Transcriptome Analysis Of Hulless Barley

Tibetan hulless barley (Hordeum vulgare var. nudum) is a cereal plant of the genus Hordeum in the family Poaceae, the staple food of Tibetans. In this study, six different tissues from hulless barley cv. Dulihuang for digital gene expression (DGE) and RNA-seq analysis were conducted with the platform of Illumina HiSeqTM2000. The clean reads (51661626) of RNA-seq were de novo assembled into86674contigs with an average length of745bp, including86385protein-encoding contigs (99.67%) that can be translated into proteins with an average length of169aa. The assembled contigs were also analyzed by the Gene Ontology (GO) annotation and the GO slim classification. The genes encoding receptor-like kinases, and those involved in hormone biosynthesis and signal transduction, anthocyanin biosynthesis and UV stress resistance among Arabidopsis, rice, barley and hulless barley were phylogenetically analyzed. The results indicated that a portion of those functional genes are conserved as single copy in those plants, but others underwent constant duplication and loss events which may affect the function conservation of them across those plants.Alternative splicing (AS) can be largely discovered by transcriptome sequencing. AS has been shown to affect mRNA structures in many plants, but how AS affects the protein coding region (CDS) and protein domain structure of genes and what genes are more or less likely to be alternatively spliced at genome-wide scale are mainly unexplored for plants. Comparative analysis of available transcript models of common barley, hulless barley and Arabidopsis showed that the frequency of AS types varies among mRNA, CDS and protein domains in plants, especially intron retention is no longer the most frequent AS type in CDS region. At genome-wide scale, the chance of AS altering the domain structure varies according to the domain types, with the highest likelihood to be alternatively spliced in non-RLK kinase domain, followed by RLK kinase domain and DNA-binding domain of transcription factor. Gene expression data analysis of multiple tissues of common barley and hulless barley showed that genes with tissue biased expression are much less likely to be alternatively spliced than those stably expressed in all tissues.