Open Access Highly Accessed Research article

Genome sequence reveals that Pseudomonas fluorescens F113 possesses a large and diverse array of systems for rhizosphere function and host interaction

Miguel Redondo-Nieto1, Matthieu Barret23, John Morrissey3, Kieran Germaine4, Francisco Martínez-Granero1, Emma Barahona1, Ana Navazo1, María Sánchez-Contreras1, Jennifer A Moynihan23, Candela Muriel1, David Dowling4, Fergal O’Gara23, Marta Martín1 and Rafael Rivilla1*

Author Affiliations

1 Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, c/Darwin, 2, Madrid, 28049, Spain

2 BIOMERIT Research Centre, Microbiology Department, University College Cork, Cork, Ireland

3 Microbiology Department, Food Science Building, University College Cork, Cork, Ireland

4 Institute of Technology, Carlow, Ireland

For all author emails, please log on.

BMC Genomics 2013, 14:54  doi:10.1186/1471-2164-14-54

Published: 25 January 2013

Additional files

Additional file 1:

Characteristics of sequenced genomes from the P. fluorescens group (as of 20-11-2012).

Format: PDF Size: 150KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

Physical map of the Pseudomonas fluorescens F113 genome. Arrows in the outer circles show CDS (in green), tRNA (in red) and rRNA (in yellow). Gene clusters described in the article are highlighted in the map. Center circle shows G/C% distribution.

Format: PDF Size: 8.7MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3:

List of F113 CDSs that are not present or are below the threshold to be considered as orthologous in other strains belonging to the P. fluorescens Subgroup I. Closest homologues are included in the Table.

Format: PDF Size: 811KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4:

Distribution of denitrification pathway in strains belonging to the P. fluorescens group.

Format: PDF Size: 333KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 5:

Distribution of chemotaxis systems in strains belonging to theP. fluorescensgroup.

Format: PDF Size: 333KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 6:

Repertoire of T2SSs, T3SSs and T6SSs in the Pseudomonas genus.

Format: XLSX Size: 24KB Download file

Open Data

Additional file 7:

Phylogenetic distribution of T2SSs within Pseudomonas species. A distance tree (Maximum-Likelihood) was calculated from 200 XcpR-like proteins of Pseudomonas spp. T2SSs of Pseudomonas spp. can be divided in two distinct phylogenetic clusters: Xcp and Hxc highlighted in red and blue, respectively. The XcpR-like proteins related to the Hpl cluster are used as out group. Genes of P. fluorescens F113 encoding potential T2SSs are represented as block arrows showing the direction of their transcription. Numbers represented the PSF113 locus IDs. Black arrows represented genes encoding the T2S machinery, whereas grey arrows represented gene encoding protein with unknown function. White arrows represented genes encoding putative T2SS-substrates.

Format: PDF Size: 570KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 8:

Phylogenetic distribution of T3SSs within Pseudomonas species. A distance tree (Maximum-Likelihood) was calculated from 146 HrcV-like proteins of Pseudomonas spp. Green, orange, and blue labels indicate HrcV-like proteins related to Hrp1, SPI-1, Rhizobiales, and Ysc systems, respectively. Genes of P. fluorescens F113 encoding T3SSs are represented as block arrows showing the direction of their transcription. Numbers represented the PSF113 locus IDs. Black arrows represented genes encoding the T3S machinery, whereas grey arrows represented gene encoding protein with unknown function. White arrows represented genes encoding putative T3SS-substrates and chaperones.

Format: PDF Size: 652KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 9:

GC content analysis of the SPI-1 clusters encoded in different strains belonging to the Pseudomonas genus. Asterisks indicate that the SPI-1 cluster is located on two different scaffolds.

Format: XLSX Size: 10KB Download file

Open Data

Additional file 10:

Phylogenetic distribution of T6SSs within Pseudomonas species. A distance tree (Maximum-Likelihood) was calculated from 345 IglA proteins of Pseudomonas spp. T6SSs of Pseudomonas spp. can be divided into five mains clusters (1, 2, 3, 4A and 4B) highlighted in red, yellow, green, blue and purple, respectively. Genes of P. fluorescens F113 encoding T6SSs are represented as block arrows showing the direction of their transcription. Numbers represented the PSF113 locus IDs. Black arrows represented genes encoding the T6S machinery, whereas grey arrows represented gene encoding protein with unknown function.

Format: PDF Size: 603KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data