Transcriptome analysis of Crimson seedless grapevine (Vitis vinifera L.) infected by grapevine berry inner necrosis virus

Grapevine fruits produced in China are often infected by grapevine berry inner necrosis virus (GINV). GINV disease is the most economically important viral disease of the grapevine, characterized by discoloration on the fruit surface and necrosis of the flesh. In this study, the transcriptome sequencing technology revealed 1700 differently expressed genes (DEGs), with 846 up-regulated and 854 down-regulated genes in Crimson seedless grapevine during the GINV infection. Both Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted to classify the DEGs. The top 10 GO terms were enriched in GINV versus mock, and these enriched GO terms were mainly classified into three categories, namely, 324 cellular components, 2062 biological processes, and 940 molecular functions. Based on the P-values, the KEGG pathway analysis indicated that 96 major pathways were identified in GINV versus mock, and 20 major enrichment pathways were significantly enriched. Using quantitative real-time polymerase chain reaction (qRT-PCR), we validated the differential expression of 12 genes. The expression patterns of 11 genes were consistent with the RNA-sequencing (RNA-seq) results, except for one gene. Thus, our study provides comprehensive transcriptome information on the GINV–grapevine interaction, thereby improving our understanding of virus–host interactions.