Project description:This work represents the first epigenomic study carried out on saffron crocus. Five accessions of saffron, showing differences in tepal pigmentation, yield of saffron and flowering time, were analysed at the epigenetic level by applying a methylation-sensitive restriction enzyme-sequencing (MRE-seq) approach. Five accession-specific hypomethylomes plus a reference hypomethylome, generated by combining the sequence data from the single accessions, were obtained. Assembled sequences were annotated against existing online databases. In the absence of the Crocus genome, the rice genome was mainly used as the reference as it is the best annotated genome among monocot plants. Comparison of the hypomethylomes revealed many differentially methylated regions, confirming the high epigenetic variability present among saffron accessions, including sequences encoding for proteins that could be good candidates to explain the accessions’ alternative phenotypes. In particular, transcription factors involved in flowering process (MADS-box and TFL) and for the production of pigments (MYB) were detected. Finally, by comparing the generated sequences of the different accessions, a high number of SNPs, likely having arisen as a consequence of the prolonged vegetative propagation, were detected, demonstrating surprisingly high genetic variability. Gene ontology (GO) was performed to map and visualise sequence polymorphisms located within the GOs and to compare their distributions among different accessions. As well as suggesting the possible existence of alternative phenotypes with a genetic basis, a clear difference in polymorphic GO is present among accessions based on their geographic origin, supporting a possible signature of selection in the Indian accession with respect to the Spanish ones.
Project description: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.
Project description:Dynamic transcriptomic and metabolic profiling reveal synthetic characters and regulators of apocarotenoids biosynthesis in Crocus sativus
