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-grapegrowing 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.Different microorganisms are able to survive in and to colonize plant water-conductive vessels (xylem). The result of this association is either beneficial or detrimental to the plant host.Of the latter, an example is the association of Xylella fastidiosa (38) with diverse plant hosts. X. fastidiosa is a fastidious, insecttransmitted, xylem-inhabiting bacterium known to cause several economically important diseases of both monocotyledonous and dicotyledonous plants (14,17,29). These diseases include Pierce's disease (PD) of grapevine and citrus variegated chlorosis (CVC), which have rather distinct symptoms and geographical distributions.PD, caused by certain strains of X. fastidiosa, is characterized by wilted, shriveled, raisin-like fruit and scorched leaves that detach, leaving bare petioles attached to the canes (37). The bark of affected canes may lignify or mature irregularly, leaving

Genomic Insights into Xylella fastidiosa Interactions with Plant and Insect Hosts

“…8.2). This accounts for 71-86 % of the largest X. fastidiosa genome, 9a5c, depending on how conservative one is in predicting genes (e.g., Simpson et al 2000;van Sluys et al 2003). Only one study addressed this question at the subspecies level (subsp.…”

“…The finding that most obvious differences among X. fastidiosa genomes are connected to phage-like sequences has led several groups to propose that the divergence of lineages leading to host specificity is mediated by laterally transferred elements (e.g., van Sluys et al 2003;Nunes et al 2003;Varani et al 2008). Thus, host adaptation in X. fastidiosa could be the result of one or few changes with large fitness benefits, despite the fact that overall pathogenicity mechanisms are similar regardless of host plant.…”

“…Among subspecies, it is evident that X. fastidiosa's flexible genome is primarily composed of laterally transferred phage-like elements, including prophages (Nunes et al 2003;van Sluys et al 2003;Varani et al 2008).…”

“…nih.gov/genome/genomes/173), representing three of the four described subspecies (subspecies sandyi being the exception; Fig. 8.2) (Chen et al 2010;Simpson et al 2000;van Sluys et al 2003). These genomes range from 2.5 to 2.…”

“…The nucleotide sequences are 51.8-52.6 % GC. Published annotations indicate that these genomes each contain from 2,066 to 2,294 protein-coding sequences, 2 ribosomal RNA operons, 49-50 tRNA genes (43 different anti-codons), and 1 tmRNA gene (van Sluys et al 2003). Draft quality genomes are available for three other isolates, each appearing to be very similar to one of the finished genomes at the coarse scale (Bhattacharyya et al 2002;Schreiber et al 2010;Zhang et al 2011), as are contigs from the shotgun sequencing of a mixed sample of subspecies multiplex and sandyi (Bhattacharyya et al 2002;Nunney et al 2012).…”