Combined use of a new SNP-based assay and multilocus SSR markers to assess genetic diversity of Xylella fastidiosa subsp. pauca infecting citrus and coffee plants
Two haplotypes of
Xylella fastidiosa
subsp.
pauca
(Xfp) that correlated with their host of origin were identified
in a collection of 90 isolates infecting citrus and coffee plants in Brazil, based on a single-nucleotide polymorphism in the
gyrB
sequence. A new single-nucleotide primer extension (SNuPE) protocol was designed for rapid identification of
Xfp
according
to the host source. The protocol proved to be robust for the prediction of the
Xfp
host source in blind tests using DNA from
cultures of the bacterium, infected plants, and insect vectors allowed to feed on
Xfp-
infected citrus plants. AMOVA and
STRUCTURE analyses of microsatellite data separated most
Xfp
populations on the basis of their host source, indicating that
they were genetically distinct. The combined use of the SNaPshot protocol and three previously developed multilocus SSR
markers showed that two haplotypes and distinct isolates of
Xfp
infect citrus and coffee in Brazil and that multiple, genetically
different isolates can be present in a single orchard or infect a single tree. This combined approach will be very useful in studies
of the epidemiology of
Xfp-
induced diseases, host specificity of bacterial genotypes, the occurrence of
Xfp
host jumping, vector
feeding habits, etc., in economically important cultivated plants or weed host reservoirs of
Xfp
in Brazil and elsewhere
[Int Microbiol 2015; 18(1):13-24].We acknowledge financial support from the EU grant ICA4-CT-2001-10005 and an ‘Intramural Project’ to B. B. Landa from the Spanish National Research Council (CSIC), as well as CNPq for a scholarship to J. R. S. Lopes in Brazil.Peer reviewe