Computational protocol: Identification and Analysis of Jasmonate Pathway Genes in Coffea canephora (Robusta Coffee) by In Silico Approach

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Protocol publication

[…] Molecular evolutionary genetic analysis software MEGA6 ( was used for sequence alignment and construction of phylogenetic trees. [...] Protein sequence of different genes involved in the JA synthesis was taken from the model plant A. thaliana using NCBI database. Those sequences were used for Basic Local Alignment Search Tool (BLAST) search[] and the Coffee Genome Hub database to identify the respective gene sequences in C. canephora. Among the matches in C. canephora, top match for each gene was taken and used for BLAST search against NCBI database. The top matches for C. canephora proteins involved in the JA pathway obtained in NCBI BLAST search were used for sequence alignment to obtain phylogeny trees using MEGA6 software.[] [...] Around 14 top matches in NCBI database for each protein involved in the JA pathway and 1 top match from coffee genome database were taken from the BLAST results and transferred the sequence data to MEGA ALIGN tool in MEGA6 software. Using CLUSTALW alignment, the obtained sequences were aligned and by neighbor-joining method with bootstrap value 1000, the phylogenic trees were constructed.[] […]

Pipeline specifications

Software tools MEGA, BLASTN, Clustal W
Databases Coffee Genome Hub
Application Phylogenetics
Organisms Coffea canephora, Coffea arabica, Arabidopsis thaliana