc_0170 to XALc_0242, phage and plasmid sequences and a housekeeping gene, respectively). Some spacers are 100% identical to corresponding sequences of strain GPE PC73 of X. albilineans. Percentage value is indicated in brackets only for spacers for which the percentage identity is less than 100%.

Format: PDF Size: 126KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data