De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq.
De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq.
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DOI：
10.1186/1471-2164-11-681
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发表时间：
2010-12-01
期刊：
影响因子：
4.4
通讯作者：
Myburg AA
中科院分区：
文献类型：
--
作者：
Mizrachi E;Hefer CA;Ranik M;Joubert F;Myburg AA
由短读长 DNA 测序技术产生的转录序列的从头组装提供了一种快速获得非模式生物表达基因目录的方法。代表世界上最重要的硬木纤维作物的桉树树种（E. grandis）的基因组序列草案将于 2010 年制作完成。来自多个组织和器官的表达基因序列的全面收集将极大地促进这种有价值的木本植物的基因组注释及其优越的生长和生产力的遗传解剖。我们提供了仅使用 Illumina mRNA-Seq 技术和从头组装构建的商业种植的巨桉 × 尾叶桉杂交克隆的广泛表达基因目录。总共 18,894 个转录衍生的重叠群，其中很大一部分代表全长蛋白质编码基因被组装和注释。装配质量、长度和多样性的分析表明，该数据集代表了任何桉树最全面的表达基因目录。 mRNA-Seq 分析还允许对不同木源和非木源组织中所有组装的转录本进行数字表达分析，这对于归因假定的基因功能非常有价值。 Illumina mRNA-Seq 读段的从头组装是在桉树和其他非模型生物体中进行转录组测序和分析的有效方法。本研究生成的转录组资源（Eucspresso，http://eucspresso.bi.up.ac.za/）对于桉树木质生物量生产的基因组分析以及木本和草本植物生长和发育的比较基因组分析具有价值。
De novo assembly of transcript sequences produced by short-read DNA sequencing technologies offers a rapid approach to obtain expressed gene catalogs for non-model organisms. A draft genome sequence will be produced in 2010 for a Eucalyptus tree species (E. grandis) representing the most important hardwood fibre crop in the world. Genome annotation of this valuable woody plant and genetic dissection of its superior growth and productivity will be greatly facilitated by the availability of a comprehensive collection of expressed gene sequences from multiple tissues and organs. We present an extensive expressed gene catalog for a commercially grown E. grandis × E. urophylla hybrid clone constructed using only Illumina mRNA-Seq technology and de novo assembly. A total of 18,894 transcript-derived contigs, a large proportion of which represent full-length protein coding genes were assembled and annotated. Analysis of assembly quality, length and diversity show that this dataset represent the most comprehensive expressed gene catalog for any Eucalyptus tree. mRNA-Seq analysis furthermore allowed digital expression profiling of all of the assembled transcripts across diverse xylogenic and non-xylogenic tissues, which is invaluable for ascribing putative gene functions. De novo assembly of Illumina mRNA-Seq reads is an efficient approach for transcriptome sequencing and profiling in Eucalyptus and other non-model organisms. The transcriptome resource (Eucspresso, http://eucspresso.bi.up.ac.za/) generated by this study will be of value for genomic analysis of woody biomass production in Eucalyptus and for comparative genomic analysis of growth and development in woody and herbaceous plants.
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