Multilocus sequencing of pseudomonads isolated from the
phyllosphere of sugar beet
A total of 230 isolates (164 from Oxford, 66 from Auckland) were
initially subjected to sequencing of seven housekeeping genes
(gapA , gltA , acnB , gyrB , coxC ,pgi and ropD ) using the universal primers (Hwang et al.,
2005). However, the rates of PCR or sequencing failure were very high,
suggesting that the leaf-colonising Pseudomonas populations are
highly diverse. After modification of the primer sequences (Table 1),
high-quality DNA sequences were obtained for three genes (gapA ,gltA , acnB ) in a total of 152 isolates (96 from Oxford, 56
from Auckland). The concatenated aligned sequences were 897 bp in
length, and encompassed 81 unique STs and 22 distinct OTUs. Rarefaction
analysis indicates near saturation of sampling at the OTU level (Fig.
1A), indicating that the sample was a good representation of the genetic
diversity. As summarised in Table 2, the number of segregation sites
ranged from 18 to 23 for each of the three genes, and 59 identified for
the concatenated sequences. Results obtained fromĀ a coalescent-based
likelihood permutation test (LPT) from LDHat (McVean, 2002) identified a
recombination point within the gapA gene (P = 0.007), but
not in the gltA or acnB genes.