Computational protocol: Four genes encoding MYB28, a major transcriptional regulator of the aliphatic glucosinolate pathway, are differentially expressed in the allopolyploid Brassica juncea

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Protocol publication

[…] The coding sequences and amino acids of the BjuMYB28 genes were predicted using the software DNASTAR (Lasergene). Multiple sequence alignments of coding sequences and the deduced amino acid sequences of MYB28 from Arabidopsis and Brassica species were performed using ClustalW. Percentage similarities among MYB28 homologues were calculated using the MegAlign module of DNASTAR.The BLASTX search of AtMYB28 and four BjuMYB28 coding sequences was performed on the publicly available database at NCBI (http://blast.ncbi.nlm.nih.gov/Blast.cgi) and phytozome (http://phytozome.net). Full-length coding sequences showing high percentage similarity scores and sequence coverage were obtained. Evolutionary history was inferred using the Maximum Likelihood method () based on the JTT matrix-based model in MEGA5 (). MYB28 like sequences reported from the following genomes were used for the analysis: Arabidopsis thaliana (AtMYB28, AtMYB29, AtMYB76); Arabidopsis lyrata (Aly_950898, Aly_487604, Aly_892702); Capsella rubella (Cru_10027861m, Cru_10001328m); Thellungiella halophila (Tha_v10004407m, Tha_v10013952m); Brassica rapa (Bra035929, Bra012961, Bra029311), and Brassica oleracea (BolC.MYB28.1/ADK38583, BolC.MYB28.2/CBI71385). The deduced proteins from the B. rapa (BraA.MYB28.1, BraA.MYB28.2); B. nigra (BniB.MYB28.1, BniB.MYB28.2), and B. juncea (BjuMYB28-1, -2, -3, and -4) genomes were also used. […]

Pipeline specifications

Software tools DNASTAR Lasergene, Clustal W, BLASTX, MEGA
Databases Phytozome
Applications Phylogenetics, Sanger sequencing
Organisms Homo sapiens, Arabidopsis thaliana, Brassica juncea, Brassica rapa, Brassica nigra