GSE40482
Transcription profiling of Arabidopsis plants overexpressing SsCBF1
Solanum lycopersicoides (LA2408), collected at higher altitudes (up to 3600 meters) than any of other solanum species, is a wild nightshade distant-allied to cultivated tomato. Many traits of Solanum lycopersicoides including cold tolerance, resistance to virus diseases and insect pests were previously confirmed. Thus, it is an ideal candidate plant for isolating cold-tolerance-related genes. In this study, we successfully cloned the full-length cDNA of the CBF1 gene from Solanum lycopersicoides which was designated as SsCBF1. In order to investigate the possible functions of SsCBF1 in plant growth and stress responses, we generated transgenic Arabidopsis overexpressing SsCBF1. We employed the RNA-seq approach to identify the differentially expressed genes between the two genotypes. Processing of RNA samples on the Illumina HiSeq 2000 system produced more than 20 million reads, each 100bp in length, encompassing 2.0 Gb of sequence data for each sample which was then mapped to the reference genome. The statistical analysis identified a total of 338 differentially expressed genes between Col-0 (WT) and transgenic Arabidopsis overexpressing SsCBF1 with the criteria of Q-value < 0.001 and fold change >2, among which 120 (35.5%) were up-regulated and 218 (64.5%) were down-regulated. Overall design: RNA-sequencing was carried out using one transgenic line (35S:SsCBF1-11) and the Col-0 (WT) plants. Total RNA was isolated with Trizol reagent (Invitrogen, USA) from the aerial parts of 4-week-old seedlings grown in parallel under unstressed conditions. Materials from 20 plants of each genotype were pooled for RNA isolation.