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

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.