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

Nicotiana tabacum and N. benthamiana are widely used models in plant biology research. However, genomic studies of these species have lagged. Here we report construction of chromosome-level reference genomes of 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 parent origins and chromosome structural changes leading to hybrid genome formation of each species. Interestingly, antiviral silencing genes RDR1, RDR6, DCL2, DCL3 and AGO2 were lost from one or both subgenomes in N. benthamiana while both homeologues were kept in N. tabacum. Furthermore, N. benthamiana genome encodes fewer immune receptors and signaling components than N. tabacum. These findings point to reason behind hyper susceptible nature of N. benthamiana. We developed user friendly Nicomics (http://lifenglab.hzau.edu.cn/Nicomics/) webserver to facilitate gene structure and expression analysis.