Transcriptomic de novo analysis of pitaya ( Hylocereus polyrhizus ) canker disease caused by Neoscytalidium dimidiatum

Background Canker disease caused by Neoscytalidium dimidiatum is the most serious disease that attacks the pitaya industry. One pathogenic fungus, referred to as ND8 , was isolated from the wild-type red-fleshed pitaya ( Hylocereus polyrhizus ) of Hainan Province. In the early stages of this disease, stems show little spots and a loss of green color. These spots then gradually spread until the stems became rotten due to infection by various strains. Canker disease caused by Neoscytalidium dimidiatum poses a significant threat to pitaya commercial plantations with the growth of stems and the yields, quality of pitaya fruits. However, a lack of transcriptomic and genomic information hinders our understanding of the molecular mechanisms underlying the pitaya defense response. Results We investigated the host responses of red-fleshed pitaya ( H. polyrhizus ) cultivars against N. dimidiatum using Illumina RNA-Seq technology. Significant expression profiles of 23 defense-related genes were further analyzed by qRT-PCR. The total read length based on RNA-Seq was 25,010,007; mean length was 744, the N50 was 1206, and the guanine-cytosine content was 44.48%. Our investigation evaluated 33,584 unigenes, of which 6209 (18.49%) and 27,375 (81.51%) were contigs and singlets, respectively. These unigenes shared a similarity of 16.62% with Vitis vinifera , 7.48% with Theobroma cacao , 6.6% with Nelumbo nucifera and 5.35% with Jatropha curcas . The assembled unigenes were annotated into non-redundant (NR, 25161 unigenes), Kyoto Encyclopedia of Genes and Genomes (KEGG, 17895 unigenes), Clusters of Orthologous Groups (COG, 10475 unigenes), InterPro (19,045 unigenes), and Swiss-Prot public protein databases (16,458 unigenes). In addition, 24 differentially expressed genes, which were mainly associated with plant pathology pathways, were analyzed in-depth. Conclusions This study provides a basis for further in-depth research on the protein function of the annotated unigene assembly with cDNA sequences.