Transcriptome dynamics provides insights into divergences of photosynthesis pathway between Saccharum officinarum and Saccharum spontaneum.

Saccharum spontaneum and Saccharum officinarum contributed to the genetic background of modern sugarcane cultivars. S. spontaneum has shown higher net photosynthetic rate and lower soluble sugar than S. officinarum. Here, we analyzed 198 RNA-seq samples to investigate the molecular mechanisms, for the divergences of photosynthesis and sugar accumulation between the two Saccharum species. We constructed gene co-expression networks based on differentially expressed genes (DEGs) both for leaf developmental gradients and diurnal rhythm. Our results suggested that the divergence of sugar accumulation may attribute to the enrichment of major carbohydrate metabolism and the oxidative pentose phosphate pathway. S. spontaneum DEGs showed high enrichment for photosynthesis and comprised of more complicated photosynthesis-related genes regulation, as compared to its counterpart. Noticeably, S. spontaneum lacked gene interactions with sulfur assimilation which is stimulated by photorespiration. In S. spontaneum, core genes related to clock and photorespiration displayed a sensitive regulation by the diurnal rhythm and phase-shift. Small subunit of Rubisco displayed higher expression in the source tissues of S. spontaneum. Additionally, it was more sensitive under diurnal rhythm, and had more complex gene networks than that in S. officinarum. This indicates that the differential regulation of Rubisco contributed to photosynthesis capacity divergence in both Saccharum species.