Transcriptomic Analysis of Tomatoes Infected with Tomato Mosaic Virus and Cucumber Mosaic Virus

Viral diseases are a major factor limiting tomato productions world-wide. To better understand molecular interaction between tomatoes and their viruses, transcriptomes of tomatoes infected with Tomato mosaic virus (ToMV) or Cucumber mosaic virus (CMV) alone or together were sequenced. Approximately 12 million Illumina reads were obtained from healthy and virus-infected tomatoes, 80% of which were mapped to the recently published tomato genome (Nature 485, 635–641). Using a criterion of p<0.05 and a minimum of 2-fold changes, we found 183 up-regulated genes and 232 down-regulated genes in ToMV-infected tomatoes and 293 up-regulated genes and 285 down-regulated genes in CMV-infected tomatoes. In double-infected tomatoes, up-regulated genes increased to 302 while down regulated genes decreased to 165. These data indicated that tomato plants responded actively to the viral infections in general and that the mixed infection by different viruses led to more genes being up-regulated than down-regulated. Expression of nearly 4% of all tomato genes were altered by the infection by these two viruses.  In contrast, only a relative small number (40) of genes  were differentially regulated between ToMV-infected and CMV-infected tomatoes, indicating that tomato plants responded via similar pathways to infections by to the two very different viruses, ToMV, a member of Virgaviridae, and CMV, a member of Bromoviridae. Further analysis revealed that nearly 11% of resistance-related genes responded to infections by these viruses.