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

TitleHigh-quality assembled and annotated genomes of Nicotiana tabacum and Nicotiana benthamiana reveal chromosome evolution and changes in defense arsenals.
Publication TypeJournal Article
Year of Publication2024
AuthorsWang J, Zhang Q, Tung J, Zhang X, Liu D, Deng Y, Tian Z, Chen H, Wang T, Yin W, Li B, Lai Z, Dinesh-Kumar SP, Baker B, Li F
JournalMol Plant
Volume17
Issue3
Pagination423-437
Date Published2024 Mar 04
ISSN1752-9867
KeywordsChromosomes, Genes, Plant, Genomics, Molecular Sequence Annotation, Nicotiana
Abstract<p>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.</p>
DOI10.1016/j.molp.2024.01.008
Alternate JournalMol Plant
PubMed ID38273657