Transcriptome Analysis of Tomato Leaves Reveals Candidate Genes Responsive to Tomato Brown Rugose Fruit Virus Infection

Abstract

Tomato brown rugose fruit virus (ToBRFV) is a newly-emerging tobamovirus which was first reported on tomatoes in Israel and Jordan, and which has now spread rapidly in Asia, Europe, North America, and Africa. ToBRFV can overcome the resistance to other tobamoviruses conferred by tomato Tm-1, Tm-2, and Tm-2² genes, and it has seriously affected global crop production. The rapid and comprehensive transcription reprogramming of host plant cells is the key to resisting virus attack, but there have been no studies of the transcriptome changes induced by ToBRFV in tomatoes. Here, we made a comparative transcriptome analysis between tomato leaves infected with ToBRFV for 21 days and those mock-inoculated as controls. A total of 522 differentially expressed genes were identified after ToBRFV infection, of which 270 were up-regulated and 252 were down-regulated. Functional analysis showed that DEGs were involved in biological processes such as response to wounding, response to stress, protein folding, and defense response. Ten DEGs were selected and verified by qRT-PCR, confirming the reliability of the high-throughput sequencing data. These results provide candidate genes or signal pathways for the response of tomato leaves to ToBRFV infection.

Keywords: tomato; tomato brown rugose fruit virus; transcriptome analysis.

Figure 1

Symptoms on tomato leaves infected by ToBRFV. (A) Typical symptoms 21 days after ToBRFV inoculation. (B) Confirmation of the accumulation of ToBRFV in tomato leaves by PCR using ToBRFV CP-specific primers.

Figure 2

Volcanic diagram of the number of differentially expressed genes between tomato leaves of 21-day infected group and control group. Red dots represent up-regulated genes and green dots represent down-regulated genes.

Figure 3

Gene ontology (GO) analyses of DEGs responsive to ToBRFV infection in tomato plants. GO analysis showing the GO terms in the categories of cellular component, molecular function, and biological process (FDR < 0.05). Red bars represent up-regulated genes and green bars represent down-regulated genes.

Figure 4

Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of DEGs responsive to ToBRFV infection in tomato plants. On the left are up-regulated genes and on the right are down-regulated genes. The number above the column indicates the number of differentially expressed genes in the enrichment process.

Figure 5

Validation of RNA-seq results. Ten differentially expressed genes were selected based on RNA-seq results, and their expression changes were analyzed by RT-qPCR with gene-specific primers. The obtained RT-qPCR data were normalized by Slactin expression level as the average value ± SD relative to the control inoculation. The asterisk indicates a statistically significant difference between the tomato plants inoculated with ToBRFV and the control. (* p < 0.05, *** p < 0.01).