Differentially expressed genes and temporal and spatial expression of genes during interactions between Mexican lime (Citrus aurantifolia) and a severe Citrus tristeza virus isolate

•430 differently expressed genes were identified in CTV-N21 infected citrus.•The majority of them were associated with primary metabolism.•Differential expression of 25 genes was confirmed by qPCR.•Temporal and spatial effect on expression of 6 genes were analyzed in a time course of CTV-N21 infection.

Determining transcriptional responses of host plants to virus infection will help understand mechanisms involved in host–virus interactions. In this study, 430 genes differentially regulated by a severe CTV isolate in lime plants were identified by using SSH. The differential expression levels of 25 ESTs in CTV-N21 infected lime were validated by qRT-PCR. The largest set of those genes involved in primary metabolism (26.0%), and then in protein metabolism (15.1%). Our results revealed a large set of genes (51 ESTs) were commonly up-regulated by two severe strains CTV-N21 and CTV-T305 in lime. The quantitative analysis for temporal and spatial transcriptional levels of six genes in lime plants infected by CTV-N21 indicated that the transcriptional levels of those genes fluctuated during CTV infection and differed in different citrus leaves.