Computational protocol: The Transcription Factor OsWRKY45 Negatively Modulates the Resistance of Rice to the Brown Planthopper Nilaparvata lugens

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Protocol publication

[…] For the phylogenetic analysis, the characterized WRKYs from different species were selected and the program MEGA 6.0 [] was used. The protein sequences aligned using the ClustalW method in MEGA 6.0 (pairwise alignment: gap opening penalty 10, gap extension penalty 0.1; multiple alignments: gap opening penalty 10, gap extension penalty 0.2, protein weight matrix using Gonnet). The residue-specific and hydrophilic penalties were on, and the end gap separation and the use negative separation matrix were off. The gap separation distance was 4, and the delay divergence cutoff (percentage) was 30. This alignment was then used to generate an unrooted tree with statistical tests (parameters for phylogeny reconstruction were neighbor-joining method [] and bootstrap, n = 1000, amino acid, Poisson model, rates among sites: uniform rates gaps/missing, data treatment: complete deletion, traditional tree without modification for graphics) using MEGA 6.0. [...] Differences in mRNA levels of genes, plant heights, concentrations of JA, SA, ethylene and H2O2, the amount of honeydew, herbivore performance, and the number of insect pests and predatory spiders as well as the severity of disease, in different lines, treatments, or treatment times were determined by analysis of variance (or Student’s t-test for comparing two treatments). All tests were carried out with Statistica (SAS Institute, Inc., Cary, NC, USA, […]

Pipeline specifications

Software tools MEGA, Clustal W, Statistica
Applications Miscellaneous, Phylogenetics
Organisms Oryza sativa, Nilaparvata lugens, Rhizoctonia solani, Magnaporthe oryzae
Diseases Byssinosis, Plant Poisoning, Machado-Joseph Disease
Chemicals Salicylic Acid