Systems analysis of cis-regulatory motifs in C(4) photosynthesis genes using maize and rice leaf transcriptomic data during a process of de-etiolation

Identification of potential cis-regulatory motifs controlling the development of C(4) photosynthesis is a major focus of current research. In this study, we used time-series RNA-seq data collected from etiolated maize and rice leaf tissues sampled during a de-etiolation process to systematically characterize the expression patterns of C(4)-related genes and to further identify potential cis elements in five different genomic regions (i.e. promoter, 5′UTR, 3′UTR, intron, and coding sequence) of C(4) orthologous genes. The results demonstrate that although most of the C(4) genes show similar expression patterns, a number of them, including chloroplast dicarboxylate transporter 1, aspartate aminotransferase, and triose phosphate transporter, show shifted expression patterns compared with their C(3) counterparts. A number of conserved short DNA motifs between maize C(4) genes and their rice orthologous genes were identified not only in the promoter, 5′UTR, 3′UTR, and coding sequences, but also in the introns of core C(4) genes. We also identified cis-regulatory motifs that exist in maize C(4) genes and also in genes showing similar expression patterns as maize C(4) genes but that do not exist in rice C(3) orthologs, suggesting a possible recruitment of pre-existing cis-elements from genes unrelated to C(4) photosynthesis into C(4) photosynthesis genes during C(4) evolution.