Analysis of the genome-wide variations among multiple strains of the plant pathogenic bacterium <it>Xylella fastidiosa</it>
<p>Abstract</p> <p>Background</p> <p>The Gram-negative, xylem-limited phytopathogenic bacterium <it>Xylella fastidiosa </it>is responsible for causing economically important diseases in grapevine, citrus and many other plant species. Despite its economic imp...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2006-09-01
|
| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/7/225 |
| _version_ | 1818701897607938048 |
|---|---|
| author | Walker M Andrew Lin Hong Yao Jiqiang Doddapaneni Harshavardhan Civerolo Edwin L |
| author_facet | Walker M Andrew Lin Hong Yao Jiqiang Doddapaneni Harshavardhan Civerolo Edwin L |
| author_sort | Walker M Andrew |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>The Gram-negative, xylem-limited phytopathogenic bacterium <it>Xylella fastidiosa </it>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.</p> <p>Results</p> <p>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 <it>X. fastidiosa </it>unique sequences exist as tandem gene clusters of 6 or more genes. Multiple alignments identified 12,754 SNPs and 14,449 INDELs in the 1528 common genes and 20,779 SNPs and 10,075 INDELs in the 194 non-coding sequences. The average SNP frequency was 1.08 × 10<sup>-2 </sup>per base pair of DNA and the average INDEL frequency was 2.06 × 10<sup>-2 </sup>per base pair of DNA. On an average, 60.33% of the SNPs were synonymous type while 39.67% were non-synonymous type. The mutation frequency, primarily in the form of external INDELs was the main type of sequence variation. The relative similarity between the strains was discussed according to the INDEL and SNP differences. 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.</p> <p>Conclusion</p> <p>INDELs and strain specific genes have been identified as the main source of variations among strains, with individual strains showing different rates of genome evolution. Based on these genome comparisons, it appears that the Pierce's disease strain Temecula-1 genome represents the ancestral genome of the <it>X. fastidiosa</it>. Results of this analysis are publicly available in the form of a web database.</p> |
| first_indexed | 2024-12-17T15:28:08Z |
| format | Article |
| id | doaj.art-02d63f0fe75c46189b1c4f703d810bd8 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-17T15:28:08Z |
| publishDate | 2006-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-02d63f0fe75c46189b1c4f703d810bd82022-12-21T21:43:14ZengBMCBMC Genomics1471-21642006-09-017122510.1186/1471-2164-7-225Analysis of the genome-wide variations among multiple strains of the plant pathogenic bacterium <it>Xylella fastidiosa</it>Walker M AndrewLin HongYao JiqiangDoddapaneni HarshavardhanCiverolo Edwin L<p>Abstract</p> <p>Background</p> <p>The Gram-negative, xylem-limited phytopathogenic bacterium <it>Xylella fastidiosa </it>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.</p> <p>Results</p> <p>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 <it>X. fastidiosa </it>unique sequences exist as tandem gene clusters of 6 or more genes. Multiple alignments identified 12,754 SNPs and 14,449 INDELs in the 1528 common genes and 20,779 SNPs and 10,075 INDELs in the 194 non-coding sequences. The average SNP frequency was 1.08 × 10<sup>-2 </sup>per base pair of DNA and the average INDEL frequency was 2.06 × 10<sup>-2 </sup>per base pair of DNA. On an average, 60.33% of the SNPs were synonymous type while 39.67% were non-synonymous type. The mutation frequency, primarily in the form of external INDELs was the main type of sequence variation. The relative similarity between the strains was discussed according to the INDEL and SNP differences. 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.</p> <p>Conclusion</p> <p>INDELs and strain specific genes have been identified as the main source of variations among strains, with individual strains showing different rates of genome evolution. Based on these genome comparisons, it appears that the Pierce's disease strain Temecula-1 genome represents the ancestral genome of the <it>X. fastidiosa</it>. Results of this analysis are publicly available in the form of a web database.</p>http://www.biomedcentral.com/1471-2164/7/225 |
| spellingShingle | Walker M Andrew Lin Hong Yao Jiqiang Doddapaneni Harshavardhan Civerolo Edwin L Analysis of the genome-wide variations among multiple strains of the plant pathogenic bacterium <it>Xylella fastidiosa</it> BMC Genomics |
| title | Analysis of the genome-wide variations among multiple strains of the plant pathogenic bacterium <it>Xylella fastidiosa</it> |
| title_full | Analysis of the genome-wide variations among multiple strains of the plant pathogenic bacterium <it>Xylella fastidiosa</it> |
| title_fullStr | Analysis of the genome-wide variations among multiple strains of the plant pathogenic bacterium <it>Xylella fastidiosa</it> |
| title_full_unstemmed | Analysis of the genome-wide variations among multiple strains of the plant pathogenic bacterium <it>Xylella fastidiosa</it> |
| title_short | Analysis of the genome-wide variations among multiple strains of the plant pathogenic bacterium <it>Xylella fastidiosa</it> |
| title_sort | analysis of the genome wide variations among multiple strains of the plant pathogenic bacterium it xylella fastidiosa it |
| url | http://www.biomedcentral.com/1471-2164/7/225 |
| work_keys_str_mv | AT walkermandrew analysisofthegenomewidevariationsamongmultiplestrainsoftheplantpathogenicbacteriumitxylellafastidiosait AT linhong analysisofthegenomewidevariationsamongmultiplestrainsoftheplantpathogenicbacteriumitxylellafastidiosait AT yaojiqiang analysisofthegenomewidevariationsamongmultiplestrainsoftheplantpathogenicbacteriumitxylellafastidiosait AT doddapaneniharshavardhan analysisofthegenomewidevariationsamongmultiplestrainsoftheplantpathogenicbacteriumitxylellafastidiosait AT civeroloedwinl analysisofthegenomewidevariationsamongmultiplestrainsoftheplantpathogenicbacteriumitxylellafastidiosait |