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Background  Chrysanthemum is an important ornamental plant all over the world. It is easily attacked by aphid,  Macrosiphoniella sanbourni . The molecular mechanisms of plant defense responses to aphid are only partially understood. Here, we investigate the gene expression changes in response to aphid feeding in chrysanthemum leaf by RNA-Seq technology.    Results  Three libraries were generated from pooled leaf tissues of  Chrysanthemum morifolium  ‘nannongxunzhang’ that were collected at different time points with (Y) or without (CK) aphid infestations and mock puncture treatment (Z), and sequenced using an Illumina HiSeq TM  2000 platform. A total of 7,363,292, 7,215,860 and 7,319,841 clean reads were obtained in library CK, Y and Z, respectively. The proportion of clean reads was >97.29% in each library. Approximately 76.35% of the clean reads were mapped to a reference gene database including all known chrysanthemum unigene sequences. 1,157, 527 and 340 differentially expressed genes (DEGs) were identified in the comparison of CK-VS-Y, CK-VS-Z and Z-VS-Y, respectively. These DEGs were involved in phytohormone signaling, cell wall biosynthesis, photosynthesis, reactive oxygen species (ROS) pathway and transcription factor regulatory networks, and so on.    Conclusions  Changes in gene expression induced by aphid feeding are shown to be multifaceted. There are various forms of crosstalk between different pathways those genes belonging to, which would allow plants to fine-tune its defense responses.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-1050) contains supplementary material, which is available to authorized users.

Gene expression profiles responses to aphid feeding in chrysanthemum (Chrysanthemum morifolium)