The first Illumina-based de novo transcriptome sequencing and analysis of safflower flowers.
The first Illumina-based de novo transcriptome sequencing and analysis of safflower flowers.
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DOI：
10.1371/journal.pone.0038653
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Shangqin H
中科院分区：
文献类型：
--
作者：
Lulin H;Xiao Y;Pei S;Wen T;Shangqin H
红花，红花，是一种世界性的油料作物，其花类黄酮含量高，是传统医学中治疗心血管疾病的重要药用资源。由于红花基因组庞大而复杂，其基因组资源的开发一直受到阻碍。第二代Illumina测序现在是产生大量序列的有效途径，这些序列可以代表大量基因及其表达水平。为了研究可能控制红花中黄酮类化合物和其他次级代谢产物的基因和途径，我们使用Illumina测序来进行红花管状花组织转录组的从头组装。我们获得了总共4.69 Gb的干净核苷酸，包括52，119，104个干净测序读段、195，320个重叠群和120，778个单基因。基于与已知蛋白质的相似性搜索，我们注释了70，342个unigenes（约占已识别unigenes的58%），截止E值为10−5。总共发现21，943个红花unigenes具有COG分类，并且BLAST2GO将26，332个unigenes分配给1，754个GO术语注释。此外，我们将30，203个unigenes分配给121个KEGG通路。当我们专注于被鉴定为有助于类黄酮生物合成和不饱和脂肪酸生物合成的基因时，这些基因分别是控制花和种子质量的重要途径，我们发现这些基因在红花基因组中与其他植物相比相当保守。本研究为红花的基因组学研究提供了丰富的数据。为红花的研究提供了全面的序列资源。我们相信，这些转录组数据集将作为一个重要的公共信息平台，以加快红花基因组的研究，并可能帮助我们确定花组织特异性和次生代谢在这种非模式植物的机制。
The safflower, Carthamus tinctorius L., is a worldwide oil crop, and its flowers, which have a high flavonoid content, are an important medicinal resource against cardiovascular disease in traditional medicine. Because the safflower has a large and complex genome, the development of its genomic resources has been delayed. Second-generation Illumina sequencing is now an efficient route for generating an enormous volume of sequences that can represent a large number of genes and their expression levels. To investigate the genes and pathways that might control flavonoids and other secondary metabolites in the safflower, we used Illumina sequencing to perform a de novo assembly of the safflower tubular flower tissue transcriptome. We obtained a total of 4.69 Gb in clean nucleotides comprising 52,119,104 clean sequencing reads, 195,320 contigs, and 120,778 unigenes. Based on similarity searches with known proteins, we annotated 70,342 of the unigenes (about 58% of the identified unigenes) with cut-off E-values of 10−5. In total, 21,943 of the safflower unigenes were found to have COG classifications, and BLAST2GO assigned 26,332 of the unigenes to 1,754 GO term annotations. In addition, we assigned 30,203 of the unigenes to 121 KEGG pathways. When we focused on genes identified as contributing to flavonoid biosynthesis and the biosynthesis of unsaturated fatty acids, which are important pathways that control flower and seed quality, respectively, we found that these genes were fairly well conserved in the safflower genome compared to those of other plants. Our study provides abundant genomic data for Carthamus tinctorius L. and offers comprehensive sequence resources for studying the safflower. We believe that these transcriptome datasets will serve as an important public information platform to accelerate studies of the safflower genome, and may help us define the mechanisms of flower tissue-specific and secondary metabolism in this non-model plant.
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影响因子：
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