Next Generation Sequencing of Arabidopsis seedlings upon Mock or GR244DO Transcriptomes

Purpose: Strigolactones (SLs), a class of carotenoid-derived plant hormones, have fundamental effects on plant development. But only a few SL-responsive genes have been identified. The goal of this study is to identify SL early responsive genes in the model system Arabidopsis thaliana. Methods: The 10-day-old wild-type seedlings were treated with GR244DO or solvent for 2 h or 4 h. The mRNA profiles were generated by deep sequencing, in triplicate, using Illumina system Hiseq2000. The sequence reads were analyzed using STAR and R package DESeq. To limit interference of circadian clock and environmental factors, GR244DO treatment at 2 h was compared to solvent treatment control at 2 h as well as the start point of treatment, and genes upregulated at both conditions were considered as up-regulated SL responsive genes at 2 h. The same comparison criteria were applied to identify down-regulated responsive genes at 4 h. qRT-PCR validation was performed using CFX 96 real-time PCR detection system. Results: We identified 99 upregulated and 57 downregulated genes at 2 h treatment, as well as 147 upregulated and 150 downregulated genes at 4 h treatment in Arabidopsis thaliana using the cutoff of fold-change more than 1.5 and P-value less than 0.05. Overall design: The mRNA profiles of 10-day-old wild-type seedlings under GR244DO or solvent treatment were generated by deep sequencing, in triplicate, using Illumina Hiseq2000.