Coix lacryma-jobi L. is a very important economic crop widely cultivated in Southeast Asia. Drought affects more than four million square kilometers every year, and is a significant factor limiting agricultural productivity. However, relatively little is known about how Coix lacryma-jobi L. responds to drought treatments. To obtain a detailed and comprehensive understanding of the mechanisms regulating the transcriptional responses of Coix lacryma-jobi L. to drought treatment, we employed high throughput short-read sequencing of cDNA prepared from polyadenylated RNA to explore global gene expression after a seven-day drought treatment. We generated a de novo assembled transcriptome comprising 65,480 unique sequences. Differential expression analysis based on RSEM-estimated transcript abundances identified 5,315 differentially expressed genes (DEGs) when comparing samples from plants following drought-treatment and from the appropriate controls. Among these, the transcripts for 3,460 genes were increased in abundance, whereas 1,855 were decreased. Real-time quantitative PCR for 5 transcripts confirmed the changes identified by RNA-Seq. The results provide a transcriptional overview of the changes in Coix lacryma-jobi L. in response to drought, and will be very useful for studying the function of associated genes and selection of molecular marker of Coix lacryma-jobi L in the future.
CIRCexplorer pipelines for circRNA annotation and quantification from non-polyadenylated RNA-seq datasets
