Abstract： Coix (Coix lachryma-jobi) is a crop, which has high value of nutrition and medicine. However, the most studies are focus on physiology and biochemistry, there is a lack of molecular biology research in coix. In order to obtain genetic datas and functions, the study carried on the transcriptome analysis of coix leaf in seedlings. In this study, 92 865 unigenes were obtained and 35 813 unigenes were successfully annotated to some databases, being 39.87% of total unigenes numbers. GO (Gene Ontology) analysis showed that 1 053 unigenes were identi?ed as potentially involved in the drought, which 409 and 125 unigenes were identified as encoding some plant hormones and osmosis synthetases. Meanwhile, some genes and enzymes were also annotated in GO database, including lipid compounds, sterol and catechol. For KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis, 6 560 unigenes were assigned to 170 known pathways. Among these pathways, "Plant hormone signal transduction" (264 DEGs), which were the more enriched metabolic pathways of differentially expressed genes. Among plant hormone signal transduction, AMPK (AMP-activated protein kinase), MAPK (mitogen-activated protein kinase) and Ca signal transduction were related to drought stress. In addition, 7 534 simple sequence repeats were detected. The most abundant microsatellites were mononucleotide repeats, with the SSR numbers being 3 068, followed by trinucleotide and double base repeats, being 3 017 and 1 288, respectively. This study will provide the foundation and reference for functional genes obtaining and molecular biology study in coix.
