Evolutionary Analysis of MYB Gene Family

The BnPIR website (http://cbi.hzau.edu.cn/bnapus, accessed on 5 March 2022) provided information on the chromosome location of BnaMYBs. After that, the distribution status of the BnaMYBs discovered on the chromosomes was shown using MapChart software. With the aid of Adobe Illustrator, the outcomes were improved.
We downloaded the protein sequences of the MYB family members of Brassica oleracea, Brassica rapa, Capsella rubella, Oryza sativa, Raphanus sativus and Zea mays. The sequences of the protein on the Brassica oleracea and Brassica rapa were collected from the Phytozome website (https://phytozome.jgi.doe.gov/pz/portal.html, accessed on 10 March 2022). The sequences of the protein in Oryza sativa and Zea mays were collected from the Ensembl website (http://plants.ensembl.org/index.html, accessed on 10 March 2022). The protein sequences of Capsella rubella and Raphanus sativus were collected from the NCBI website (https://www.ncbi.nlm.nih.gov/, accessed on 10 March 2022). OrthoMCL software (v2.0.3) [62 (link)] was used to search for orthologous, co-orthologous, and paralogous genes in Arabidopsis thaliana, Brassica oleracea, Brassica rapa, Capsella rubella, Oryza sativa, Raphanus sativus and Zea mays using entire R2R3-MYB protein sequences. The E-value cut-off of an all-against-all BLASTP alignment process was set at 1 × 10⁻¹⁰, and the alignments with a match cut-off value lower than 50 were eliminated.
These plants’ MYB protein sequences were analyzed using Clustal W after the protein sequences of MYB family members from B. napus, Arabidopsis, B. oleracea, B. rapa, Capsella rubella, Oryza sativa, Raphanus sativus and Zea mays were retrieved. Additionally, MEGA 11.0 software was used to create the evolutionary tree using the neighbor joining method (NJ) once the results of sequence alignment were obtained [63 (link),64 (link)]. Finally, we used Evolview (http://www.omicsclass.com/article/671, accessed on 13 March 2022) to visualize the evolutionary tree.