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To obtain better insight into the mechanisms of selenium hyperaccumulation in Stanleya pinnata, transcriptome-wide differences in root and shoot gene expression levels were investigated in S. pinnata and related nonaccumulator Stanleya elata grown with or without 20 M selenate. Genes predicted to be involved in sulfate/selenate transport and assimilation or in oxidative stress resistance (glutathione-related genes and peroxidases) were among the most differentially expressed between species; many showed constitutively elevated expression in S. pinnata. A number of defense-related genes predicted to mediate synthesis and signaling of defense hormones jasmonic acid (JA, reported to induce sulfur assimilatory and glutathione biosynthesis genes), salicylic acid (SA) and ethylene were also more expressed in S. pinnata than S. elata. Several upstream signaling genes that upregulate defense hormone synthesis showed higher expression in S. pinnata than S. elata and might trigger these selenium-mediated defense responses. Thus, selenium hyperaccumulation and hypertolerance in S. pinnata may be mediated by constitutively upregulated JA, SA and ethylene-mediated defense systems, associated with elevated expression of genes involved in sulfate/selenate uptake and assimilation or in antioxidant activity. Genes pinpointed in this study may be targets of genetic engineering of plants that may be employed in biofortification or phytoremediation.