Computational protocol: An easy, simple inexpensive test for the specific detection of Pectobacterium carotovorum subsp. carotovorum based on sequence analysis of the pmrA gene

Similar protocols

Protocol publication

[…] The PCR-amplified fragments of pmrA were purified and the sequencing reactions were performed with a Big-Dye Terminator v3.1 (Applied Biosystems). The pmrA sequences which we determined and the sequences of the reference strains of members of the family Enterobacteriaceae obtained from the GenBank databases were analyzed. The pmrA sequences were first aligned by using the Clustal W program [], and then the alignments were corrected by hand. Evolutionary trees for the data set were inferred by using the Neighbor-Joining program of MEGA [,]. The stability of relationships was assessed by performing bootstrap analyses of the Neighbor-Joining data based on 500 resamplings. The entire sequences corresponding to positions 4317866-4318532 of the reference sequence of the subspecies. […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Organisms Solanum tuberosum, Pectobacterium carotovorum, Pectobacterium atrosepticum, Pectobacterium wasabiae