Figure 4
Comparison of MSGI 1.0 and Mt3.0 cds as reference sequences for digital gene expression analysis. For a subset of genes involved in stem development independent of genotypic variation, Log2(PES/ES) values from the RNA-Seq data (x-axis) generated using (A) the Medicago sativa Gene Index (MSGI1.0) or (B) the Medicago truncatula coding sequences (Mt3.0 cds) as reference sequences were plotted against Log2(PES/ES) values from the GeneChip data (y-axis) previously generated [25]. For 63 randomly selected genes (C) and 34 selected cell wall genes (D), Log ratio values from the RNA-Seq data (x-axis) generated using MSGI1.0 (O) and Mt3.0 cds (Δ) as reference sequences were plotted against ΔΔCT values obtained from the qRT-PCR data (y-axis).