Abstract
Saffron (Crocus sativus L.) is commonly known as world’s most expensive spice with rich source of apocarotenoids and possesses magnificent medicinal properties. To understand the molecular basis of apocarotenoid biosynthesis/accumulation, we performed transcriptome sequencing from five different tissues/organs of C. sativus using Illumina platform. After comprehensive optimization of de novo transcriptome assembly, a total of 105, 269 unique transcripts (average length of 1047 bp and N50 length of 1404 bp) were obtained from 206 million high-quality paired-end reads. Functional annotation led to the identification of many genes involved in various biological processes and molecular functions. In total, 54% of C. sativus transcripts could be functionally annotated using public databases. Transcriptome analysis of C. sativus revealed the presence of 16721 SSRs and 3819 transcription factor encoding transcripts. Differential expression analysis revealed preferential/specific expression of many transcripts involved in apocarotenoid biosynthesis in stigma. We have revealed the differential expression of transcripts encoding for transcription factors (MYB, MYB related, WRKY, C2C2-YABBY and bHLH) involved in secondary metabolism. Overall, these results will pave the way for understanding the molecular basis of apocarotenoid biosynthesis and other aspects of stigma development in C. sativus.
Highlights
Saffron (Crocus sativus L.) is commonly known as world’s most expensive spice with rich source of apocarotenoids and possesses magnificent medicinal properties
We present the transcriptome analysis of C. sativus in five different tissues/organs to understand the molecular basis of apocarotenoid biosynthesis and discovery of molecular markers
De novo transcriptome analysis provides an excellent platform to generate a comprehensive resource of the gene space in an organism without whole genome sequencing and allows the discovery of novel genes, molecular markers and tissue-specific expression patterns
Summary
RNA sequencing and de novo transcriptome assembly. De novo transcriptome analysis provides an excellent platform to generate a comprehensive resource of the gene space in an organism without whole genome sequencing and allows the discovery of novel genes, molecular markers and tissue-specific expression patterns. We identified the genes encoding for all the enzymes catalyzing different intermediate reactions involved in apocarotenoid biosynthetic pathway (Fig. 6) from the C. sativus transcriptome. All these transcript sequences were highly conserved at the amino acid sequence level in Arabidopsis. The expression analysis of transcripts involved in key enzymatic steps of apocarotenoid biosynthesis, such as carotenoid cleavage dioxygenase (CCD), glucosyltransferases, aldehyde dehydrogenases and beta glucosidases revealed their higher expression levels in stigma as compared to other tissues (Fig. 6). The expression analysis was performed for selected genes belonging to apocarotenoid biosynthesis pathway, such as phytoene synthase (PS), beta carotene hydrolase (BCH), carotenoid cleavage dioxygenase (CCD) and glucosyltransferases (GTs) and a few TF (MADS, C2C2-YABBY and C2H2) encoding transcripts (Fig. 7). It is anticipated that these data will pave the way for elucidating the exact molecular mechanism for apocarotenoid biosynthesis in C. sativus
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