In silico evaluation of molecular probes for detection and identification of Ralstonia solanacearum and Clavibacter michiganensis subsp. sepedonicus.
Ralstonia solanacerum and Clavibacter michiganensis subsp. sepedonicus are the two most relevant bacterial pathogens of potato for which a large number of molecular diagnostic methods using specific DNA sequences have been developed. About one hundred oligonucleotides have been described and thoroughly tested experimentally. After having compiled and evaluated all these primers and probes in silico to check their specificity, many discrepancies were found. A detailed analysis permitted the recognition of different possible reasons for such discrepancies: sequencing errors in public sequences, wrong supposed specificity (sometimes due to more recent sequences than the oligonucleotides being evaluated) or even typing errors in the oligonucleotides. Although this study is an exercise about in silico evaluation using two potato bacterial pathogens as a model, the conclusions reflect not only information useful for phytopathologists but, in a broader scope, draw the main situations that can be found during an evaluation of probes, which can be surely found in other scenarios.
Arahal
David R
DR
Departamento de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain.
Llop
Pablo
P
Alonso
Manuel Pérez
MP
López
María M
MM
D000192:Actinomycetales / Q000145:classification* / Q000235:genetics*; D001483:Base Sequence; D017931:DNA Primers; D015345:Oligonucleotide Probes; D043368:Ralstonia solanacearum / Q000145:classification* / Q000235:genetics*; D012680:Sensitivity and Specificity; D011198:Solanum tuberosum / Q000382:microbiology
D017931:DNA Primers; D015345:Oligonucleotide Probes