Transcriptome analysis reveals the hawthorn response to the infection of apple chlorotic leaf spot virus

Viral diseases have become an important disease in the growth and development of fruit trees. Apple chlorotic leaf spot virus (ACLSV) is one of the most important viruses that harm fruit trees. We performed a high-throughput sequencing study to identify the differentially expressed genes (DEGs) induced by ACLSV in hawthorn using uninfected plants as a control. The results indicated that we have identified 125,469 unigenes, of which 9910 were expressed differentially. GO and KEGG enrichment analysis of the DEGs revealed that most DEGs were in the “stimulus response” GO term of “biological processes” and the “plant-pathogen interaction” KEGG pathway. Quantitative RT-PCR analysis about some defense-related genes showed a high consistency with the transcriptome data. This is the first study characterizing changes in plants when challenged with ACLSV through the transcriptome.