Understanding the triacylglycerol-based carbon anabolic differentiation in Cyperus esculentus and Cyperus rotundus developing tubers via transcriptomic and metabolomic approaches

Abstract

Background Yellow nutsedge (YSD, Cyperus esculentus) and purple nutsedge (XFZ, Cyperus rotundus), closely related Cyperaceae species, exhibit significant differences in triacylglycerol (TAG) accumulation within their tubers, a key factor in carbon flux repartitioning. Previous studies have attempted to elucidate the carbon anabolic discrepancies between these two species, however, a lack of comprehensive genome-wide annotation has hindered a detailed understanding of the underlying molecular mechanisms. Results This study utilizes transcriptomic analysis, supported by a comprehensive YSD reference genome, and metabolomic profiling to uncover the mechanisms of TAG-based carbon anabolic differentiation between the developing tubers of YSD and XFZ germplasms harvested in Yunnan province, China. Our findings indicate distinct expression patterns of key regulatory genes involved in TAG biosynthesis and lipid droplet formation, including ABI3 transcriptional factor, rate-limiting enzymes GPAT3/6/9 and DGAT2/3, and oleosin and caleosin homologs. Furthermore, our omics data suggest that these differences in gene expression are not the sole contributors to the diverse tuber compositions. Instead, complex interactions among highly regulated catalytic reactions, governing carbohydrate, protein, and species-specific metabolite metabolisms, collectively contribute to the pronounced carbon anabolic differentiation primarily evident in TAG accumulation, as well as the starch properties in mature tubers. Conclusion This study offers new metabolic insights into the high-value underground non-photosynthetic tissues of Cyperaceae species. The detailed omics analyses aim to deepen our understanding of the Cyperaceae species, which could significantly enhance their resource utilization and industrial applications in contemporary agricultural production.