In silico analyses of gene families involved in xyloglucan synthesis in barley (Hordeum vulgare L.)

Barley (Hordeum vulgare L.) is a cereal that has always been one of the key plants to cultivate since ancient times. Today, it is the fifth most produced crop in the world. Because of its economic importance, barley has been investigated in many studies and scientific works. Xyloglucans (XyGs) is an important component of barley cell walls, and is involved in the process of cell growth. The backbone of XyGs is synthesized by cellulose synthase-like C (CSLC) enzymes, whilst xylosyl substitution, added by xyloglucan xylosyl transferases (XXT) is the most common side chain. Many different sidechains patterns have been observed on xyloglucan, which are added through the catalytic activities of enzymes such as xyloglucan galactosyl transferase (XGT), xyloglucan o-acetyl transferase (O-AcT), and fucosyl transferase (FUT) transferase. To date, they are not any publications that have systematically investigated all the genes involved in XyG synthesis, in any plant. This study aimed to analyze, at the in silico level, the gene families that are involved in XyG synthesis in barley. Since there are many different polysaccharides present in barley, the second goal was to determine the co-expression patterns of all these genes, in order to find the most likely candidates involved in XyG synthesis. For this study, five different gene groups, CSLC, XXT, XGT, O-AcT, and FUT were investigated. Protein sequence alignments and phylogenetic trees were used to determine the level of relatedness within each group. In addition, their expression levels were investigated using public RNA-seq data, with calculations of their FPKM values. Values were analyzed using Pearson Correlation to find co-expression levels between each of the genes. Since CSLC enzymes are crucial to xyloglucan structure, the analysis focused onto co-expression with these genes. HvCSLC3 in particular showed the highest number of correlating genes, including XXTs, XGTs, O-AcTs, and somewhat surprisingly, several FUTs. Tissues from 4-6 weeks barley plants generally gave higher FPKM values for the studied genes, so the need for xyloglucan might be increase at that time interval in barley. This study should lead to further investigations into the biosynthesis of XyG in barley, not only at mRNA/protein levels, but also in polysaccharide/carbohydrate levels and fine structural analyses.