Comparative Analysis of Sequence, Chromosomal Arrangement and Cis-Regulatory Elements of SQS Genes Across Brassicaceae

Plant sterols are known to be involved in plant growth and development and also in plants' response to stress conditions. Squalene synthase (SQS) is an important enzyme for the biosynthesis of sterols and triterpenoids. Owing to their crucial role in plants, SQS genes have been identified and characterized in several plants, however not much is known about their cis-regulatory regions. In our previous study, we identified Brassicaceae specific duplications of the gene, providing an ideal opportunity to explore the diversification of the regulatory regions across the gene copies. In this study we identified 49 SQS genes from 12 species of Brassicaceae and analyzed their genomic distribution, physicochemical properties, subcellular localization, cis-regulatory element (CRE) landscape and sequence evolution (Ka/Ks ratios). The SQS proteins were predicted to be highly stable, dominated by aliphatic amino acids, hydrophilic in nature and localized within the endoplasmic reticulum. In-silico promoter analysis identified 50 types of CREs with the predominance of light-responsive (22), followed by hormone-responsive (9), stress-responsive (7) and plant growth and development (9) elements. We identified differences both in the type and distribution of CREs across the SQS duplicates suggestive of regulatory divergence of the paralogs. The Ka/Ks analysis depicted that all the SQS genes are under purifying selection pressure. The information generated in this study would provide a useful resource for further investigations in SQS genes in Brassicaceae.