Dynamic transcriptomic and metabolic profiling reveal synthetic characters and regulators of apocarotenoids biosynthesis in Crocus sativus

Background: Crocus sativus L. belongs to the Iridaceae family and its dried stigma, called saffron, is one of the world’s most expensive spice. C. sativus is also a famous medicinal plant on account of producing significant pharmaceutical apocarotenoids like crocins, crocetin, picrocrocin and safranal. These metabolites have been reported to play important pharmacological efficiency towards many diseases. However, the regulatory mechanism of saffron apocarotenoids biosynthesis and stigma specific accumulation remains poorly understood. Results: In this work, we performed deep transcriptomic sequencing and dynamic metabolomic profiling of different developmental stage stigmas, and firstly integrated the dynamic changes of apocarotenoids with dynamic transcriptomic data. As a result, a co-expression network was constructed, and 41 pathway genes, 5 TF genes were identified as hub genes probably participating in apocarotenoid biosynthesis, validated by qRT-PCR. The reliability of these results was validated by previous research of several genes, which were also screened out by the co-expression network. Conclusions: This work provides novel insights into the mechanism by which the apocarotenoids is synthesized and regulated. Such gene-to-apocarotenoid landscapes associated with different developmental stigma are fundamental of deeply understanding the biosynthesis and metabolic engineering of saffron apocarotenoids in the C. sativus and other plant. Total RNA profiles of RED, -2DAY, 0DAY stage stigmas from Crocus. sativus were generated by deep sequencing, in triplicate, using Illumina HiSeq2500.