Computational protocol: TaNAC1 acts as a negative regulator of stripe rust resistance in wheat, enhances susceptibility to Pseudomonas syringae, and promotes lateral root development in transgenic Arabidopsis thaliana

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Protocol publication

[…] Gene sequences were analyzed using DNAMAN software (Lynnon Biosoft, USA), BLAST and ORF Finder on the NCBI website. Conserved domains and motifs were predicted using the PROSITE Scan tool. The coding sequence of TaNAC1 was deduced from its isolated cDNA clone, and the closest homologs in other plants were identified using TBLASTX. Multiple alignments of protein sequences were performed with the program Clustal X version 2.0 program (). The phylogenetic comparison of isolated full-length TaNAC1 and characterized NAC proteins based on the literature (; ; ; ; ; ) and GenBank were constructed with the neighbor-joining algorithm using MEGA4 program (). Bootstrap values were calculated from 1000 bootstrap replicates. […]

Pipeline specifications

Software tools DNAMAN, Open Reading Frame Finder, TBLASTX, Clustal W, MEGA
Databases PROSITE
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Arabidopsis thaliana, Flavobacterium sp., Pseudomonas syringae, Triticum aestivum, Barley stripe mosaic virus, Pseudomonas syringae pv. tomato str. DC3000