Hyper-variations of a protease locus, PD0218 (pspB), in Xylella fastidiosa almond leaf scorch and Pierce's disease strains in California

USDA-ARS, Parlier, San Joaquin Valley Agricultural Sciences Center, 9611 S. Riverbend Ave., Parlier, CA 93648; USDA-APHIS, Center for Plant Health Science and Technology, Pest Epidemiology and Risk Assessment Laboratory, 1730 Varsity Dr., Suite 300, Raleigh, NC 27606; Department of Plant Pathology, University of California, Davis, CA 95616; Paramount Farming Co. 33141 E. Lerdo Hwy, Bakersfield, Calif., 93308

^* To whom correspondence should be addressed. Email: Jianchi.chen{at}ars.usda.gov.

	Abstract

Xylella fastidiosa is a Gram negative plant pathogenic bacterium that causes almond leaf scorch disease (ALSD) and Pierce's disease (PD) of grape in many regions of North America and Mexico. Among the two 16S rRNA gene genotypes described in California, A-genotype strains cause ALSD only and G-genotype strains cause both PD and ALSD. While G-genotype strains cause two different diseases, little is known about their genetic variation. In this study, we identified a putative protease locus, PD0218 (pspB), in the genome of X. fastidiosa and evaluated the variation at this locus in X. fastidiosa populations. PD0218 contains tandem repeats of ACDCCA, translated to threonine and proline (TP), upstream of the putative protease conserved domain. Among 116 X. fastdiosa ALSD and PD strains isolated from seven locations in California, tandem repeat numbers (TRNs) varied from 9 to 47 with a total of 30 TRN genotypes, indicating that X. fastidiosa possesses an active mechanism of contracting and expanding tandem repeats at this locus. A significant TRN variation was found among PD strains (Mean=29.9), which could be further divided into two TRN groups: PD-G_small (Mean=17.3) and PD-G_large (Mean=44.3). Less variation was found in ALSD strains (Mean=21.7). Variation was even smaller after ALSD strains were sub-divided into the A- and G-genotype (Mean=13.3, for G-genotype; Mean=27.1, for A-genotype). Genetic variation at PD0218 locus is potentially useful for sensitive discrimination of X. fastidiosa strains. However, TRN stability, variation range, and correlation to phenotypes should be evaluated in epidemiological applications such as pathotype identification and delineation of pathogen origin.