De novo assembly and characterization of transcriptome using Illumina paired-end sequencing and identification of CesA gene in ramie (Boehmeria nivea L. Gaud).
De novo assembly and characterization of transcriptome using Illumina paired-end sequencing and identification of CesA gene in ramie (Boehmeria nivea L. Gaud).
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使用 Illumina 双端测序对转录组进行从头组装和表征，并鉴定苎麻 (Boehmeria nivea L. Gaud) 中的 CesA 基因
DOI：
10.1186/1471-2164-14-125
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发表时间：
2013-02-26
期刊：
影响因子：
4.4
通讯作者：
Tang S
中科院分区：
文献类型：
--
作者：
Liu T;Zhu S;Tang Q;Chen P;Yu Y;Tang S
背景
苎麻纤维是从营养器官茎韧皮中提取的，是最重要的天然纤维之一。了解苎麻营养生长和韧皮纤维形成发育的分子机制对于提高苎麻纤维的产量和品质至关重要。然而，公共数据库中仅有 418 个苎麻表达标签序列 (EST)，远远不足以理解其分子机制。因此，为了发现基因，特别是纤维素合酶（CesA）基因等基因，高通量转录组测序对于生成大量苎麻转录本序列至关重要。
结果
使用 Illumina 双端测序，生成了约 5300 万个测序读数。从头组装产生 43,990 个 Unigene，平均长度为 824 bp。通过搜索已知蛋白质的序列相似性，总共对 34,192 个（77.7%）基因的功能进行了注释。在这些带注释的unigenes中，16,050和13,042个unigenes分别被分配到基因本体和直系同源组簇。检索京都基因和基因组通路数据库百科全书（KEGG）表明，19,846个unigenes被映射到126个KEGG通路，565个基因被分配到与纤维素生物合成相关的http://starch和sucrose代谢通路。此外，还鉴定了 51 个参与纤维素生物合成的 CesA 基因。对51个CesA基因的组织特异性表达模式分析表明，有36个基因在茎皮中表达水平相对较高，这表明它们很可能负责韧皮纤维的生物合成。
结论
据我们所知，本研究首次对苎麻转录组进行了表征，获得的大量转录本将加速对苎麻营养生长和发育机制的理解。此外，茎皮中表达水平相对较高的36个CesA基因的发现将为了解苎麻韧皮纤维的形成和发育机制提供机会。
Background
Ramie fiber, extracted from vegetative organ stem bast, is one of the most important natural fibers. Understanding the molecular mechanisms of the vegetative growth of the ramie and the formation and development of bast fiber is essential for improving the yield and quality of the ramie fiber. However, only 418 expressed tag sequences (ESTs) of ramie deposited in public databases are far from sufficient to understand the molecular mechanisms. Thus, high-throughput transcriptome sequencing is essential to generate enormous ramie transcript sequences for the purpose of gene discovery, especially genes such as the cellulose synthase (CesA) gene.
Results
Using Illumina paired-end sequencing, about 53 million sequencing reads were generated. De novo assembly yielded 43,990 unigenes with an average length of 824 bp. By sequence similarity searching for known proteins, a total of 34,192 (77.7%) genes were annotated for their function. Out of these annotated unigenes, 16,050 and 13,042 unigenes were assigned to gene ontology and clusters of orthologous group, respectively. Searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG) indicated that 19,846 unigenes were mapped to 126 KEGG pathways, and 565 genes were assigned to http://starch and sucrose metabolic pathway which was related with cellulose biosynthesis. Additionally, 51 CesA genes involved in cellulose biosynthesis were identified. Analysis of tissue-specific expression pattern of the 51 CesA genes revealed that there were 36 genes with a relatively high expression levels in the stem bark, which suggests that they are most likely responsible for the biosynthesis of bast fiber.
Conclusion
To the best of our knowledge, this study is the first to characterize the ramie transcriptome and the substantial amount of transcripts obtained will accelerate the understanding of the ramie vegetative growth and development mechanism. Moreover, discovery of the 36 CesA genes with relatively high expression levels in the stem bark will present an opportunity to understand the ramie bast fiber formation and development mechanisms.
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