Computational protocol: A Drought Resistance-Promoting Microbiome Is Selected by Root System under Desert Farming

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Protocol publication

[…] 16S rRNA gene sequences were aligned using the ClustalX software and the output file was used to define operational taxonomic units (OTUs) using DOTUR . A quantitative matrix was created basing on the absence/presence of each polymorphic OTU calculated at 99% nucleotide similarity. Cluster analysis has been performed with the XLSTAT software using the Pearson correlation coefficient.Number of Taxa, Shannon, Evenness, Simpson and Dominance indexes of the OTUs, defined at 99% of similarity, have been calculated using the PAST software .The alignment of ACCd rhizobacteria sequences and the construction of the phylogenetic tree were performed using the neighbor-joining method of MEGA version 4 . […]

Pipeline specifications

Software tools Clustal W, DOTUR, MEGA
Applications Phylogenetics, 16S rRNA-seq analysis
Organisms Capsicum annuum