They encoded proteins with a wide range of biological functions. Those cBRs highly accumulated in dry mature grains and their accumulation gradually decreased over the course of seed germination. This raises the possibility that these cBRs encoded proteins involved in seed development and maturation. The highly accumulated transcripts were degraded over the course of seed germination. Barley and rice diverged from their common ancestor 50 million years ago. However, they share a great similarity morphologically and physiologically in germination and seedling growth. In this study, we measured the 
transcriptomes of germinating rice grains at dry, mid- and end points of seed germinations, which should represent the most distinct stages of the dynamic transcriptional changes over seed germination process. Having determined transcriptomes of rice at the three equivalent stages, we designed a systems and evolutionary strategy to compare the dynamic transcriptomic changes over the course of seed germination to gain an insight into divergence and conservation of gene regulatory programs underlying rice and barley germination. One-Way ANOVA analysis of the transcriptomes revealed that 2537 barley and 13813 rice genes were differentially regulated over the course of seed germination. Comparing their encoding protein sequences and expression patterns identified 322 sets of conserved barley and rice genes sharing strong similarity in both protein sequences and gene expression patterns. The collection of cBRs contained 368 barley genes and 388 rice genes. Thus, only a very small percentage of the germination-regulated genes preserved their protein sequences and gene expression patterns; and a significant divergence occurred in transcriptional regulatory programs underlying rice and barley germination since the barley-rice divergence. As expected, protein sequence similarity of germination regulated barley and rice genes positively correlated to the similarity of their expression patterns, suggesting co-evolution of protein functions and gene expression patterns. Biological functions of genes are mainly determined by their protein sequences and their expression patterns. Both protein sequences and expression patterns change quickly if the genes have no Diacerein functional significance. Therefore, we hypothesized that the germination regulated expression patterns and protein sequences of the barley and rice genes in each cBR have been preserved for 50 million years after the split of rice and barley from their common ancestor because the genes are functionally important to seed germination, and should contribute to the characteristics shared by rice and barley germination. Additionally, 60 of the 322 cBRs were multi-gene cBRs. Each multi-gene cBRs contained at least one pair of paralogs. Duplicated paralogous genes are subjected to little functional constrains, and offer a great opportunity for their sub-functionalization or neofunctionalization through divergence of their protein sequence and/or expression patterns. Preserving germination regulated expression patterns and protein sequences of those paralogous genes in the multi-gene cBRs suggests that they may be subjected to negative selection, and provides additional Atropine sulfate evidence supporting their functional significance in seed germination. We identified a number of biological pathways enriched with cBRs of similar expression patterns, suggesting that their underlying transcriptional regulatory programs are highly conserved in rice and barley.