Computational protocol: Population Structure of the Bacterial Pathogen Xylella fastidiosa among Street Trees in Washington D.C.

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Protocol publication

[…] All sequence data was processed using the software Geneious v6.1.6 []. The forward and reverse read of each locus were quality-trimmed, de novo assembled, and ambiguities were resolved with visual analysis of the chromatograph and re-sequencing when necessary. The consensus sequence was extracted from each assembly and sequences were aligned using the Geneious alignment option []. In order to compare the strains in our study to those published in, an additional set of primers were required in order to meet the sequence requirements necessary for website entry. The new primers were designed to span the gene region at each locus not formerly covered by the original primers used in the analysis. The newly designed primers were created using the primer3 v0.4.0 plug-in for Geneious []. Alleles for each strain at each of the seven MLST loci were further sequenced and included in the sample assemblies before an allelic profile of each host species was submitted to (PubMLST ID: 519–525). Bacterial strains in this study were identical to previously identified strains in the Washington D.C. region on the website [,]. All X. fastidiosa alleles found for each host species was uploaded to GenBank, accession numbers KM487213-KM487276 and KM590452-KM590457. […]

Pipeline specifications

Software tools Geneious, Primer3
Databases PubMLST
Application qPCR
Organisms Bacteria, Xylella fastidiosa, Escherichia coli, Quercus rubra, Platanus occidentalis
Diseases Hepatitis D