Computational protocol: Analysis of the grape MYB R2R3 subfamily reveals expanded wine quality-related clades and conserved gene structure organization across Vitis and Arabidopsis genomes

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Protocol publication

[…] To place the obtained sequences in a phylogenetic context, a phylogeny reconstruction was performed with the single DNA-binding domain and full predicted amino acid sequences of grape MYB genes and then integrated in the Arabidopsis phylogenetic tree. Alignments were performed using the BLOSUM matrix (Gap opening and extension penalties of 25 and 1, respectively) using the ClustalW algorithm-based AlignX module from Mega4 software []. The phylogenetic tree was constructed using the Neighbour Joining Tree Method in Mega4 and confirmed with Mega3. Tree nodes were evaluated by bootstrap analysis for 1000 or 2000 replicates. All positions containing gaps and missing data were eliminated from the dataset (Complete deletion option in Mega4 software). Evolutionary distances were computed using the Poisson correction method and are represented as amino acid substitutions per site. Sequences of all 126 Arabidopsis R2R3 MYB proteins were downloaded from the TAIR Arabidopsis genome annotation version 7.0, released on April 2007. […]

Pipeline specifications

Software tools Clustal W, Vector NTI Advance, MEGA
Applications Phylogenetics, Protein sequence analysis
Organisms Arabidopsis thaliana, Oryza sativa