National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi Province, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330299, China.
National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China.
Mol Plant. 2024 Mar 4;17(3):423-437. doi: 10.1016/j.molp.2024.01.008. Epub 2024 Jan 24.
Nicotiana tabacum and Nicotiana benthamiana are widely used models in plant biology research. However, genomic studies of these species have lagged. Here we report the chromosome-level reference genome assemblies for N. benthamiana and N. tabacum with an estimated 99.5% and 99.8% completeness, respectively. Sensitive transcription start and termination site sequencing methods were developed and used for accurate gene annotation in N. tabacum. Comparative analyses revealed evidence for the parental origins and chromosome structural changes, leading to hybrid genome formation of each species. Interestingly, the antiviral silencing genes RDR1, RDR6, DCL2, DCL3, and AGO2 were lost from one or both subgenomes in N. benthamiana, while both homeologs were kept in N. tabacum. Furthermore, the N. benthamiana genome encodes fewer immune receptors and signaling components than that of N. tabacum. These findings uncover possible reasons underlying the hypersusceptible nature of N. benthamiana. We developed the user-friendly Nicomics (http://lifenglab.hzau.edu.cn/Nicomics/) web server to facilitate better use of Nicotiana genomic resources as well as gene structure and expression analyses.
烟草和黄花烟是植物生物学研究中广泛使用的模式物种。然而，这些物种的基因组研究相对滞后。本研究报道了黄花烟和烟草的染色体水平参考基因组组装，其完整性分别估计为 99.5%和 99.8%。开发了灵敏的转录起始和终止位点测序方法，用于烟草的准确基因注释。比较分析揭示了每个物种的亲本来源和染色体结构变化的证据，导致杂种基因组的形成。有趣的是，抗病毒沉默基因 RDR1、RDR6、DCL2、DCL3 和 AGO2 在黄花烟的一个或两个亚基因组中丢失，而在烟草中则保留了两个同源基因。此外，黄花烟基因组编码的免疫受体和信号成分比烟草少。这些发现揭示了黄花烟高度敏感特性的可能原因。我们开发了用户友好的 Nicomics（http://lifenglab.hzau.edu.cn/Nicomics/）网络服务器，以方便更好地利用烟草基因组资源以及基因结构和表达分析。
