Comprehensive transcriptome analysis of Crocus sativus for discovery and expression of genes involved in apocarotenoid biosynthesis.
Comprehensive transcriptome analysis of Crocus sativus for discovery and expression of genes involved in apocarotenoid biosynthesis.
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DOI：
10.1186/s12864-015-1894-5
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发表时间：
2015-09-15
期刊：
影响因子：
4.4
通讯作者：
Ashraf N
中科院分区：
文献类型：
--
作者：
Baba SA;Mohiuddin T;Basu S;Swarnkar MK;Malik AH;Wani ZA;Abbas N;Singh AK;Ashraf N
番红花柱头形成了丰富的类胡萝卜素来源，如藏红花素、苦藏红花素和藜芦醛，它们除了赋予番红花香料颜色、风味和香气外，还具有巨大的药理学特性。尽管它们的重要性，番红花脱辅基类胡萝卜素的生物合成途径尚未完全阐明。此外，其柱头特异性积累的机制仍不清楚。因此，对番红花柱头和其余花组织进行了深度转录组测序，以鉴定参与这些化合物生物合成的基因和转录调控因子。使用Illumina Genome Analyzer IIx平台对柱头和花组织的其余部分的转录组进行测序，其产生64，604，402朵花和51，350，714个柱头读数。使用Trinity位一体从头组装序列，得到64，438个转录物，其被分类为32，204个单基因，包括9853个簇和22，351个单基因。进行了全面的功能注释和基因本体（GO）分析。58.5%的转录本与公共数据库中存在的序列相似，而其余转录本可能是番红花属的特异性转录本。5789个转录本与76个家族的转录因子相似，其中Myb家族的转录因子最多。本研究首次发现了类胡萝卜素/脱辅基类胡萝卜素途径中的多种基因，包括zeta-胡萝卜素异构酶和去饱和酶、类胡萝卜素异构酶和番茄红素环化酶。GO分析表明，在生物过程类别中占主导地位的是代谢过程，其次是细胞过程和初级代谢过程。KEGG图谱分析表明，核糖体、碳、淀粉和蔗糖代谢途径在该基因中具有较高的代表性。差异表达分析表明，类胡萝卜素/脱辅基类胡萝卜素途径的关键基因八氢番茄红素合成酶、八氢番茄红素去饱和酶和类胡萝卜素裂解双加氧酶2在柱头中富集，为柱头是脱辅基类胡萝卜素合成的位点提供了分子证据。这些数据将为了解番红花类胡萝卜素/脱辅基类胡萝卜素代谢提供丰富的资料。该数据库还将有助于调查与花的生物学有关的许多问题，包括花的发育。本文的在线版本（doi：10.1186/s12864-015-1894-5）包含补充材料，可供授权用户使用。
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. 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. 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. The online version of this article (doi:10.1186/s12864-015-1894-5) contains supplementary material, which is available to authorized users.