Genome-wide identification and comparative analyses of key genes involved in C photosynthesis in five main gramineous crops.

Compared to C species, C plants showed higher photosynthetic capacity as well as water and nitrogen use efficiency due to the presence of the C photosynthetic pathway. Previous studies have shown that all genes required for the C photosynthetic pathway exist in the genomes of C species and are expressed. In this study, the genes encoding six key C photosynthetic pathway enzymes (β-CA, PEPC, ME, MDH, RbcS, and PPDK) in the genomes of five important gramineous crops (C: maize, foxtail millet, and sorghum; C: rice and wheat) were systematically identified and compared. Based on sequence characteristics and evolutionary relationships, their C functional gene copies were distinguished from non-photosynthetic functional gene copies. Furthermore, multiple sequence alignment revealed important sites affecting the activities of PEPC and RbcS between the C and C species. Comparisons of expression characteristics confirmed that the expression patterns of non-photosynthetic gene copies were relatively conserved among species, while C gene copies in C species acquired new tissue expression patterns during evolution. Additionally, multiple sequence features that may affect C gene expression and subcellular localization were found in the coding and promoter regions. Our work emphasized the diversity of the evolution of different genes in the C photosynthetic pathway and confirmed that the specific high expression in the leaf and appropriate intracellular distribution were the keys to the evolution of C photosynthesis. The results of this study will help determine the evolutionary mechanism of the C photosynthetic pathway in Gramineae and provide references for the transformation of C photosynthetic pathways in wheat, rice, and other major C cereal crops.