Computational protocol: Specific Detection and Identification of American Mulberry-Infecting and Italian Olive-Associated Strains of Xylella fastidiosa by Polymerase Chain Reaction

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Protocol publication

[…] Four complete genomes of X. fastidiosa strains, Temecula 1 (AE009442) from Pierce’s-diseased grapevine, 9a5c (AE003849) from variegated chlorosis-diseased citrus, and M12 (CP000941) and M23 (CP001011) from leaf scorch-diseased almond, as well as the draft genome of the mulberry-infecting strain Mul-MD (AXDP00000000) [], were downloaded from NCBI’s whole genome and shotgun reads database. Proteins encoded by predicted genes of the five X. fastidiosa strains were compared using a bi-directional BLAST between amino acid sequences from the five strains. The e-value threshold was e-04 or less for two proteins to be considered a match. A protein was considered strain specific if BLAST yielded no hits or all hits had an e-value greater than e-04. Mul-MD strain-unique genes were then compared with the genome of the other mulberry strain MUL0034 (CP006740.1), and with other complete and draft genomes of X. fastidiosa strains in GenBank, to ensure their uniqueness. Primers were designed based on a unique gene selected using the criteria and software as described previously []. A search for nucleotide sequence matches of the primers and amplicons was conducted using BLASTn to query the nucleotide collection (nr/nt) and whole-genome shotgun contigs (wgs) databases in GenBank. […]

Pipeline specifications

Software tools BiDiBlast, BLASTN
Applications Genome annotation, WGS analysis
Organisms Xylella fastidiosa
Diseases Coinfection
Chemicals Nucleotides