title: De novo transcriptome assembly and comprehensive expression profiling in Crocus sativus to gain insights into apocarotenoid biosynthesis.
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.
authors.affiliation: Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India.|School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
authors.forename: Mukesh
authors.initials: M
authors.lastname: Jain
authors.affiliation: Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India.
authors.forename: Prabhakar Lal
authors.initials: PL
authors.lastname: Srivastava
authors.affiliation: Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India.
authors.forename: Mohit
authors.initials: M
authors.lastname: Verma
authors.affiliation: Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India.
authors.forename: Rajesh
authors.initials: R
authors.lastname: Ghangal
authors.affiliation: Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India.
authors.forename: Rohini
authors.initials: R
authors.lastname: Garg
mesh_terms: D002338:Carotenoids / Q000096:biosynthesis*; D027622:Crocus / Q000235:genetics / Q000378:metabolism*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000502:physiology*; D010940:Plant Proteins / Q000096:biosynthesis* / Q000235:genetics; D059467:Transcriptome / Q000502:physiology*
chemical_list: D010940:Plant Proteins; D002338:Carotenoids; C004984:apocarotenal