Table 1.
Genetic typing of isolates of X. fastidiosa from Costa Rica indicating, in addition to the genetic data, the plant host sampled and the location.
Figure 1.
Distance tree showing the relationship of the two atypical Sequence Types (ST) of Xylella fastidiosa from Costa Rica.
ST53 and ST61, (each marked with an arrow) are shown relative to all other published sequence types of X. fastidiosa. CR X. f. subsp. fastidiosa defines STs from Costa Rica. Bootstrap values showing the separation of STs 53 and 61 from the other STs are shown (other bootstrap values are not relevant to the hypothesis being tested and are omitted for clarity).
Figure 2.
Distance tree of all known Xylella fastidiosa pilU alleles.
Distance tree showing the close relationship of the novel pauca-like alleles 27 and 28 found in Costa Rica to the single allele (#10) found in the Brazilian X. f. subsp. pauca. The strong percentage bootstrap support for grouping these Costa Rican alleles with subsp. pauca, rather than with the other three subspecies is shown. The tree includes previously unpublished pilU data from Costa Rican X. f. subsp. fastidiosa isolates previously typed using MLST (11) (see text), including four new alleles (boxed). Alleles previously identified as involved in intersubspecific homologous recombination are indicated by: *, allele derived from X. f. subsp. fastidiosa, but found in recombinant X. f. subsp. multiplex; **, allele derived from X. f. subsp. multiplex, but found in X. f. subsp. fastidiosa; ***, allele characteristic of X. f. subsp. fastidiosa, but also found in recombinant X. f. subsp. multiplex and in X. f. subsp. morus [4], [12], [15]. Published pilU data from refs. [4], [13], [15].
Figure 3.
Distance tree of unique sequence types (STs) based on five MLST loci leuA, petC, malF, holC, and gltT plus the non-MLST locus pilU.
Tree showing the grouping of the Costa Rica (CR) sequence type ST53 with the Brazilian X. f. subsp. pauca instead of grouping with the native (CR) X. f. subsp. fastidiosa. The 100% bootstrap support for this separation, and values within X. f. subsp. pauca are shown (other bootstrap values are omitted to aid clarity). The figure excludes STs that become identical to another ST when the alleles at cysG and nuoL are omitted.
Figure 4.
Distance trees of the alleles at the MLST loci cysG, holC, and nuoL.
Tree showing that the “alleles of unknown origin” cysG#24, nuoL#16 and holC#16 map to a position close to, but distinct from, the South American subspecies X. f. subsp. pauca. The generally strong bootstrap support for grouping these alleles close to, but distinct from, subsp. pauca, rather than with the other three subspecies is also shown. In the cysG tree, *: allele #4 derived from X. f. subsp. multiplex, but found in X. f. subsp. fastidiosa; **: alleles #6, 8, 18 derived from X. f. subsp. multiplex and X. f. subsp. fastidiosa found in the recombinant X. f. subsp. multiplex and/or X. f. subsp. morus; ***: allele #12 derived from and found in X. f. subsp. fastidiosa, but also found in the recombinant X. f. subsp. multiplex [4], [12], [14], [15]. In the holC tree, *: alleles #5, eight derived from X. f. subsp. fastidiosa, but found in X. f. subsp. morus; **: allele #7 derived from X. f. subsp. multiplex and X. f. subsp. fastidiosa found in the recombinant X. f. subsp. multiplex [4], [12].