Data from: Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges

Gordon JL, Lefeuvre P, Escalon A, Barbe V, Cruveiller S, Gagnevin L, Pruvost O

Date Published: December 28, 2015

DOI: http://dx.doi.org/10.5061/dryad.8t53k

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title Xanthomonas citri - 44 strain Mugsy genome alignment
Downloaded 13 times
Description A multiple genome alignment of 44 strains of Xanthomonas citri output from the Mugsy genome alignment software
Download Xanthomonas_citri_44_strain_Mugsy_genome_...nt.maf (232.1 Mb)
Details View File Details
Title Xanthomonas citri - 44 strain PhyML phylogeny SYM model
Downloaded 11 times
Description A maximum likelihood phylogenetic tree constructed with PhyML from the genome alignment of 44 strains of Xanthomonas citri. Regions of recombination were removed from the alignment as well as gap-containing columns and +/- 20bp from a gap-containing column. The evolutionary model used was SYM, as chosen with jModeltest 2.1.7.
Download Xanthomonas_citri_44_strain_PhyML_phyloge...el.nwk (1.686 Kb)
Details View File Details
Title Xanthomonas citri - 44 strain concatenated genome alignment (recombination, gaps +/- 20nt removed) FASTA format
Downloaded 9 times
Description A FASTA format multiple sequence alignment used for phylogenetic reconstruction. The alignment was constructed by concatenating blocks from a whole genome multiple alignment using the IAPAR 306 strain to order blocks. Regions of recombination detected using RDP were removed, as were gap-containing columns and 20 nt surrounding gap-containing columns.
Download Xanthomonas_citri_44_strain_concatenated_g...fasta (158.6 Mb)
Details View File Details
Title Xanthomonas citri - 36 strain PhyML phylogeny GTR model, Reduced A-strain distribution, Contains recombination
Downloaded 10 times
Description A maximum likelihood phylogenetic tree constructed with PhyML from the genome alignment of 36 strains of Xanthomonas citri. The alignment contains regions of recombination and the distibution of A pathotype strains is reduced to only those containing recombination Event 16. The evolutionary model used was GTR.
Download Xanthomonas_citri_36_strain_concatenated_...el.nwk (1.371 Kb)
Details View File Details
Title Xanthomonas citri - 36 strain concatenated genome alignment (gaps +/- 20nt removed) FASTA format, Contains recombination
Downloaded 11 times
Description A FASTA format multiple sequence alignment used for phylogenetic reconstruction. The alignment was constructed by concatenating blocks from a whole genome multiple alignment using the IAPAR 306 strain to order blocks. Gap-containing columns and 20 nt surrounding gap-containing columns were removed. The alignment contains regions of recombination and the distibution of A pathotype strains is reduced to only those containing recombination event 16.
Download Xanthomonas_citri_36_strain_concatenated_g...fasta (140.8 Mb)
Details View File Details

When using this data, please cite the original publication:

Gordon JL, Lefeuvre P, Escalon A, Barbe V, Cruveiller S, Gagnevin L, Pruvost O (2015) Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges. BMC Genomics 16: 1098. http://dx.doi.org/10.1186/s12864-015-2310-x

Additionally, please cite the Dryad data package:

Gordon JL, Lefeuvre P, Escalon A, Barbe V, Cruveiller S, Gagnevin L, Pruvost O (2015) Data from: Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.8t53k
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: