De novo assembly and transcriptome analysis of five major tissues of Jatropha curcas L. using GS FLX titanium platform of 454 pyrosequencing.
De novo assembly and transcriptome analysis of five major tissues of Jatropha curcas L. using GS FLX titanium platform of 454 pyrosequencing.
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DOI：
10.1186/1471-2164-12-191
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发表时间：
2011-04-15
期刊：
影响因子：
4.4
通讯作者：
Parani M
中科院分区：
文献类型：
--
作者：
Natarajan P;Parani M
麻疯树是一种重要的非食用油料作物，在生物柴油生产中具有广阔的应用前景。但是，油脂产量、油脂成分、油饼中的有毒物质、病虫害等因素限制了其商业潜力。使用克隆基因的成熟的基因工程方法可以用来解决这些限制。此前，报道了来自Sanger测序的10983个独特基因，以及来自454个非克隆cdna焦磷酸测序的3484个独特组装转录本。为了加快基因发现的进程，我们对从麻树的根、成熟叶、花、发育中的种子和胚胎中制备的标准化cdna进行了454焦磷酸测序。从383,918个原始reads中，我们获得了381,957个经过质量过滤和修剪的reads，适合转录本序列的组装。这些reads的从头组装产生17,457个组装转录本（contigs）和54,002个单基因。转录本的平均长度为916 bp。约30%的转录本长度超过1000个碱基，最长的转录本长度为7173个碱基。BLASTX分析显示，其中2589个转录本是全长的。通过RT-PCR对28个转录本进行验证。结果表明，转录本组装正确，代表了活跃表达的基因。KEGG通路图谱显示，2320个转录本与包括油脂生物合成途径在内的主要生化途径相关。总的来说，本研究报告了14,327个新组装的转录本，其中包括2589个全长转录本和27个直接参与石油生物合成的转录本。本研究报道的大量转录本以及现有的est和转录本序列将为麻疯树作物改良提供宝贵的遗传资源。这些参与油脂生物合成的基因序列信息可用于麻疯树的代谢工程，以提高油的含量，改变油的成分。
Jatropha curcas L. is an important non-edible oilseed crop with promising future in biodiesel production. However, factors like oil yield, oil composition, toxic compounds in oil cake, pests and diseases limit its commercial potential. Well established genetic engineering methods using cloned genes could be used to address these limitations. Earlier, 10,983 unigenes from Sanger sequencing of ESTs, and 3,484 unique assembled transcripts from 454 pyrosequencing of uncloned cDNAs were reported. In order to expedite the process of gene discovery, we have undertaken 454 pyrosequencing of normalized cDNAs prepared from roots, mature leaves, flowers, developing seeds, and embryos of J. curcas. From 383,918 raw reads, we obtained 381,957 quality-filtered and trimmed reads that are suitable for the assembly of transcript sequences. De novo contig assembly of these reads generated 17,457 assembled transcripts (contigs) and 54,002 singletons. Average length of the assembled transcripts was 916 bp. About 30% of the transcripts were longer than 1000 bases, and the size of the longest transcript was 7,173 bases. BLASTX analysis revealed that 2,589 of these transcripts are full-length. The assembled transcripts were validated by RT-PCR analysis of 28 transcripts. The results showed that the transcripts were correctly assembled and represent actively expressed genes. KEGG pathway mapping showed that 2,320 transcripts are related to major biochemical pathways including the oil biosynthesis pathway. Overall, the current study reports 14,327 new assembled transcripts which included 2589 full-length transcripts and 27 transcripts that are directly involved in oil biosynthesis. The large number of transcripts reported in the current study together with existing ESTs and transcript sequences will serve as an invaluable genetic resource for crop improvement in jatropha. Sequence information of those genes that are involved in oil biosynthesis could be used for metabolic engineering of jatropha to increase oil content, and to modify oil composition.
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影响因子：
4.3
作者：
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通讯作者：
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