The barcoding protocol within Xanthomonas
Based on a partial sequence of the Gyrase B gene (GyrB) of approximately 760 bp (Parkinson et al, 2007), it is possible to identify the regulated species X. fragariae, X. oryzae, X. vesicatoria, the three pathovars of X. translucens (pv’s translucens, undulosa, and cerealis), as well as the regulated pathovar X. cynarae pv. gardneri, and several species that represent complex pathovar clusters containing both regulated as well as non-regulated pathovars. The species studied in QBOL that can be regarded as complex pathovar clusters are X. euvesicatoria, X. phaseoli and X. citri. An accessory gene, the AvrBs2 gene (Hajri et al, 2009), is used to identify regulated pathovars within these complex clusters. These pathovars include:
- X. euvesicatoria pv. euvesicatoria
- X. euvesicatoria pv. perforans
- X. phaseoli pv. phaseoli
- X. phaseoli pv. dieffenbachiae (from Anthurium)
- X. citri pv. phaseoli
- X. citri pv. fuscans
- X. citri pv. aracearum
- X. citri pv. citri
- X. citri pv. aurantifolii.
The protocol for the conventional PCR gyrB for Xanthomonas species identification is available in the annex 2, section 2.5 of PM 7/129.
The protocol for the conventional PCR avrBs2 for Xanthomonas pathovars identification is available in the annex 2, section 2.6 of PM 7/129.