De novo transcriptome assembly of the Chinese pearl barley, adlay, by full-length isoform and short-read RNA sequencing

• Published in: PloS one 2018-12, Vol.13 (12), p.e0208344-e0208344
• Main Authors: Kang, Sang-Ho, Lee, Jong-Yeol, Lee, Tae-Ho, Park, Soo-Yun, Kim, Chang-Kug
• Format: Article
• Language: English
• Subjects: Asian medicine; Assembly; Barley; Biology and life sciences; Biosynthesis; Breeding; Cancer; Cardiovascular diseases; Chronic diseases; Coix - genetics; Coix - metabolism; Computer and Information Sciences; Corn; Coronary artery disease; Deoxyribonucleic acid; DNA; Gene expression; Gene families; Gene sequencing; Genes; Genetic aspects; Genomes; Genomics; Heart; Heart diseases; Herbal medicine; Metabolism; Metabolites; Physical sciences; Physiology; Plant tissues; Prolamins - metabolism; Protein Isoforms - genetics; Proteins; Quality; Research and analysis methods; Retirement benefits; Ribonucleic acid; RNA; RNA sequencing; Seeds; Sequence Analysis, RNA - methods; Sorghum; Sorghum - genetics; Tocopherol; Traditional Chinese medicine; Transcription (Genetics); Transcriptome - genetics; Vitamin E; Vitamin E - metabolism; Vitamins; Zea mays - genetics
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0208344

Adlay (Coix lacryma-jobi) is a tropical grass that has long been used in traditional Chinese medicine and is known for its nutritional benefits. Recent studies have shown that vitamin E compounds in adlay protect against chronic diseases such as cancer and heart disease. However, the molecular basis of adlay's health benefits remains unknown. Here, we generated adlay gene sets by de novo transcriptome assembly using long-read isoform sequencing (Iso-Seq) and short-read RNA-Sequencing (RNA-Seq). The gene sets obtained from Iso-seq and RNA-seq contained 31,177 genes and 57,901 genes, respectively. We confirmed the validity of the assembled gene sets by experimentally analyzing the levels of prolamin and vitamin E biosynthesis-associated proteins in adlay plant tissues and seeds. We compared the screened adlay genes with known gene families from closely related plant species, such as rice, sorghum and maize. We also identified tissue-specific genes from the adlay leaf, root, and young and mature seed, and experimentally validated the differential expression of 12 randomly-selected genes. Our study of the adlay transcriptome will provide a valuable resource for genetic studies that can enhance adlay breeding programs in the future.