Comprehensive transcriptome analysis of Crocus sativus for discovery and expression of genes involved in apocarotenoid biosynthesis

Abstract

BackgroundCrocus sativus stigmas form rich source of apocarotenoids like crocin, picrocrocin and saffranal which besides imparting color, flavour and aroma to saffron spice also have tremendous pharmacological properties. Inspite of their importance, the biosynthetic pathway of Crocus apocarotenoids is not fully elucidated. Moreover, the mechanism of their stigma specific accumulation remains unknown. Therefore, deep transcriptome sequencing of Crocus stigma and rest of the flower tissue was done to identify the genes and transcriptional regulators involved in the biosynthesis of these compounds.ResultsTranscriptome of stigma and rest of the flower tissue was sequenced using Illumina Genome Analyzer IIx platform which generated 64,604,402 flower and 51,350,714 stigma reads. Sequences were assembled de novo using trinity resulting in 64,438 transcripts which were classified into 32,204 unigenes comprising of 9853 clusters and 22,351 singletons. A comprehensive functional annotation and gene ontology (GO) analysis was carried out. 58.5 % of the transcripts showed similarity to sequences present in public databases while rest could be specific to Crocus. 5789 transcripts showed similarity to transcription factors representing 76 families out of which Myb family was most abundant. Many genes involved in carotenoid/apocarotenoid pathway were identified for the first time in this study which includes zeta-carotene isomerase and desaturase, carotenoid isomerase and lycopene epsilon-cyclase. GO analysis showed that the predominant classes in biological process category include metabolic process followed by cellular process and primary metabolic process. KEGG mapping analysis indicated that pathways involved in ribosome, carbon and starch and sucrose metabolism were highly represented. Differential expression analysis indicated that key carotenoid/apocarotenoid pathway genes including phytoene synthase, phytoene desaturase and carotenoid cleavage dioxygenase 2 are enriched in stigma thereby providing molecular proof for stigma to be the site of apocarotenoid biosynthesis.ConclusionsThis data would provide a rich source for understanding the carotenoid/apocarotenoid metabolism in Crocus. The database would also help in investigating many questions related to saffron biology including flower development.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1894-5) contains supplementary material, which is available to authorized users.

Functional Characterization of CsBGlu12, a β-Glucosidase from Crocus sativus, Provides Insights into Its Role in Abiotic Stress through Accumulation of Antioxidant Flavonols

“…Identification, Cloning, and Phylogenetic Analysis of CsBGlu12-Previously, our laboratory developed a transcriptome database from Crocus stigma and flower tissues (18). Fifteen sequences from this database exhibited homology with plant ␤-glucosidases.…”

“…To assess their biological function, it is imperative to know about the physiological substrates of a particular ␤-glucosidase and the conditions under which they come into contact. Against this backdrop, 15 ␤-glucosidases were identified from C. sativus transcriptome (18). Among these, Csbglu12 exhibited higher expression in stigma of the flower, the main site of biosynthesis and accumulation of many secondary metabolites in C. sativus, which include, but are not limited to, flavonols and apocarotenoids (29,30).…”

“…Identification and Cloning of Csbglu12-Previously our laboratory had carried out the whole transcriptome sequencing of C. sativus (18). From this transcriptome, we identified 15 ␤-glucosidase cDNA sequences.…”

UGT709G1: a novel uridine diphosphate glycosyltransferase involved in the biosynthesis of picrocrocin, the precursor of safranal in saffron (Crocus sativus)

“…Recently, RNA sequencing (RNAseq) has revolutionized the exploration of gene expression in nonmodel plant species with nonsequenced genomes. Deep transcriptomes are currently available from two Crocus species, C. sativus and Crocus sieberi (Baba et al, 2015;Jain et al, 2016;Ahrazem et al, 2018), which serve as an important public information database for gene expression and structural and functional genomics studies in Crocus.…”

Microarray analysis of differentially expressed genes in L929 mouse fibroblast cells exposed to leptin and hypoxia

“…The GO annotation () provides a descriptive framework and functional annotation of DEGs, and is comprised of biological processes, cellular components and molecular functions. In addition, Kyoto Encyclopedia of Genes and Genomes (KEGG; ) pathway enrichment analysis was performed to map the potential pathways of the DEGs (24). The P-value cut-off associated with this analysis was set at P<0.05 in order to identify significantly enriched functional terms and pathways.…”