Transcriptome analysis of chrysanthemum in responses to white rust

Chrysanthemum white rust (CWR), one of the primary diseases on chrysanthemum, has been considered as a quarantine disease in many countries. Few studies have been conducted on the molecular mechanisms of white rust resistance in chrysanthemum. In this study, we performed transcriptome and digital gene expression profiling to investigate the responses of chrysanthemum to white rust infection. By using RNA-Seq technology, we aimed to screen the differentially expressed genes (DEGs) for functional annotation and metabolic pathway analysis. The resistant (CO29) and susceptible (C008) cultivars were sequenced by Illumina HiSeq (TM) 2000. 20,597,533, 19,519,160, 20,570,705 and 20,301,157 total reads were obtained from four libraries, respectively, and for all samples, clean reads were over 97.34% of the total. We obtained 392,137 unigenes through sequencing assembly and we gained 213,531 complete protein coding sequences by annotation. 433 significant DEGs were obtained between R0 (resistant cultivar control) and R1 (resistant cultivar with inoculation), and 787 DEGs were obtained between S0 (susceptible cultivar control) and S1 (susceptible cultivar with inoculation) through expression quantity analysis and functional annotation in 194,179 genes. There were 14 genes which had differential expressions in both two comparison groups. These DEGs were involved in the pentose phosphate pathway, phenylpropanoid biosynthesis pathway, carbon metabolism pathway and phenylalanine metabolism pathway. The results of the qRT-PCR indicated that the expression tendency of DEGs was consistent with that of the transcriptome sequencing results. Our transcriptome sequencing can help to fill the gaps in the literature on CWR transcriptome and enrich sequence information of chrysanthemum transcriptome. It also offers candidate genes that can be used to guide future studies attempting to breed resistant cultivars, and provides a theoretical basis for exploring the mechanism of response of chrysanthemum to white rust.