Drought stress severely affects plant growth and crop yield. Coix lachryma-jobi L (Coix) commonly known as Job’s tears, is a member of the grass family in the tribe Maydeae. To understand the transcriptome dynamics and explore the important drought resistant genes during drought stress in coix seedlings, in this study,YiLiao 5, with good resistant drought was taken as the experimental material. The results showed 92,865 unigenes were detected and the average gene length was 737.85 bp, the N50 was 1,26bp. A comparison of the treatment and the control samples revealed that 1,128 differentially expressed genes (DEGs) were expressed, including 662 and 466 genes that were up-and down-regulated, respectively. According to the Gene Ontology (GO) database, among biological processes the metabolic process group was the largest group (14,908 genes, 24.28%) and contained high frequency of differentially expressed genes (352 genes, 24.22%). The DEGs are involved in 170 metabolic pathways. The plant hormone signal transduction and starch and sucrose metabolism were relatively obvious. Some DEGs and proteins were found, such as response to abscisic acid genes, 9-cis-epoxycarotenoid dioxygenase, some Transcription factors (TFs), protein serine/threonine phosphatase, late embryogenesis abundant protein (LEA). Eight genes analyzed by Quantitative Real-time PCR (qRT-PCR) confirmed the transcriptome results. Overall, this study had done the transcriptome sequencing and established a genomics database of Coix for the first time. Meanwhile the results also provided a molecular basis and theoretical resource for mechanistic studies on drought resistance in Coix
