Computational protocol: Biocontrol of Bacterial Leaf Blight of Rice and Profiling of Secondary Metabolites Produced by Rhizospheric Pseudomonas aeruginosa BRp3

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Protocol publication

[…] CTAB method (Ausubel et al., ) was used to extract total genomic DNA of strain BRp3. Universal primers P1 and P6 were used to amplify 16S rRNA gene (Tan et al., ). QIAquick Gel Extraction Kit (QIAGEN Sciences, Maryland 20874, USA) was used to clean the amplified PCR product about 1.5 Kb of 16S rRNA gene. Amplified PCR products were commercially sequenced by Macrogen, Inc. (Seoul, South Korea). Available sequences of bacterial lineage in NCBI were used to align and compare the sequence data using BLAST. Accession numbers were allocated after submitting the sequences to NCBI GenBank database (Yasmin et al., ).For calculating phylogenetic tree of strain BRp3, closely related sequences were downloaded and aligned using CLUSTAL X and MacClade 4.05 (Thompson et al., ; Maddison and Maddison, ). Maximum Parsimony (MP), maximum likelihood (ML) and neighbor joining (NJ) methods were used for sequences analysis as mentioned by Mirza et al. (). […]

Pipeline specifications

Software tools Clustal W, MacClade
Applications Phylogenetics, 16S rRNA-seq analysis
Organisms Xanthomonas oryzae, Oryza sativa, Pseudomonas aeruginosa
Chemicals Phosphorus