Submitted to: Current Microbiology
Publication Type: Peer reviewed journal
Publication Acceptance Date: 9/13/2004
Publication Date: 2/14/2005
Citation: Chen, J., Civerolo, E.L., Jarret, R.L., Van Sluys, M., De Oliveira, M. 2005. Genetic discovery in Xylella fastidiosa through sequence analysis of selected randomly amplified polymorphic DNAs. Current Microbiology. 50(2):78-83. Interpretive Summary: It has long been speculated that Xylella fastidiosa Pierce's disease strain in California has its origin from the southeastern U. S. Yet, supports for this hypothesis are limited because of the technical difficulty in collecting evidences. The publication of the whole genome sequence of a California X. fastidiosa Pierce's disease strain (PD-Temecula) opens a venue for PD strain sequence comparison. While the current technology does not allow sequencing of whole genome from every bacterial strain, we obtained five sections of genome sequences from a Florida PD strain through random PCR primers. Four of the five sequences showed very high degree of sequence similarity to the genome sequence of PD-Temecula, a strong indication that PD strains from California and the southeastern U. S. are from a common source. The discrepant DNA was later determined to be related to a bacterial phage, or mobile genetic element. This is the first report showing evidence of active horizontal gene transfers among X. fastidiosa strains.
Technical Abstract: Five randomly amplified polymorphic DNA (RAPD) fragments from a strain of X. fastidiosa causing Pierce's disease (PD) of grapevine in Florida were sequenced. These sequences were used to search for similarities in the genome sequence databases of four X. fastidiosa strains that cause PD (PD-Temecula), almond leaf scorch disease (ALSD-Dixon), and oleander leaf scorch disease (OLSD-Ann-1) in California and citrus variegated chlorosis (CVC-9a5c) in Brazil. Four of the five nucleotide sequences from the Florida PD strain were most similar to PD-Temecula, indicating the homogeneity of X. fastidiosa PD strains from both Florida and California. CVC-9a5c was the most distantly related to the Florida PD strain. The discrepant RAPD, PDX3-1 (547 bp), shared no homology with regions in the genomes of PD-Temecula and CVC-9a5c, but did show homology with two regions in ALSD-Dixon and one in OLSD-Ann-1. PDX3-1 contained the C-terminal portion of an integrase gene (int), highly similar (>40% identities, or, >60% positives) to those in the phage family of Podoviridae, commonly found in Enterobacteriaceae. A 43-bp sequence at the 3' end of PDX3-1 was almost identical (42/43) to that of the anti-codon and T C arms of the two tRNAlys genes found in all of the four X. fastidiosa genomes. This sequence could be the att site for DNA integration.