Characteristics of the alleles found in the clade A X. fastidiosa subsp. multiplex isolates of Parker et al. (44)a

LocusSubgroupX. fastidiosa allele subgroup (bp difference)bRegion of IHRMaximum length (bp)Ratio(s)P value(s)
subsp. multiplexsubsp. fastidiosa
acvBAllAll (0)All (45)None0:45
copBAllAll (4)All (2)(1 to 789)c7894:2<0.001d
cvaCRag, ElmOak1 (15)All (0)1 to 28528515:0<0.001d
BB1, -2, and -3Plum (8)All (9)(135 to 13) to (220 to 222)2851:5 vs 7:0 vs 0:40.010, 0.015, combined = 0.0014
Alm2Oak1 (0)All (15)None2850:15
fimAAllOak1 (4)Ca05 (4)(268 to 378) to 5065060:4 vs 4:00.029
gaaAllOak1 (0)All (13)None1,0640:13
pglAAll (−Elm)Lupine (8)All (2)1 to 4974978:2<0.001d
ElmLupine (6)All (4)1 to (374 to 395)4976:1 vs 0:30.067
pilABB1,-2, and -3; RagPlum (7)All (49)None3537:49
Alm2Lupine (7)All (48)None3537:48
ElmOak1 (0)All (54)None3530:54
rpfFAll (−Rag)All (0)All (36)None7770:36
RagAll (4)All (32)1 to (94 to 158)7774:1 vs 0:310.0002
xadABB1 and -3, Alm2Redbud (9)Gafl (14)(834 to 901) to 10601,0602:12 vs 7:20.0083
BB2Redbud (0)Gafl (22)None1,0600:22
RagLupine (2)Gafl (21)None1,0602:21
ElmRedbud (1)Gafl (22)None1,0601:21
  • a Regions of suspected intersubspecific homologous recombination (IHR) in the alleles found in clade A based on our analysis are identified and in boldface. All differences were statistically significant (see P values). Parker et al. (44) divided clade A into 6 subgroups: Ragweed (Rag), Elm, Blueberry1 (BB1), BB2, BB3, and Almond2 (Alm2). Only Elm and BB3 are not represented in the present study (see the text).

  • b The number of base pair differences between each clade A allele and the most similar allele from their clade B X. fastidiosa subsp. multiplex isolates and from the X. fastidiosa subsp. fastidiosa isolates is shown in parentheses. For additional details, see Table 1.

  • c Excludes the minisatellite region at positions 69 to 356 (based on Elm).

  • d Based on a comparison of the observed ratio to a 1:11 ratio (see Table 1).