De novo transcriptome assembly and comprehensive expression profiling in Crocus sativus to gain insights into apocarotenoid biosynthesis

Jain, Mukesh, Srivastava, Prabhakar Lal ORCID: https://orcid.org/0000-0002-8219-6419, Verma, Mohit, Ghangal, Rajesh and Garg, Rohini 2016. De novo transcriptome assembly and comprehensive expression profiling in Crocus sativus to gain insights into apocarotenoid biosynthesis. Scientific Reports 6 (1) , 22456. 10.1038/srep22456

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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.

Item Type:	Article
Date Type:	Published Online
Status:	Published
Schools:	Chemistry
Publisher:	Nature Publishing Group
ISSN:	2045-2322
Date of First Compliant Deposit:	13 July 2020
Date of Acceptance:	15 February 2016
Last Modified:	16 Jan 2024 02:21
URI:	https://orca.cardiff.ac.uk/id/eprint/133385

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