Comparative bioinformatics analysis of Pyrroline-5-carboxylate synthase (P5CS), Betaine aldehyde dehydrogenase (BADH) and Ferritin encoding genes in several crop species

Abstract

Improving abiotic stress tolerance in crops using both conventional breeding and transgenic techniques has become highly important. Of them, the transgenic technique provides means for the introgression of novel genes across species. Prior knowledge of conserved regions of a gene throughout the evolutionary process and the evolutionary divergence of genes among different plant species and families for coding sequences is vitally important in the genetic engineering processes. The genes: Pyrroline-5-carboxylate synthase (P5CS), Betaine aldehyde dehydrogenase (BADH) and Ferritin have been reported to be involved in delivering tolerance to abiotic stresses in crops. In this study, bioinformatics analysis was used to study coding sequences of the three genes encoding P5CS, BADH and Ferritin in nine different crop species. Coding sequences were retrieved from National Center for Biotechnology Information (NCBI) and ClustalW multiple sequence alignment was performed using MEGA₅ software. A phylogenetic tree following the maximum likelihood approach with 100 bootstrap analysis and pairwise distances was obtained. DnaSP₅ software was used to analyze the conserved regions. P5CS, BADH and Ferritin genes recorded sixteen, seven and six conserved regions respectively with significant (P≤ 0.05) conservation and homozygosity values. Phylogenetic trees of P5CS and BADH showed three distinct clusters whereas only two clusters were observed for the Ferritin gene. There was a significant evolutionary divergence among CDS of P5CS (0.011 - 0.458), BADH (0.017 - 0.406) and Ferritin (0.009 - 0.509) genes. The results revealed the three genes to possess several regions conserved throughout the evolutionary process. Phylogeny reconstruction of the genes revealed the existence of two groups, separating monocot from dicot plants. The information derived will be important in the genetic engineering of crops for abiotic stress tolerance.

KEYWORDS: BADH, Conserved regions, evolutionary divergence, Ferritin, P5CS, phylogenetic relationships