Comprehensive transcriptome analysis of Crocus sativus for discovery and expression of genes involved in apocarotenoid biosynthesis
| Autor: | Nazia Abbas, Zahoor Ahmed Wani, Mohit Kumar Swarnkar, Aubid Hussain Malik, Swaraj Basu, Anil Kumar Singh, Shoib Ahmad Baba, Tabasum Mohiuddin, Nasheeman Ashraf |
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| Rok vydání: | 2015 |
| Předmět: |
Phytoene desaturase
ved/biology.organism_classification_rank.species Biology Transcriptome chemistry.chemical_compound Primary metabolic process Illumina Gene Expression Regulation Plant Crocus sativus De novo assembly Genetics Cluster Analysis Phylogeny Apocarotenoids Crocus Phytoene synthase ved/biology Gene Expression Profiling Computational Biology High-Throughput Nucleotide Sequencing Reproducibility of Results food and beverages Molecular Sequence Annotation biology.organism_classification Carotenoids Picrocrocin Saffron chemistry Apocarotenoid biology.protein Research Article Transcription Factors Biotechnology |
| Zdroj: | BMC Genomics |
| ISSN: | 1471-2164 |
| Popis: | 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. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1894-5) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
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