Abstract
Xylella fastidiosa infects a wide range of plant hosts and causes economically serious diseases, including Pierce's disease (PD) of grapevines. X. fastidiosa biocontrol strain EB92-1 is infectious to grapevines but does not cause symptoms. The draft genome of EB92-1 reveals that it may be missing 10 potential pathogenicity effectors.
GENOME ANNOUNCEMENT
Xylella fastidiosa is a fastidious, insect-vectored, plant xylem-colonizing bacterial pathogen that causes a variety of diseases in a wide range of plant species (12). Among the most damaging X. fastidiosa diseases are Pierce's disease (PD) of grapes, almond leaf scorch, and citrus variegated chlorosis (CVC). CVC is a USDA select agent (http://www.aphis.usda.gov/programs/ag_selectagent/) found only in South America. Five complete pathogenic X. fastidiosa genomes are available: PD strains Temecula1 (17) and GB514 (14), almond leaf scorch strains M12 and M23 (4), and CVC strain 9a5c (15). Two draft X. fastidiosa genomes are also available, strain Ann-1, isolated from oleander, and strain Dixon, isolated from almond (3). In 1992, D. L. Hopkins (10) isolated an X. fastidiosa strain, EB92-1, from elderberry; this strain infects grapevines and survives for many years, yet causes no symptoms and provides effective biocontrol against PD.
The 2,478,730 bp (∼194× coverage) draft genome of X. fastidiosa strain EB92-1 was obtained using Roche 454 GS (FLX titanium) pyrosequencing; based on the size of the Temecula1 genome (2,519,802 nucleotides [nt]), this draft EB92-1 genome is ∼98% complete. The genome was assembled into 168 contigs with an average contig length of 12,977 bp using Newbler version 2.3 (454 Life Sciences). There were 2,343 predicted protein-encoding genes. By far the majority of the primary BLAST (1) hits were to Temecula1; 92% of predicted EB92-1 proteins had more than 99% identity with Temecula1 proteins. Comparisons using Mauve 2.3.1 (6) revealed a high level of synteny with Temecula1. A plasmid sequence similar to the Temecula plasmid (pXFPD1.3) was also found in EB92-1. No unique or additional genes were found in EB92-1 that were not previously identified in Temecula1. However, 11 genes found in Temecula1 were not found in EB92-1; 10 of these encoded predicted secreted pathogenicity effectors.
The complete repertoire of Temecula1 type I system components and effectors (3 colicins and 8 hemolysins) was found in EB92-1 and confirmed to be identical or nearly identical to its Temecula1 homologs. Two predicted Temecula1 type II secreted enzymes, a serine protease (PD0956) and a lipase (PD1703), appeared to be missing from EB92-1. PD1703 is a homolog of LipA from Xanthomonas oryzae that is important in pathogenicity on rice (2, 11, 13). Two of three predicted zonula occludens toxin (Zot) genes, PD0928 and PD0915, also appeared to be missing in EB92-1. Zot is an important secreted virulence factor for Vibrio cholerae (16) and has been suggested as a potential virulence factor in CVC strain 9a5c (7). Surprisingly, all six predicted hemagglutinin-like proteins (PD0986, PD1792, PD2108, PD2110, PD2116, and PD2118) appeared to be missing in EB92-1. Two of these (PD1792 and PD2118) carry a type V two-partner secretion (TPS) domain (5); the remaining four have no TPS domain. Independent knockout mutations of PD1792 and PD2118 in Temecula1 caused an increase in virulence (9). In contrast, a knockout of the only functional hemagglutinin-like protein with a TPS domain in Xanthomonas axonopodis pv. citri caused a loss of virulence (8). Experiments designed to functionally test the roles of these 10 potential secreted pathogenicity factors are under way.
Nucleotide sequence accession number.
This whole-genome shotgun sequence has been deposited at DDBJ/EMBL/GenBank under accession number AFDJ00000000. The version described in this paper is the first version, AFDJ01000000. The sequence and annotation are also available at the ICBR public access site (http://vision.biotech.ufl.edu/mycap/jsp/project/projects.jsp).
Acknowledgments
Funding for this project was provided by the University of California Pierce's Disease Research Grants Program, project 2009-244.
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