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首页> 外文期刊>BMC Genomics >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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De novo assembly and characterization of transcriptome using Illumina paired-end sequencing and identification of CesA gene in ramie (Boehmeria nivea L. Gaud)

机译：从头组装和使用Illumina的双端测序和script麻中CesA基因的鉴定来表征转录组。

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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 e xpressed t ag s equences (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 webcite 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.
机译：背景Ram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the麻营养生长以及韧皮纤维的形成和发育的分子机制对于提高the麻纤维的产量和质量至关重要。但是，仅存于公共数据库中的418 x麻突变序列（EST）不足以了解其分子机制。因此，高通量转录组测序对于产生大量麻转录本序列，对于基因发现尤其是诸如纤维素合酶（CesA）基因之类的基因而言至关重要。结果使用Illumina的双末端测序，产生了约5300万个测序读数。从头组装产生了43,990个单基因，平均长度为824 bp。通过序列相似性搜索已知的蛋白质，总共注释了34,192（77.7％）个基因的功能。在这些带注释的单基因中，分别将16,050和13,042个单基因分配给基因本体和直系同源群。通过对《京都议定书》的基因和基因组途径数据库进行搜索，发现有19,846个单基因被映射到126条KEGG途径，其中565个基因被分配给http：//淀粉和蔗糖Webcite代谢途径，这与纤维素的生物合成有关。另外，鉴定了涉及纤维素生物合成的51个CesA基因。对51个CesA基因的组织特异性表达模式的分析表明，茎皮中存在36个相对较高表达水平的基因，这表明它们最有可能是韧皮纤维的生物合成的原因。结论据我们所知，这项研究是第一个表征the麻转录组的研究，获得的大量转录本将加速对the麻营养生长和发育机理的了解。此外，在茎皮中发现具有相对较高表达水平的36个CesA基因将为了解the麻韧皮纤维的形成和发育机制提供机会。

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