Preliminary in silico Analysis of CHS1 Gene in Commelinids Clade: Family Zingiberaceae, Costaceae, and Poaceae

Abstract

The chalcone synthase (CHS) gene families are known to be conserved in plants and have been well-studied in many plants, and they have an important role in the physiological and biological processes of plants. One of the studied CHS gene families is the CHS1 gene. CHS1 gene is known for its function in the flavonoid biosynthetic pathway. However, not many studies have been reported on the CHS1 gene in the Commelinids clade, especially the evolution of this gene within three families: Zingiberaceae, Costaceae, and Poaceae. Thus, this study aimed to perform a preliminary in silico comparative analysis of the CHS1 gene across these three families. Through this in silico comparative analysis, 20 partial sequences of the CHS1 gene, which are restricted to 565 bp regions, were analysed. The partial sequences were extracted from the National Center for Biotechnology Information database comprised of 16 Zingiberaceae species, three Costaceae species, and one Poaceae species. From the analysis, these targeted regions showed a low polymorphic site (18.23%) with 103 positions of single nucleotide polymorphisms and three mutations (substitution, insertion, and deletion). Meanwhile, phylogenetic analysis showed no clear evolutionary pattern within the three studied families. In conclusion, the studied partial sequences of the CHS1 gene in Zingiberaceae, Costaceae, and Poaceae showed that the gene is conserved within the Commelinids clade. Further studies to understand the consequences of low polymorphism and mutations as well as adaptive evolution in the CHS1 gene, accompanied by biochemistry and gene expression studies, should be done in these 20 species of Zingiberaceae, Costaceae, and Poaceae.