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

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 forN. 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 inN. 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 genesRDR1,RDR6,DCL2,DCL3, andAGO2were lost from one or both subgenomes in N. benthamiana, while both homeologs were kept in N. tabacum. Furthermore, theN. benthamianagenome encodes fewer immune receptors and signaling components than that ofN. tabacum. These find-ings uncover possible reasons underlying the hypersusceptible nature ofN. benthamiana. We developedthe user-friendly Nicomics (http://lifenglab.hzau.edu.cn/Nicomics/) web server to facilitate better use ofNicotianagenomic resources as well as gene structure and expression analyses.