Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria.
Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria.
BMC Genomics. 2019 Jul 19;20(1):594. doi: 10.1186/s12864-019-5960-2.
The allotetraploid tobacco species Nicotiana benthamiana native to Australia has become a popular host for recombinant protein production. Although its usage grows every year, little is known on this plant's genomic and transcriptomic features. Most N. benthamiana accessions currently used in research lack proper documentation of their breeding history and provenance. One of these, the glycoengineered N. benthamiana line ΔXT/FT is increasingly used for the production of biopharmaceutical proteins.
Based on an existing draft assembly of the N. benthamiana genome we predict 50,516 protein -encoding genes (62,216 transcripts) supported by expression data derived from 2.35 billion mRNA-seq reads. Using single-copy core genes we show high completeness of the predicted gene set. We functionally annotate more than two thirds of the gene set through sequence homology to genes from other Nicotiana species. We demonstrate that the expression profiles from leaf tissue of ΔXT/FT and its wild type progenitor only show minimal differences. We identify the transgene insertion sites in ΔXT/FT and show that one of the transgenes was inserted inside another predicted gene that most likely lost its function upon insertion. Based on publicly available mRNA-seq data, we confirm that the N. benthamiana accessions used by different research institutions most likely derive from a single source.
This work provides gene annotation of the N. benthamiana genome, a genomic and transcriptomic characterization of a transgenic N. benthamiana line in comparison to its wild-type progenitor, and sheds light onto the relatedness of N. benthamiana accessions that are used in laboratories around the world.
原产于澳大利亚的异源四倍体烟草物种黄花烟已成为重组蛋白生产的热门宿主。尽管其使用量逐年增加，但对该植物的基因组和转录组特征知之甚少。目前在研究中使用的大多数黄花烟品种缺乏对其育种历史和起源的适当记录。其中之一，经过糖基工程改造的黄花烟 ΔXT/FT 品系越来越多地用于生物制药蛋白的生产。
基于现有的黄花烟基因组草案组装，我们预测了 50516 个编码蛋白的基因（62216 个转录本），这些基因的表达数据来自 23.5 亿个 mRNA-seq reads。使用单拷贝核心基因，我们表明预测基因集的完整性很高。我们通过与其他黄花烟物种的基因进行序列同源性来对超过三分之二的基因集进行功能注释。我们证明 ΔXT/FT 及其野生型亲本的叶片组织的表达谱仅显示出最小的差异。我们确定了 ΔXT/FT 中的转基因插入位点，并表明其中一个转基因插入到另一个预测基因内，该基因很可能在插入后失去了功能。基于公开的 mRNA-seq 数据，我们确认不同研究机构使用的黄花烟品种很可能来自单一来源。
这项工作提供了黄花烟基因组的基因注释，比较了其转基因黄花烟品系与野生型亲本的基因组和转录组特征，并阐明了世界各地实验室使用的黄花烟品种的亲缘关系。
