Computational protocol: Gene expression and metabolite profiling of gibberellin biosynthesis during induction of somatic embryogenesis in Medicago truncatula Gaertn

Similar protocols

Protocol publication

[…] To identify Medicago truncatula genes encoding the enzymes of the GA biosynthetic pathway, Arabidopsis thaliana protein sequences of known function from the TAIR data base, were used as queries to search the Medicago truncatula JCVI Mt 4.0v1 data base. The NGS transcription library of the M9-10a embryogenic line from all time-points during the SE induction phase were used for additional BLAST analysis conducted with the Geneious software (Biomatters Ltd). Protein BLAST were used to obtain protein sequences from the NBCI data base for Brassica napus, Cicer arietinum, Glycine max, Oryza sativa, Pisum sativum, Phaseolus vulgaris, and Solanum lycopersicum. For the sequence-based phylogeny, multiple sequence alignments of protein sequence were performed using the ClustalW. The phylogenetic analysis was conducted using the Geneious 6.1 software [] with the Neighbor-Joining tree building method and Jukes-Cantor genetic distance model. The trees were resampled 1000 times using the bootstrap method and out-groups were used for rooting of phylogenetic trees. The candidate Medicago truncatula genes are summarized in . […]

Pipeline specifications

Software tools Geneious, DELTA-BLAST, Clustal W
Databases TAIR
Applications Phylogenetics, Amino acid sequence alignment
Organisms Medicago truncatula, Caenorhabditis elegans
Chemicals Gibberellins