RT Journal
T1 BIOINFORMATICS ANALYSIS OF CODON USAGE BIAS AND RNA SECONDARY STRUCTURES FOR SALT STRESS RESPONSIVE GENES IN ARABIDOPSIS THALIANA AND SOLANUM LYCOPERSICUM
A1 B. Sadia
A1 W. N. Hamzazai
A1 I. A. Baloch
A1 S. Kazmi
A1 Asyia
A1 P. S. Jan
A1 S. Irfan
JF Journal of Animal and Plant Sciences
JO JAPS
SN 1018-7081
VO 28
IS 5
SP 1532
OP 1536
YR 2018
FD 2018/10/01
DO DOI NA
AB Salt stress is one of the most important abiotic stresses for agricultural crops and other plants. Salinity highly affects physical, physiological and metabolic responses of plants. Codon usage bias (CUB) and RNA secondary structures (RSS) were analyzed for salt stress responsive ( SSR) genes of Arabidopsis thaliana and Solanum lycopersicum. Four salt stress resistant genes SOS1 (salt overly sensitive 1), BZIP (basic lucien zipper protein), HVA22-like protein and CDPK1 (calcium-dependent protein kinase 1) of Arabidopsis thaliana as well as Solanum lycopersicum were compared for CUB and RSS. All genes expressed similarity for codon usage, as both plants showed to prefer more than 50% (65%, 50%, 60%, and 80%) similar codon usage for all four selected salt stress responsive genes. RSS analysis revealed that three SSR genes had significant difference in minimum free energy ( MFE) while two differed in number of loops and stems depicting overall mix behavior. These findings can further help to engineer the salt resistant genes by adjusting the codon usage through genetic screening and by using bioinformatics tools. of base pairing within a single molecule as well as in a set
K1 Codon usage bias; Genetic code; Salinity responsive genes; Secondary structure.
PB Pakistan Agricultural Scientists Forum
LK https://thejaps.org.pk/AbstractView.aspx?mid=2018-JAPS-537