03. Codon usage bias and RNA secondary structures analysis for virus resistant genes in Arabidopsis thaliana and Oryza sativa
Abstract
The current study is based upon the relationship of the codon usage bias (CUB) and RNA secondary structures (RSS) analysis between virus resistant (biotic stress) and housekeeping genes in Arabidopsis thaliana (ath) and Oryza sativa (osa). A total of seventeen genes (including thirteen virus resistant and four housekeeping genes) were subjected for the CUB and RSS analysis. The CUB analysis revealed that nine (out of thirteen) virus resistant genes showed similarity by more than 50% in the usage of codons for Arabidopsis thaliana and Oryza sativa and only one (out of four) ATC8 (housekeeping gene) showed similarity in the usage of codons by more than 50%. On the other hand Mfold algorithms for RNA secondary structure prediction revealed that six virus resistant genes showed significant difference in minimum free energy, two in number of loops and one in the number of stems. Whereas for the housekeeping genes, none showed significant difference in minimum free energy, number of loops & number of stems of RNA secondary structures. It can be concluded from the results that on the basis of RNA secondary structure virus resistant genes show mix behavior while housekeeping genes show uniform behavior. CUB analysis helps us to engineer the virus resistant crops through adjusting specific codon usage.
Keywords: Biotic stress; CUB; Housekeeping genes; RNA secondary structures
