Comparative Analyses of the Complete Genome Sequences of Pierce's Disease and Citrus Variegated Chlorosis Strains of Xylella fastidiosa
ABSTRACT
MATERIALS AND METHODS
Genome sequence and assembly.
Genome annotation and analysis.
PCR analysis of genomic islands in different strains of X. fastidiosa.
Nucleotide sequence accession numbers.
RESULTS AND DISCUSSION
Genome features.
Genome reorganization.
Genomic islands.
ADDENDUM IN PROOF
Disease | Length (bp) | GC content (%) | Coding region (% chromo- some size) | No. of predicted ORFs | Avg ORF length (bp) | % of: | No. of: | Plasmid length (bp) | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ORFs with a functional assignment | Conserved hypothetical ORFs | Hypo- thetical ORFs | tRNAs | rRNA operons | tmRNAs | |||||||||||
PDb | 2,519,802 | 51.8 | 79.9 | 2,066 | 979 | 65.9 | 33.3 | 0.8 | 49 | 2 | 1 | 1,345 | ||||
CVCc | 2,679,305 | 52.7 | 80.6 | 2,249 | 964 | 57.4 | 38.2 | 4.4 | 49 | 2 | 1 | 1,285 and 51,158 |
Strain | No. and type of: | ||
---|---|---|---|
Strain-specific genes | Genes with frameshift and/or stop codon in frame | ||
Temecula | 16 Hypothetical | 7 Conserved hypothetical | |
16 Conserved hypothetical | 10 Mobile genetic elements | ||
13 Mobile genetic elements | 2 Hemagglutinin-secreted proteins | ||
2 DNA methyltransferases | 1 Fimbrial adhesin | ||
1 Type II restriction enzyme | 3 Type I restriction-modification enzymes (R, S, and M) | ||
1 HicA-related protein | |||
1 Hydrolase | 1 DNA methyltransferase | ||
1 Integral membrane protein | 1 Aconitate hydratase | ||
1 Mg2+ transporter | |||
1 Heat shock protein (HslU) | |||
1 Anthranilate synthase component I | |||
1 Penicillin binding protein | |||
9a5c | 99 Hypothetical | 2 Conserved hypothetical | |
21 Conserved hypothetical | 7 Mobile genetic elements | ||
19 Mobile genetic elements | 1 Integral membrane protein | ||
2 DNA methyltransferases | 1 Polygalacturonase precursor | ||
1 Single-stranded DNA binding protein | |||
1 O antigen acetylase | 2 Type I restriction-modification enzymes (R and M) | ||
1 Transport protein | 1 DNA damage-inducible protein | ||
1 NADH flavin oxidoreductase | 1 Aconitate hydratase | ||
1 Oxidoreductase | 1 Ribosomal protein S6 modification protein | ||
1 HTP reductase | |||
4 Transcriptional regulators | |||
1 Drug resistance translocase |
Host | Strain | Origin | Distribution of: | ||
---|---|---|---|---|---|
giCVC1 (kb)a | giPD1 | ||||
Grapevine | Temecula | United States | − (4.5) | + | |
Grapevine | Fetzer | United States | − (4.5) | + | |
Grapevine | Traver | United States | − (4.5) | + | |
Grapevine | IAPAR 9715 | United States | − (4.5) | + | |
Grapevine | ATCC 35881 | United States | − (4.5) | − | |
Grapevine | ATCC 35877 | United States | − (4.5) | − | |
Mulberry | ATCC 35868 | United States | − (4.5) | − | |
Mulberry | ATCC 35869 | United States | − (4.5) | − | |
Oleander | ATCC 700598 (Ann1) | United States | − (4.5) | − | |
Almond | ATCC 35870 | United States | − (4.5) | + | |
Almond | ATCC 700965 (Dixon) | United States | − (2.9) | − | |
Elm | ATCC 35873 | United States | − (2.9) | − | |
Red oak | ATCC 35874 | United States | − (2.9) | ND | |
Plum | ATCC 35871 | United States | − (2.9) | − | |
Plum | IAPAR 9746 | Brazil | − (2.9) | − | |
Periwinkle | ATCC 35878 | United States | − (2.9) | − | |
Periwinkle | IAPAR 12319 | Brazil | + | − | |
Hibiscus | Hib#6-CCSM-BR | Brazil | + | − | |
Coffee | Inst. Biológico | Brazil | + | − | |
Coffee | C13-CCSM-BR | Brazil | + | − | |
Coffee | CCT 6755 | Brazil | + | − | |
Citrus | 9a5c | Brazil | + | − | |
Citrus | CCT 5671 | Brazil | + | − | |
Citrus | 20.06/HC16 | Brazil | + | − | |
Citrus | Rep15 | Brazil | + | − | |
Citrus | 5R1 | Brazil | + | − | |
Citrus | X1 | Brazil | + | − | |
Citrus | IAPAR 11834 | Brazil | + | + | |
Citrus | IAPAR 11775 | Brazil | + | + | |
Citrus | IAPAR 11066 | Brazil | + | + |
Acknowledgments
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