Comparative Analysis of TT2 and MYB5 in Brassica

The TT2 and MYB5 protein sequences of the six Brassica species and Arabidopsis were used to generate phylogenetic trees via ClustalX [26 (link)] and MAFFT sofaware (Katoh and Standley, 2013) multiple sequence alignments with the default parameters. A maximum likelihood (ML) phylogenetic tree was constructed using FastTree2 software (v2.1.11), in which JTT (Jones-Taylor-Thornton) model was the best substitution model [52 (link)]. The TT2 and MYB5 promoter regions of 2000 bp regions upstream of the translational start sites ATG were examined based on their positions in the genomes of six Brassica species and Arabidopsis using Samtools software (v 1.8), which was used to identify the cis-elements in the promoters according to the online PlantCARE database (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/). The gene structures of TT2 and MYB5 were analyzed according to the GFF annotation file of the gene position information in the six Brassica crops and Arabidopsis database. The MEME online tool (https://meme-suite.org/meme/) was used to investigate conserved domains, and the WEBLoGo online tool (https://weblogo.berkeley.edu/) and SWISS-MODEL online tool (https://swissmodel.expasy.org/) was used to draw spatial structure. TBtools software (v0.67) was used to draw the TT2 and MYB5 to the different copies of each Brassica species, including phylogenetic, promoter characteristics, gene structure, conserved motifs [4 ].

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Chen D., Chen H., Dai G., Zhang H., Liu Y., Shen W., Zhu B., Cui C, & Tan C. (2023). Genome-wide identification and expression analysis of the anthocyanin-related genes during seed coat development in six Brassica species. BMC Genomics, 24, 103.

Publication 2023

Arabidopsis Brassica Crops Gene Gene position Gene structure Genomes Protein sequences Sequence alignments Translational

Corresponding Organization : Sichuan Academy of Agricultural Sciences

Other organizations : Gannan Normal University

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Variable analysis

independent variables

TT2 and MYB5 protein sequences of the six Brassica species and Arabidopsis

dependent variables

Phylogenetic trees generated via ClustalX and MAFFT multiple sequence alignments
Cis-elements identified in the promoters of TT2 and MYB5 genes
Gene structures of TT2 and MYB5
Conserved domains identified using MEME online tool
Spatial structures drawn using WEBLoGo and SWISS-MODEL online tools

control variables

Default parameters used in ClustalX and MAFFT multiple sequence alignments
JTT (Jones-Taylor-Thornton) model used as the best substitution model in FastTree2 software
2000 bp regions upstream of the translational start sites ATG examined for the TT2 and MYB5 promoter regions

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