Kurotani Ken-Ichi, Hirakawa Hideki, Shirasawa Kenta, Tagiri Koya, Mori Moe, Ramadan Abedelaziz, Ichihashi Yasunori, Suzuki Takamasa, Tanizawa Yasuhiro, An Jiyuan, Winefield Christopher, Waterhouse Peter M, Miura Kenji, Nakamura Yasukazu, Isobe Sachiko, Notaguchi Michitaka
Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601, Japan.
Department of Frontier Research and Development, Kazusa DNA Research Institute, Kazusa-kamatari, Kisarazu, 292-0818, Japan.
Plant J. 2025 Jan;121(1):e17178. doi: 10.1111/tpj.17178. Epub 2024 Dec 3.
Nicotiana benthamiana has long served as a crucial plant material extensively used in plant physiology research, particularly in the field of plant pathology, because of its high susceptibility to plant viruses. Additionally, it serves as a production platform to test vaccines and other valuable substances. Among its approximately 3.1 Gb genome, 57 583 genes have been annotated within a 61 Mb region. We created a comprehensive and easy-to-use platform to use transcriptomes for modern annotation. These tools allow to visualize gene expression profiles, draw molecular evolutionary phylogenetic trees of gene families, perform functional enrichment analyses, and facilitate output downloads. To demonstrate their utility, we analyzed the gene expression profiles of enzymes within the nicotine biosynthesis pathway, a secondary metabolic pathway characteristic of the Nicotiana genus. Using the developed tool, expression profiles of the nicotine biosynthesis pathway genes were generated. The expression patterns of eight gene groups in the pathway were strongly expressed in the roots and weakly expressed in leaves and flowers of N. benthamiana. The results were consistent with the established gene expression profiles in Nicotiana tabacum and provided insights into gene family composition and expression trends. The compilation of this database tool can facilitate genetic analysis of N. benthamiana in the future.
本氏烟草长期以来一直是植物生理学研究中广泛使用的关键植物材料，特别是在植物病理学领域，因为它对植物病毒高度敏感。此外，它还作为测试疫苗和其他有价值物质的生产平台。在其约31亿碱基对的基因组中，在6100万碱基对的区域内已注释了57583个基因。我们创建了一个全面且易于使用的平台，用于利用转录组进行现代注释。这些工具可用于可视化基因表达谱、绘制基因家族的分子进化系统发育树、进行功能富集分析，并便于输出下载。为了证明它们的实用性，我们分析了尼古丁生物合成途径中酶的基因表达谱，尼古丁生物合成途径是烟草属特有的次生代谢途径。使用开发的工具，生成了尼古丁生物合成途径基因的表达谱。该途径中八个基因组的表达模式在本氏烟草的根中强烈表达，而在叶和花中弱表达。结果与烟草中已建立的基因表达谱一致，并为基因家族组成和表达趋势提供了见解。这个数据库工具的编制可以促进未来对本氏烟草的遗传分析。
