Abstract

Recent genome comparisons of a growing number of Brassicaceae genome assemblies revealed the extent of conserved non-coding sequences (CNS). Despite these evolutionary constraints, little is known about their function. We assembled the genome of Arabis alpina, which diverged _{30 million years ago from A. thaliana and sequenced the transcriptomes of both species at 12 time points of two consecutive days. Over} 4,000 orthologous genes showed daytime-dependent expression. Comprehensively analyzing CNS for cis-regulatory elements revealed 50 putatively daytime specifying motifs, including all those shown to be involved in diurnal expression so far. Moreover, absence or presence of many elements has significant impact on the degree of conservation in gene expression, evidencing their role in gene regulation. On average diurnal genes are delayed by two hours in A. alpina as compared to A. thaliana. The plant circadian clock can be divided into three intervening loops, but intriguingly this shift is only present in the morning and evening loops, but not in the core loop. GO enrichment and pathway analyses revealed striking differences between pathways conserved for their daytime and those being shifted. Conserved pathways include photosynthesis and primary metabolite biosynthesis, whereas shifted pathways are enriched for secondary metabolites biosynthesis.