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Dendrobium officinale is a traditional medicinal herb with a variety of bioactive components. Alkaloid is one of the major active ingredients of Dendrobium plants, and its immune regulatory effects have been well-studied. Although a number of genes involved in the biosynthetic pathway of alkaloids have been elucidated, the regulation mechanism underlying the methyl-jasmonate (MeJA)-induced accumulation of alkaloids in D. officinale is largely unknown. In our study, a total of 4,857 DEGs, including 2,943 up- and 1,932 down-regulated genes, were identified between the control and MeJA-treated groups. Kyoto Encyclopedia of Genes and Genomes annotation showed that a number of DEGs were associated with the putative alkaloid biosynthetic pathway in D. officinale. The main group of Dendrobium alkaloids are sesquiterpene alkaloids, which are the downstream products of mevalonate (MVA) and methylerythritol 4-phosphate (MEP) pathway. Several MVA and MEP pathway genes were significantly up-regulated by the MeJA treatment, suggesting an active precursor supply for the alkaloid biosynthesis under MeJA treatment. A number of MeJA-induced P450 family genes, aminotransferase genes and methyltransferase genes were identified, providing several important candidates to further elucidate the sesquiterpene alkaloid biosynthetic pathway of D. officinale. Furthermore, a large number of MeJA-induced transcript factor encoding genes were identified, suggesting a complex genetic network affecting the sesquiterpene alkaloid metabolism in D. officinale. Our data aids to reveal the regulation mechanism underlying the MeJA-induced accumulation of sesquiterpene alkaloids in D. officinale. [ABSTRACT FROM AUTHOR]