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Background  Agarwood, is a resinous portion derived from  Aquilaria sinensis , has been widely used in traditional medicine and incense. 2-(2-phenylethyl)chromones are principal components responsible for the quality of agarwood. However, the molecular basis of 2-(2-phenylethyl)chromones biosynthesis and regulation remains almost unknown. Our research indicated that salt stress induced production of several of 2-(2-phenylethyl)chromones in  A. sinensis  calli. Transcriptome analysis of  A. sinensis  calli treated with NaCl is required to further facilitate the multiple signal pathways in response to salt stress and to understand the mechanism of 2-(2-phenylethyl)chromones biosynthesis.    Results  Forty one 2-(2-phenylethyl)chromones were identified from NaCl-treated  A. sinensis  calli. 93 041 unigenes with an average length of 1562 nt were generated from the control and salt-treated calli by Illmunina sequencing after assembly, and the unigenes were annotated by comparing with the public databases including NR, Swiss-Prot, KEGG, COG, and GO database. In total, 18 069 differentially expressed transcripts were identified by the transcriptome comparisons on the control calli and calli induced by 24 h or 120 h salinity stress. Numerous genes involved in signal transduction pathways including the genes responsible for hormone signal transduction, receptor-like kinases, MAPK cascades, Ca 2+  signal transduction, and transcription factors showed clear differences between the control calli and NaCl-treated calli. Furthermore, our data suggested that the genes annotated as chalcone synthases and  O -methyltransferases may contribute to the biosynthesis of 2-(2-phenylethyl)chromones.    Conclusions  Salinity stress could induce the production of 41 2-(2-phenylethyl)chromones in  A. sinensis  calli. We conducted the first deep-sequencing transcriptome profiling of  A. sinensis  under salt stress and observed a large number of differentially expressed genes in response to salinity stress. Moreover, salt stress induced dynamic changes in transcript abundance for novel classes of responsive genes involved in signal transduction, including the genes responsible for hormone signal transduction, receptor-like kinases, MAPK cascades, Ca 2+  signal transduction, and transcription factors. This study will aid in selecting the target genes to genetically regulate  A. sinensis  salt-stress signal transduction and elucidating the biosynthesis of 2-(2-phenylethyl)chromones under salinity stress.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-016-0803-7) contains supplementary material, which is available to authorized users.

bmc plant biology

Salinity stress induces the production of 2-(2-phenylethyl)chromones and regulates novel classes of responsive genes involved in signal transduction in Aquilaria sinensis calli