Comparative Network Analysis of C4 Photosynthesis in Grass Species

Transcriptional regulatory networks are complex molecular systems that determine differential gene expression in response to environmental or developmental signals. Transcriptional regulation relies on the combinatorial interplay of trans-acting protein complexes, and cis-regulatory sequence elements located in or near target genes. C₄ photosynthesis is an example of a complex metabolic pathway that requires special and temporal expression of specific gene combination for its proper function. The C₄ pathway coordinates its function between two distinct, specialized leaf cell types, mesophyll (ME) and bundle sheath (BS). The C₄ pathway has evolved independently in at least 60 lineages of angiosperms, and at least 17 times in the grasses alone, however, we still don’t fully understand its complex function. In the current work, RNA-seq data from three developmental stages of each BS and M cells, were used to analyzeand compare transcriptional regulatory networks in three C₄ species, Zea mays, Sorghum bicolor, and Setaria viridis. These three species represent two independent events of C₄ photosynthesis. We used dGCNA to directly compare each of the three gene co-expression networks (GCNs) against the other two GCNs in a pairwise fashion. Combined with our cell type specific and high resolution data, our results allow us to detect gene-gene relationships for each species comparison, and better understand how C₄ photosynthesis functions, and how it evolved.