Identification of differentially expressed genes in response to infection of a mild Citrus tristeza virus isolate in Citrus aurantifolia by suppression subtractive hybridization

Citrus tristeza virus (CTV) is the most serious viral pathogen of citrus. Pathogenicity differentiation among CTV isolates has been found in some countries. In order to better understand the responses of Mexican lime (Citrus aurantifolia) to the infection of a mild CTV isolate (CTV-N4), we constructed two suppression subtractive hybridization (SSH) libraries. A total of 589 expressed sequence tags (ESTs) were screened from two SSH libraries by dot blot analysis. Sequencing results showed that these ESTs represented 202 genes, of which 111 and 91 genes were up-regulated and down-regulated, respectively. The differential expression of 10 out of 13 selected genes was confirmed by quantitative real-time RT-PCR (qRT-PCR). All differently expressed genes were functionally categorized into eight groups, of which the majority was associated with stress and disease defenses. The transcriptional levels of three genes in lime plants with the infection of a mild isolate CTV-N4 and a severe isolate CTV-N21 were comparatively analyzed by qRT-PCR over a 120 days time course. Results indicated that transcriptional changes of three studied genes were more greatly induced by CTV-N21 than those induced by CTV-N4. The obtained results provided novel information on genes potentially involved in citrus responses to CTV infection.

► We detected many genes differently expressed in CTV-N4 infected citrus.
► The majority of them were associated with stress response and disease defense.
► Differential expression of some genes was confirmed by qPCR.
► Transcriptional interference depended on CTV strains.