Jasmonic acid is a natural plant hormone that induces native defense responses in plants. Sugarbeet (Beta vulgaris L.) root unigenes that were differentially expressed 2 and 60 days after a postharvest jasmonic acid treatment are presented. Data include changes in unigene expression relative to water-treated controls, unigene annotations against nonredundant (Nr), Swiss-Prot, Clusters of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) protein databases, and unigene annotations with Gene Ontology (GO) terms. Putative defense unigenes are compiled and annotated against the sugarbeet genome. Differential gene expression data were generated by RNA sequencing. Interpretation of the data is available in the research article, "Jasmonic acid causes short- and long-term alterations to the transcriptome and the expression of defense genes in sugarbeet roots" (K.K. Fugate, et al., Plant Gene 9:50-63) Resources in this dataset:Resource Title: Short- and long-term changes in sugarbeet (Beta vulgaris L.) gene expression due to postharvest jasmonic acid treatment - Data. File Name: Web Page, url: https://www.sciencedirect.com/science/article/pii/S2352340917300276 Data in Brief: Data on sugarbeet root unigenes that were differentially expressed due to a postharvest jasmonic acid (JA) treatment are presented. Data identify unigenes that were differentially expressed 2 and 60 d after JA treatment. Data include the logarithm of the fold change in expression due to JA treatment, relevant statistics related to changes in expression, unigene annotations generated by BLASTx search against nonredundant (Nr), Swiss-Prot, Clusters of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) protein databases, and Gene Ontology (GO) annotations (Tables 1 and 2). In addition, differentially expressed genes with putative defense functions were identified, compiled, and further annotated by comparison to the sugarbeet genome.