Population genomic analysis of a bacterial plant pathogen: novel insight into the origin of Pierce's disease of grapevine in the U.S

Abstract

Invasive diseases present an increasing problem worldwide; however, genomic techniques are now available to investigate the timing and geographical origin of such introductions. We employed genomic techniques to demonstrate that the bacterial pathogen causing Pierce's disease of grapevine (PD) is not native to the US as previously assumed, but descended from a single genotype introduced from Central America. PD has posed a serious threat to the US wine industry ever since its first outbreak in Anaheim, California in the 1880s and continues to inhibit grape cultivation in a large area of the country. It is caused by infection of xylem vessels by the bacterium Xylella fastidiosa subsp. fastidiosa, a genetically distinct subspecies at least 15,000 years old. We present five independent kinds of evidence that strongly support our invasion hypothesis: 1) a genome-wide lack of genetic variability in X. fastidiosa subsp. fastidiosa found in the US, consistent with a recent common ancestor; 2) evidence for historical allopatry of the North American subspecies X. fastidiosa subsp. multiplex and X. fastidiosa subsp. fastidiosa; 3) evidence that X. fastidiosa subsp. fastidiosa evolved in a more tropical climate than X. fastidiosa subsp. multiplex; 4) much greater genetic variability in the proposed source population in Central America, variation within which the US genotypes are phylogenetically nested; and 5) the circumstantial evidence of importation of known hosts (coffee plants) from Central America directly into southern California just prior to the first known outbreak of the disease. The lack of genetic variation in X. fastidiosa subsp. fastidiosa in the US suggests that preventing additional introductions is important since new genetic variation may undermine PD control measures, or may lead to infection of other crop plants through the creation of novel genotypes via inter-subspecific recombination. In general, geographically mixing of previously isolated subspecies should be avoided.

Figure 1. The phylogeny of the major groups of X. fastidiosa showing the patterns that can detect recombination of X. fastidiosa subsp. multiplex DNA into X. fastidiosa subsp. fastidiosa.

The top figure shows the relationships of the four subspecific clades (from Schuenzel et al. 2005) labeled with the sequenced genomes: M23 and Temecula-1 (X. fastidiosa subsp. fastidiosa), Ann1 (X. fastidiosa subsp. sandyi), and M12 (X. fastidiosa subsp. multiplex) from the US, and 9a5c (X. fastidiosa subsp. pauca) from Brazil. To track recombination, a unique SNP is shown (O) in the X. fastidiosa subsp. multiplex branch. The lower trees show how recombinational transfer of X. fastidiosa subsp. multiplex DNA to one of the X. fastidiosa subsp. fastidiosa forms leaves a characteristic pattern with the non-recombining X. fastidiosa subsp. fastidiosa remaining identical to X. fastidiosa subsp. sandyi. Note that the same patterns would be created if recombination involved the transfer of a unique SNP from X. fastidiosa subsp. sandyi. Branch lengths are not scaled to divergence.

Figure 2. Maximum likelihood phylogeny of X. fastidiosa showing U.S. X. fastidiosa subsp. fastidiosa sequence types (STs) nested within the Costa Rican STs.

The circle encompasses all X. fastidiosa subsp. fastidiosa STs. The other subspecies are named on their ancestral branch. All unique STs are shown from 83 U.S. and 24 Costa Rican (CR) samples of subsp. fastidiosa and 21 US samples of subsp. sandyi. The number of isolates/ST is shown by xN. All CR isolates were from coffee except 3 from grape (designated by “grp”). X. fastidiosa subspp. multiplex and pauca are represented by a sample of sequence types (see Table 1). All bootstrap values >80% are shown and the scale bar defines 1% sequence divergence.