Computational protocol: Characterization of rhizobia isolates obtained from nodules of wild genotypes of common bean

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Protocol publication

[…] CSU, TST and genotypic characterization data were transformed into a binary matrix. The binary matrices were used for the construction of a similarity matrix using the Jaccard coefficient. The UPGMA (Unweighted pair-group method) was applied to transform the similarity matrix into a similarity dendrogram using NTSYSpc® software.Data obtained from the greenhouse experiment were subjected to analysis of variance; when F was significant, the Scott Knott test of means was applied with a 5% probability using SISVAR statistical software. Pearson correlation analyses were also performed for NDM and SDM, LA and N-Total using R statistical software.For the 16S rRNA-based phylogeny, the sequences obtained were submitted to NCBI BLAST against a non-redundant nucleotide database for getting homologous sequences. Sequences showing degree of similarity were aligned using the CLUSTAL W program. The evolutionary history was inferred using the Maximum-likelihood method, with tree consensus being inferred from 500 replicates using bootstrap. The evolutionary distances were computed using the Maximum Composite Likelihood method proposed by Tamura et al. All positions containing gaps and missing data were eliminated. There were a total of 989 positions in the final dataset. Evolutionary analyses were conducted in MEGA6. […]

Pipeline specifications

Software tools NTSYSpc, BLASTN, Clustal W, MEGA
Applications Phylogenetics, Population genetic analysis
Organisms Rhizobium tropici
Chemicals Carbon, Sodium Chloride