Data for: Induction of C4 genes during de-etiolation of Gynandropsis gynandra evolved through changes in cis allowing integration into ancestral C3 gene regulatory networks

C4 photosynthesis has evolved repeatedly and in doing so repurposed existing enzymes to drive a carbon pump that limits the oxygenation reaction of RuBisCO. C4 proteins accumulate to levels matching those of the photosynthetic apparatus, and to allow this gene expression must be modified over evolutionary time. To better understand this rewiring of gene expression we undertook RNA-SEQ and DNaseI-SEQ on de-etiolating seedlings of C4 Gynandropsis gynandra which is evolutionarily proximate to C3 A. thaliana. Changes in chloroplast ultrastructure and C4 gene expression in G. gynandra were coordinated and rapid. C3 and C4 photosynthesis genes showed similar induction patterns, but C4 genes from G. gynandra were more strongly induced than orthologs from A. thaliana. The cistrome of G. gynandra was enriched in TGA, TCP and homeodomain binding sites. Furthermore, in vivo binding data in G. gynandra highlighted TGA and homeodomain as well as light responsive elements such as G- and I-box motifs ..., Gynandropsis gynandra seeds were sown directly from intact pods and germinated on moist filter papers in the dark at 32°C for 24 hours. Germinated seeds were then transferred to half strength Murashige and Skoog (MS) medium with 0.8% (w/v) agar (pH 5.8) and grown for three days in a growth chamber at 26°C. De-etiolation was induced by exposure to white light with a photon flux density (PFD) of 350 μmol m-2 s-1 and photoperiod of 16 hours. Whole seedlings were harvested at 0.5, 2, 4 and 24 hours after illumination (starting at 8:00 with light cycle 6:00 to 22:00). Tissue was flash frozen in liquid nitrogen and stored at -80°C prior to processing.
RNA and DNaseI sequencing
Before processing, frozen samples were divided into two, the first being used for RNA-SEQ analysis and the second for DNaseI-SEQ. Samples were ground in a mortar and pestle and RNA extraction carried out with the RNeasy Plant Mini Kit (74904; QIAGEN) according to the manufacturer’s instructions. RNA quality and integrit...,