Cold suppresses virus accumulation and alters the host transcriptomic response in the turnip mosaic virus - Arabidopsis halleri system

To examine the effect of temperature on TuMV infected plants, virus was inoculated to un-infected Arabidopsis halleri plants and incubated under warm (25 degree C /20 degree C, day/night at 12 h day length) and cold (10 degree C /5 degree C, day/night at 12 h day length) conditions. As a mock inoculated control, buffer solution without TuMV was inoculated. Inoculation was made on the ninth and tenth leaves from the top. To evaluate host responses, we performed transcriptome analyses using RNA-seq for inoculated leaves and systemic leaves (fifth and sixth extant leaves upper from the inoculated ones) in biological 9 replicates at 8, 15 and 28 dpi in the warm and cold. We excluded systemic leaves at 8 and 15 dpi in the cold from the analyses because no virus accumulation was detected. In total, we obtained RNA-seq data for 10 dpi-position-temperature combinations.