Transcriptional dynamics of two seed compartments with opposing roles in Arabidopsis seed germination

Seed germination is a critical stage in the plant life cycle and the first step towards successful plant establishment. Understanding germination is therefore of important ecological and agronomical relevance. Previous research revealed that different seed compartments (testa, endosperm and embryo) control germination, but little is known about the underlying spatial and temporal transcriptome changes that lead to seed germination. We analyzed genome-wide expression in germinating Arabidopsis thaliana seeds with both temporal and spatial detail and provide web accessible visualizations of the data reported (vseed.nottingham.ac.uk). We show the potential of this high resolution data set for the construction of meaningful co-expression networks, which provide insight into the genetic control of germination. The data set reveals two transcriptional phases during germination that are separated by testa rupture. The first phase is marked by large transcriptome changes as the seed switches from a dry, quiescent state to a hydrated and active state. At the end of this first transcriptional phase the number of differentially expressed genes between consecutive time points drop. This increases again at testa rupture, the start of the second transcriptional phase. Transcriptome data indicates a role for mechano-induced signalling at this stage, and subsequently highlights the fates of the endosperm and radicle; senescence and growth respectively. Finally, using a phylotranscriptomic approach we show that expression levels of evolutionary young genes drop during the first transcriptional phase and increase during the second phase. Evolutionary old genes show an opposite pattern, suggesting a more conserved transcriptome prior to the completion of germination.