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Open Access Research article

Analysis of the genome-wide variations among multiple strains of the plant pathogenic bacterium Xylella fastidiosa

Harshavardhan Doddapaneni1, Jiqiang Yao2, Hong Lin3, M Andrew Walker1 and Edwin L Civerolo3*

Author Affiliations

1 University of California Davis, Department of Viticulture and Enology, Davis, CA 95616, USA

2 Citrus Research Board, 323 W. Oak, P.O. Box 230, Visalia, CA 93279, USA

3 USDA-ARS. San Joaquin Valley Agricultural Science Center, 9611 So. Riverbend Ave. Parlier, CA 93648, USA

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BMC Genomics 2006, 7:225  doi:10.1186/1471-2164-7-225

Published: 1 September 2006

Additional files

Additional File 1:

Conserved unique gene sequences. List of X. fastidiosa conserved unique genes.

Format: XLS Size: 43KB Download file

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Additional file 2:

Pair wise analysis of conserved genes with internal INDELs that cause frame shifts. List of conserved genes causing frame shift mutations.

Format: XLS Size: 42KB Download file

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Additional file 3:

Highly conserved genes. List of highly conserved genes among the four sequenced X. fastidiosa strains.

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Additional file 4:

Unique gene clusters in strain 9a5c. List of gene clusters that are unique to strain 9a5c.

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Additional file 5:

Unique gene clusters in strain Temecula-1. List on gene clusters that are unique to strain Temecula-1.

Format: XLS Size: 16KB Download file

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Additional file 6:

Codon usage analysis. Codon usage analysis of the native and putative xenologues (marked by a colon before the gene name) for 9a5c (6), Ann1 (7) and Dixon (8) strains. Support trees were generated for the hierarchical clusters using the TMEV software with 1000 bootstrap samples.

Format: JPEG Size: 1023KB Download file

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Additional file 7:

Codon usage analysis. Codon usage analysis of the native and putative xenologues (marked by a colon before the gene name) for 9a5c (6), Ann1 (7) and Dixon (8) strains. Support trees were generated for the hierarchical clusters using the TMEV software with 1000 bootstrap samples.

Format: JPEG Size: 844KB Download file

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Additional file 8:

Codon usage analysis. Codon usage analysis of the native and putative xenologues (marked by a colon before the gene name) for 9a5c (6), Ann1 (7) and Dixon (8) strains. Support trees were generated for the hierarchical clusters using the TMEV software with 1000 bootstrap samples.

Format: JPEG Size: 491KB Download file

Open Data

Additional file 9:

Relative neutrality plots. Relative neutrality plots for native and putative xenologues gene groups in the four X. fastidiosa strains. GC12 values are plotted as a function of the GC3 value and the slope of the correlation was determined.

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