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Background  Hickory ( Carya cathayensis ), a woody plant with high nutritional and economic value, is widely planted in China. Due to its long juvenile phase, grafting is a useful technique for large-scale cultivation of hickory. To reveal the molecular mechanism during the graft process, we sequenced the transcriptomes of graft union in hickory.    Results  In our study, six RNA-seq libraries yielded a total of 83,676,860 clean short reads comprising 4.19 Gb of sequence data. A large number of differentially expressed genes (DEGs) at three time points during the graft process were identified. In detail, 777 DEGs in the 7 d vs 0 d (day after grafting) comparison were classified into 11 enriched Gene Ontology (GO) categories, and 262 DEGs in the 14 d vs 0 d comparison were classified into 15 enriched GO categories. Furthermore, an overview of the PPI network was constructed by these DEGs. In addition, 20 genes related to the auxin-and cytokinin-signaling pathways were identified, and some were validated by qRT-PCR analysis.    Conclusions  Our comprehensive analysis provides basic information on the candidate genes and hormone signaling pathways involved in the graft process in hickory and other woody plants.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-3182-4) contains supplementary material, which is available to authorized users.

Analysis of transcriptome in hickory (Carya cathayensis), and uncover the dynamics in the hormonal signaling pathway during graft process