Characterization of expansin genes in sugar beet genome by bioinformatics analysis

Expansin proteins were first discovered in cucumbers in 1992, and in later years it was revealed that they were found in all branches of the plant kingdom and some microorganisms. The expansin gene family has been divided into four subclasses: EXPA, EXPB, EXLA and EXLB. Expansin proteins mediate cell wall expansion processes. Expansin proteins have important biological roles in plants, especially due to their ability to shift cell wall polymers from polysaccharide molecules to the plant cell wall and to contribute to cell wall remodeling. Today, expansin genes are seen as important factors in plant development at all stages from germination to fruiting. Although there are many studies on expansin genes in plants, this study on the characterization of expansin genes in sugar beet whose full genome sequence has been determined is the first. 31 expansin genes have been identified in the sugar beet (Beta vulgaris L.) genome. They were named according to their location on chromosomes as BvuEXPA-01-BvuEXPA-19, BvuEXPB-01 and BvuEXPB-02, BvuEXLA-01-BvuEXLA-07, and BvuEXLB-01-BvuEXLB-03. It has been determined that all BvuEXP genes contain introns and based on phylogenetic tree proteins of the expansin family are divided into four main clusters. miRNA analysis showed that often 3 expansin genes are targeted by 40 different miRNAs, especially miR478 and miR390 being the most abundant of different miRNAs. Among the sugar beet expansin genes, 72 tandem duplications and 268 segmental duplications were observed. Looking at the gene orthologs in other organisms, the most orthologous genes were observed with Arabidopsis, followed by rice, maize and poplar genes. While maize expansin genes were the earliest to separate from sugar beet expansin genes with 350 Million years ago (Mya), this was followed by rice, Arabidopsis and poplar genes with average seperation rates of 338, 211 and 178 Mya, respectively. The ontology of the expansin proteins was also examined and their predicted biological roles in plant cells were determined. In addition, β sheet structures were observed to be the dominant structure in the predicted 3-dimensional structures of the expansin proteins. The study data are thought to contribute to the further investigation of the expansin genes in sugar beet, to increase the sugar content and plant biomass and to improve the plant characteristics to provide resistance to biological stress.