title: Comprehensive transcriptome analysis of Crocus sativus for discovery and expression of genes involved in apocarotenoid biosynthesis.
abstract: BACKGROUND
  Crocus 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.
  
  
  RESULTS
  Transcriptome 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.
  
  
  CONCLUSIONS
  This 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.
authors.affiliation: Plant Biotechnology Division, CSIR- Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, J&K-190005, India. shoaibnazir25@gmail.com.|Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi, 110 001, India. shoaibnazir25@gmail.com.
authors.forename: Shoib Ahmad
authors.initials: SA
authors.lastname: Baba
authors.affiliation: Plant Biotechnology Division, CSIR- Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, J&K-190005, India. tabsumji@gmail.com.|Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi, 110 001, India. tabsumji@gmail.com.
authors.forename: Tabasum
authors.initials: T
authors.lastname: Mohiuddin
authors.affiliation: Stazione Zoologica Anton Dohrn di Napoli, Naples, Italy. projectbasu@gmail.com.
authors.forename: Swaraj
authors.initials: S
authors.lastname: Basu
authors.affiliation: Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, India. mohitswarnkar@gmail.com.
authors.forename: Mohit Kumar
authors.initials: MK
authors.lastname: Swarnkar
authors.affiliation: Plant Biotechnology Division, CSIR- Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, J&K-190005, India. aubidmalik_iiim@yahoo.com.|Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi, 110 001, India. aubidmalik_iiim@yahoo.com.
authors.forename: Aubid Hussain
authors.initials: AH
authors.lastname: Malik
authors.affiliation: Plant Biotechnology Division, CSIR- Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, J&K-190005, India. zawani1986@gmail.com.|Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi, 110 001, India. zawani1986@gmail.com.
authors.forename: Zahoor Ahmed
authors.initials: ZA
authors.lastname: Wani
authors.affiliation: Plant Biotechnology Division, CSIR- Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, J&K-190005, India. aizan105@gmail.com.
authors.forename: Nazia
authors.initials: N
authors.lastname: Abbas
authors.affiliation: Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, India. anils13@gmail.com.
authors.forename: Anil Kumar
authors.initials: AK
authors.lastname: Singh
authors.affiliation: Plant Biotechnology Division, CSIR- Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, J&K-190005, India. nashraf@iiim.ac.in.|Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi, 110 001, India. nashraf@iiim.ac.in.
authors.forename: Nasheeman
authors.initials: N
authors.lastname: Ashraf
mesh_terms: D002338:Carotenoids / Q000096:biosynthesis*; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D027622:Crocus / Q000235:genetics* / Q000378:metabolism*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D015203:Reproducibility of Results; D014157:Transcription Factors / Q000235:genetics; D059467:Transcriptome
chemical_list: D014157:Transcription Factors; D002338:Carotenoids