Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/29/2006
Publication Date: 9/1/2006
Citation: Doddapaneni, H., Yao, J., Lin, H., Walker, A., Civerolo, E.L. 2006. Analysis of the genome-wide variations among multiple strains of the plant pathogenic bacterium xylella fastidiosa. Biomed Central (BMC) Genomics. Available: http://www.biomedcentral.com/1471-2164/7/225
Interpretive Summary: We categorized the genome-wide variations in the four sequenced genomes of Xylella fastidiosa strains that have direct applicability in pathogen detection and strain characterization, in understanding disease epidemiology and pathogen biology, and development of novel disease management strategies. The results are presented in a database format.
Technical Abstract: The Gram-negative, xylem-limited phytopathogenic bacterium Xylella fastidiosa is responsible for causing economically important diseases in grapevine, citrus and many other plant species. Despite its economic impact, relatively little is known about the genomic variations among strains isolated from different hosts and their influence on the population genetics of this pathogen. With the availability of genome sequence information for four strains, it is now possible to perform genome-wide analyses to identify and categorize such DNA variations and to understand their influence on strain functional divergence. There are 1,579 genes and 194 non-coding homologous sequences present in the genomes of all four strains, representing a 76. 2% conservation of the sequenced genome. About 60% of the X. fastidiosa unique sequences exist as tandem gene clusters of 6 or more genes. Multiple alignments identified 15,061 SNPs and 14,670 INDELs in coding sequences and 20,779 SNPs and 10,075 INDELs in the non-coding sequences in these conserved regions. The average SNP frequency was 1.29 × 10 e-2 per base pair of DNA and the average INDEL frequency was 3.35 × 10 e-2 per base pair of DNA. The mutation rate and INDEL frequency are closely associated, with external INDELs being the major type. The relative similarity between the strains was identified as- 9a5c+Temecula-1 > Ann1+Temecula-1 >> Dixon+Temecula-1 > Ann1+Dixon > 9a5c+Ann1 >> 9a5c+Dixon. The number of genes unique to each strain were 60 (9a5c), 54 (Dixon), 83 (Ann1) and 9 (Temecula-1). A sub-set of the strain specific genes showed significant differences in terms of their codon usage and GC composition from the native genes suggesting their xenologous origin. Tandem repeat analysis of the genomic sequences of the four strains identified associations of repeat sequences with hypothetical and phage related functions. External INDELs have been identified as the main source of genome variation among strains, with individual strains showing different rates of genome evolution. Based on these genome comparisons, it appears that the Xf-Pierce’s disease strain Temecula-1 genome represents the ancestral genome of the X. fastidiosa. Results of this analysis are publicly available in the form of a web database. http://fresno.ars.usda.gov/citrusdisease/CVC_index.htm