In silico analysis of XTH gene family from barley (Hordeum vulgare L.) and their comparative expression analysis during germination

Changes in plant cell walls are critical for expansion and growth. Xyloglucan endotransglycosylase/hydrolase (XTH) enzymes are the major modifiers of xyloglucan within the cell wall and are present as large gene families. Despite the paucity of xyloglucan in barley, our analyses of the barley genome revealed at least 42 XTH genes, the most XTH members recorded for a monocot genome to date. In this paper, we show a detailed look at the barley XTH gene family, including detailed bioinformatics analyses of conserved protein motifs and structure, phylogenetic relationships, and a comparison of the expression patterns during germination and seedling growth using RT-qPCR and RNA-Seq analyses. Overall, there was a good correlation between RT-qPCR and RNA-Seq data for similar tissues. RNA-Seq data showed many different expression profile patterns, from broad, high level expression for some XTH genes to highly tissue specific patterns for others. RT-qPCR expression patterns also varied widely between genes. The highest expressing gene, HvXET4, had levels around five times that of the highest control gene tubulin. Given the low levels of xyloglucan found in barley, this high level of expression suggests that the enzyme may be catalysing reactions with other cell wall polysaccharides. We propose roles for many of the HvXTH genes based on the results shown here.