Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa

Abstract

Xylella fastidiosa is a xylem-dwelling, insect-transmitted, gamma-proteobacterium that causes diseases in many plants, including grapevine, citrus, periwinkle, almond, oleander, and coffee. X. fastidiosa has an unusually broad host range, has an extensive geographical distribution throughout the American continent, and induces diverse disease phenotypes. Previous molecular analyses indicated three distinct groups of X. fastidiosa isolates that were expected to be genetically divergent. Here we report the genome sequence of X. fastidiosa (Temecula strain), isolated from a naturally infected grapevine with Pierce's disease (PD) in a wine-grape-growing region of California. Comparative analyses with a previously sequenced X. fastidiosa strain responsible for citrus variegated chlorosis (CVC) revealed that 98% of the PD X. fastidiosa Temecula genes are shared with the CVC X. fastidiosa strain 9a5c genes. Furthermore, the average amino acid identity of the open reading frames in the strains is 95.7%. Genomic differences are limited to phage-associated chromosomal rearrangements and deletions that also account for the strain-specific genes present in each genome. Genomic islands, one in each genome, were identified, and their presence in other X. fastidiosa strains was analyzed. We conclude that these two organisms have identical metabolic functions and are likely to use a common set of genes in plant colonization and pathogenesis, permitting convergence of functional genomic strategies.

FIG. 1.

Global comparison of PD X. fastidiosa Temcula and CVC X. fastidiosa 9a5c proteomes. The distribution of protein-coding gene sequence identity along each genome is shown. Amino acid identity was determined by a reciprocal BLAST analysis of one proteome against the other. The positions of the genomic islands (giPD1 and giCVC1) are illustrated at the top of each genome graph. The colored arrows at the top of each graph indicate the positions of rearranged sequences (see Fig. 2B).

FIG. 2.

Chromosome alignment of PD X. fastidiosa Temecula and CVC X. fastidiosa 9a5c. (A) Nucleotide sequence alignment of both genomes, starting at the putative origins of replication, as determined with MUMmer. (B) Chromosome backbones of both genomes, showing the relative positions, sizes, and orientations of colinear chromosome regions detected in panel A. The direction of the arrow within each chromosome fragment indicates its relative orientation. Black triangles illustrate the positions of phage-related regions and genomic islands within each chromosome.

FIG. 3.

Comparative analysis of giPD1 and giCVC1 insertion sites. Shaded nucleotides represent the target duplication sites for each genomic island insertion. Underlined bases indicate substitutions or indels. Numbers on both sides indicate the coordinates of each genome. The coordinates for the primers used in the PCR analysis of the islands are as follows: for giPD1—P1 (PD, 1179403 to 1179420; CVC, 1608980 to 1608963), P2 (PD, 1180466 to 1180449), P3 (PD, 1194838 to 1194855), and P4 (PD, 1196338 to 1196321; CVC, 1607835 to 1607852); for giCVC1—XFUN01 (PD, 1280237 to 1280220; CVC, 1638293 to 1638310), XFCVC01R (CVC, 1639020 to 1639003), XFCVC01F (CVC, 1707041 to 1707058), and XFUN03 (PD, 1275650 to 1275667; CVC, 1707862 to 1707845).