Computational protocol: Genome-wide identification and expression analysis of the ClTCP transcription factors in Citrullus lanatus

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Protocol publication

[…] Information on the chromosomal locations of all AtTCP genes was obtained from The Arabidopsis Information Resource (TAIR; http://www.arabidopsis.org), and that for all ClTCP genes was obtained through BLASTN searches against the Cucurbit Genomics Database (http://www.icugi.org). All TCP genomic data were visualized in a circos map using CIRCOS software (http://circos.ca). [...] The sequences of 24 TCP family members in the genome of Arabidopsis were retrieved from TAIR (http://www.arabidopsis.org) or PlantTFDB (http://planttfdb.cbi.pku.edu.cn/). Twenty-seven ClTCP genes were identified from a BLAST analysis of the Cucurbit Genomics Database (http://www.icugi.org). A multiple sequence alignments of the amino acid sequences of the TCP proteins of Citrullus lanatus and Arabidopsis was generated with ClustalX 2.0 software with the default settings as described by Thompson et al. []. An unrooted phylogenetic tree based on the sequence alignments was constructed using MEGA 5.0 software (http://www.megasoftware.net/) [] and the neighbor-joining method with the following parameters: pairwise alignment, 1000 bootstrap replicates, Poisson correction model, uniform substitution rates and complete deletion. In addition, a separate phylogenetic tree was constructed for all of the TCP protein sequences from Citrullus lanatus for further analysis. [...] AtTCP and ClTCP protein sequences were submitted to online searches with the Pfam (http://pfam.xfam.org) and SMART (http://smart.embl-heidelberg.de) tools to identify conserved TCP domains. The R domain was obtained from PlantTFDB (http://planttfdb.cbi.pku.edu.cn/). The method of identifying miR319-targeting TCP genes was described previously []. To visualize protein domain structures, IBS 1.0 software (http://www.mybiosoftware.com/ibs-illustrator-of-biological-sequences.html) was used. […]

Pipeline specifications

Software tools Clustal W, MEGA, IBS
Databases PlantTFDB TAIR Pfam CuGenDB
Applications Phylogenetics, Proteome data visualization
Organisms Citrullus lanatus, Arabidopsis thaliana