Computational protocol: The Infection of Cucumber (Cucumis sativus L.) Roots by Meloidogyne incognita Alters the Expression of Actin-Depolymerizing Factor (ADF) Genes, Particularly in Association with Giant Cell Formation

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Protocol publication

[…] Sequence information for 11 A. thaliana ADF genes were retrieved from previous study (Ruzicka et al., ). To assess the corresponding cucumber orthologs, a basic local alignment search tool (BLAST) was performed for each one of the A.thaliana ADF protein sequences against the Cucumber Genome Database (http://cucumber.genomics.org.cn/page/cucumber/index.jsp). Those with the highest amino acid percentage identity were selected. Cucumber ADFs were named according to the annotation of the Cucumber Genome Database. The multiple sequence alignment of CsGID1s and related CsGID1 proteins was performed using ClustalW within the MEGA5 software package (Tamura et al., ), and the highlighting conserved sequences were drawn by using BoxShade (http://www.ch.embnet.org/software/BOX_form.html). The phylogenetic tree was constructed using the Neighbor-Joining (NJ) method (Saitou and Nei, ) with the Poisson model and 1000 bootstrap replicates test by MEGA5 (Liu et al., ). The gene numbers corresponding to every CsADF gene in the Cucumber Genome Database are shown in Supplementary Table . The PCR primers used for cloning CsADF genes are listed in Supplementary Table . […]

Pipeline specifications

Software tools BLASTN, Clustal W, MEGA, BoxShade
Databases ADFS Cucumber Genome DataBase
Applications Phylogenetics, Proteome data visualization
Diseases Infection, Nematode Infections, Parasitic Diseases
Chemicals Cytochalasin D