High-quality assembled and annotated genomes of Nicotiana benthamiana and Nicotiana tabacum reveal chromosome evolution and changes in defense arsenals

Authors: WANG, JUBIN - Huazhong Agricultural University; ZHANG, QINGLING - Huazhong Agricultural University; TUNG, JEFFREY - University Of California Berkeley; ZHANG, XI - Huazhong Agricultural University; LIU, DAN - Huazhong Agricultural University; DENG, YINGTIAN - Huazhong Agricultural University; TIAN, ZHENGDONG - Huazhong Agricultural University; CHEN, HUILAN - Huazhong Agricultural University; WANG, TAOTAO - Huazhong Agricultural University; YIN, WEIXIAO - Huazhong Agricultural University; LI, BO - Huazhong Agricultural University; LAI, ZHIBING - Huazhong Agricultural University; SAVITHRAMMA, DINESH-KUMAR - University Of California, Davis; Baker, Barbara; LI, FENG - Huazhong Agricultural University

Submitted to: Molecular Plant
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/21/2024
Publication Date: 3/4/2024
Citation: Wang, J., Zhang, Q., Tung, J., Zhang, X., Liu, D., Deng, Y., Tian, Z., Chen, H., Wang, T., Yin, W., Li, B., Lai, Z., Savithramma, D.P., Baker, B.J., Li, F. 2024. High-quality assembled and annotated genomes of Nicotiana benthamiana and Nicotiana tabacum reveal chromosome evolution and changes in defense arsenals. Molecular Plant. 17(3):423-437. https://doi.org/10.1016/j.molp.2024.01.008.
DOI: https://doi.org/10.1016/j.molp.2024.01.008

Interpretive Summary: High-quality assembled and annotated genomes of Nicotiana benthamiana and Nicotiana tabacum. Nicotiana benthamiana and N. tabacum are two important model plants used widely in plant research and biotechnology applications. They belong to the Solanaceae family that includes many important crops, such as potato, tomato, and pepper, which are threatened by a plethora of pathogens. Despite their importance in plant biology and biotechnology, genomic studies of N. benthamiana and N. tabacum have lagged. In this study, we generated high quality chromosome-level reference genomes for N. benthamiana and N. tabacum and developed sensitive RNA sequencing approaches for improved genome annotation. Using these genomic resources, we identified immune gene repertoires and determined their expression during plant microbe interactions. We developed user-friendly web analysis tools based on our high-quality genome assemblies and improved gene annotation that support dissection of genetic mechanisms underlying important plant process and contribute to crop improvement and biotechnological applications.

Technical Abstract: Nicotiana benthamiana and N. tabacum chromosome evolution and changes in defense arsenals Nicotiana benthamiana and N. tabacum are widely used models for understanding molecular mechanisms of plant-microbe interactions. However, lack of high-quality reference genome and annotation considerably hinders genetic research and limits the great potential of these two plant species in plant biology and biotechnology. In this study, chromosome-level reference genomes of N. benthamiana and N. tabacum were assembled using long read sequencing and 3-D genome analysis. We provide insight on the parent origin and chromosome structural changes leading to the hybrid genome formation of each species. Based on their high-quality genome assemblies. Highly sensitive transcription start site-sequencing (TSS-seq) and transcription termination site-sequencing (TTS-seq) methods were developed to facilitate genome annotation in conjunction with messenger RNA-seq data. Immunity-related genes were characterized, showing fewer immune receptors and antiviral RNA silencing genes in N. benthamiana than in N. tabacum, providing basis for further investigation of hyper- susceptibility of N. benthamiana to various pathogens. To facilitate user-friendly access to these two genomes, we created the Nicomics web server gene structure, expression and functions can be explored.