Computational protocol: Genetic Diversity of Nitrogen-Fixing and Plant Growth Promoting Pseudomonas Species Isolated from Sugarcane Rhizosphere

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Protocol publication

[…] To perform molecular phylogenetic analysis and evolutionary relationship analysis, the 16S rRNA gene sequences of the isolated Pseudomonas strains were compared with reference strain sequences deposited in the National Center for Biotechnology Information (NCBI) GenBank public database. The sequences were aligned by ClustalW (Saitou and Nei, ) and the phylogenetic tree was reconstructed using MEGA software version 7.0 (Kumar et al., ) and unweighted pair group method with arithmetic mean (UPGMA) (Sneath and Sokal, ) in a Kimura two-parameter model (Tamura et al., ). To obtain the confidence values, the gaps were treated by pairwise deletions and bootstrap analysis was carried out by the method of Felsenstein () using 1,000 pseudoreplications. […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Organisms Pseudomonas entomophila
Chemicals Nitrogen, Tryptophan