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Reaumuria soongorica is one of the typical desert plants that present excellent tolerance to adverse environments. However, its molecular response to UV-B radiation remains poorly understood. To test the response and tolerance mechanisms of R. soongorica to the increasing UV-B radiation, the differentially expressed genes (DEGs) were investigated between the control and UV-B radiation groups. A total of 2150 DEGs were detected between the two groups, of which 561 were up-regulated and 1589 were down-regulated. For functional analysis, DEGs were divided into three groups: (i) Chloroplast-localized proteins, including photosynthesis-associated proteins, ribulose-phosphate-3-epimerase, and ATP-dependent Clp protease. Their transcripts were inhibited, implying that the normal function of chloroplast was affected by UV-B radiation. (ii) Proteins involved in signaling transduction, such as phototropins and GTP-binding proteins. The transcriptional alternation of phototropins may reduce the penetration of UV-B radiation by regulating phototropism, stomatal opening, and chloroplast relocation. The down regulation of GTP-binding proteins may inhibit replication of potentially damaged DNA through preventing cell division; and (iii) proteins for lipid transfer and flavonoids biosynthesis. The up-regulation of these genes suggested that lipid transfer and flavonoids may have a protective function in response to UV-B radiation. Thus, IN-B radiation may lead to the disruption of chloroplasts function. The induction of genes for signal transduction and protective proteins may be a strategy for responding to UV-B radiation in R. soongorica. (C) 2015 Elsevier B.V. All rights reserved.