Bioinformatics
Shadi Heidari; Peivand Heidari
Abstract
Brassica napus field plant, as an important oilseed, has undergone extensive genome reconstruction after interspecies hybridization of its ancestors. To elucidate the evolutionary mechanisms underlying the diversity of secondary metabolites, insilico comparative analysis of different genes between three ...
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Brassica napus field plant, as an important oilseed, has undergone extensive genome reconstruction after interspecies hybridization of its ancestors. To elucidate the evolutionary mechanisms underlying the diversity of secondary metabolites, insilico comparative analysis of different genes between three Brasica species was performed. After assembling the preliminary EST sequence of libraries using EGassembler software, the contigs were analyzed by X-blast using CLC Protein Workbench software against non-redundant proteins databank. IDEG6 software and Audic-Claverie statistics were used to determine the differential expression of genes. To identify orthologs and paralogs, the Ensembl Plants website and CLUSTALW were used for a pairwise alignment for each pair of proteins. The discovery of the DNA motif is a first step in many systems to study gene function, so the MEME website and STAMP webtool were used to explore the DNA binding motif and determine the similarity of the motif sequences of the paralogs. The results showed a significant difference between 18 genes in the functional groups of secondary metabolism and transcriptional regulation. Most of the genes involved in the glucosinolate diversity in B. napus have ortholog genes in the ancestral species and Arabidopsis, which have diverged during evolutionary processes. While most transcriptional regulatory genes, including MYB28 and bHLH, have paralog genes that have been functionally altered within B. napus as a result of duplication and mutation following changes in allopolyploidy. The ancestral genome of B. napus provides valuable resources for insilico analysis in understanding the genetic consequences of polyploidy, evolution and breeding of B. napus.
