The Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
Physiol Plant. 2011 Nov;143(3):207-18. doi: 10.1111/j.1399-3054.2011.01500.x. Epub 2011 Sep 15.
Ginkgo biloba is monotypic species native to China and has old, dioecious, medicinally important characteristics. The functional genes related to these characteristics have not been effectively explored due to a limited number of expressed sequence tags (ESTs) from Ginkgo. To discover novel functional genes efficiently and to understand the development of a living fossil tree, Ginkgo, we used massive parallel pyrosequencing on the Roche 454 GS FLX Titanium platform to generate 64 057 ESTs. The ESTs combined with the 21 590 Ginkgo ESTs in genbank were assembled into 22 304 unique putative transcripts, in which 13 922 novel unique putative transcripts were identified by 454 sequencing. After being assigned to putative functions with Gene Ontology terms, a detailed view of the Ginkgo biological systems was displayed, including characterization of unique putative transcripts with homology to known key enzymes and transcription factors involved in ginkgolide/bilobalide and flavonoid biosynthetic pathways, as well as unique putative transcripts related to development, response to disease and defence. The fact that three full-length Ginkgo genes encoding key enzymes were found and cloned, suggests that high-throughput sequencing technology is superior to traditional gene-by-gene approach in discovery of genes. Additionally, a total of 204 simple sequence repeat motifs were detected. Our study not only lays the foundations for transcriptome-led studies in biosynthetic mechanisms, but also contributes significantly to the understanding of functional genomics and development in non-model plants.
银杏是原产于中国的单种植物，具有古老的、雌雄异株的、药用重要特征。由于银杏的表达序列标签 (EST) 数量有限，与这些特征相关的功能基因尚未得到有效探索。为了有效地发现新的功能基因，并了解活化石树银杏的发育情况，我们使用 Roche 454 GS FLX Titanium 平台上的大规模平行焦磷酸测序技术生成了 64057 条 EST。将这些 EST 与 genbank 中的 21590 条银杏 EST 组合，组装成 22304 个独特的假定转录本，其中 13922 个新的独特假定转录本通过 454 测序鉴定。在利用 Gene Ontology 术语将这些 EST 分配到假定功能后，展示了银杏生物系统的详细视图，包括对同源已知关键酶和转录因子的独特假定转录本的特征描述，以及与发育、疾病反应和防御相关的独特假定转录本。发现并克隆了三个全长银杏基因，这些基因编码关键酶，这一事实表明，高通量测序技术在发现基因方面优于传统的逐个基因方法。此外，还检测到 204 个简单序列重复基序。我们的研究不仅为生物合成机制的转录组研究奠定了基础，而且对非模式植物的功能基因组学和发育研究也有重要贡献。
