Ken-ichi Kurotani, Hideki Hirakawa, Kenta Shirasawa, Yasuhiro Tanizawa, Yasukazu Nakamura, Sachiko Isobe, Michitaka Notaguchi

Plant and Cell Physiology, pcac168, https://doi.org/10.1093/pcp/pcac168

Published: 09 February 2023

Abstract

Nicotiana benthamiana is widely used as a model plant for dicotyledonous angiosperms. In fact, the strains used in research are highly susceptible to a wide range of viruses. Accordingly, these strains are subject to plant pathology and plant–microbe interactions. In terms of plant–plant interactions, N. benthamiana is one of the plants that exhibit grafting affinity with plants from different families. Thus, N. benthamiana is a good model for plant biology and has been the subject of genome sequencing analyses for many years. However, N. benthamiana has a complex allopolyploid genome, and its previous reference genome is fragmented into 141,000 scaffolds. As a result, molecular genetic analysis is difficult to perform. To improve this effort, de novo whole-genome assembly was performed in N. benthamiana with Hifi reads, and 1,668 contigs were generated with a total length of 3.1 Gb. The 21 longest scaffolds, regarded as pseudomolecules, contained a 2.8-Gb sequence, occupying 95.6% of the assembled genome. A total of 57,583 high-confidence gene sequences were predicted. Based on a comparison of the genome structures between N. benthamiana and N. tabacum, N. benthamiana was found to have more complex chromosomal rearrangements, reflecting the age of interspecific hybridization. To verify the accuracy of the annotations, the cell wall modification genes involved in grafting were analyzed, which revealed not only the previously indeterminate untranslated region, intron and open reading frame sequences but also the genomic locations of their family genes. Owing to improved genome assembly and annotation, N. benthamiana would increasingly be more widely accessible.

See https://academic.oup.com/pcp/advance-article/doi/10.1093/pcp/pcac168/7031347?login=false

Figure 1: The N. benthamiana genome. (A) The distribution of retrotransposons and genes in 21 scaffolds. Circles indicate the concentration of Ty3-gypsy (yellow) and Ty1-copia (blue), gene content (orange) and G+C% (light blue) from inner to outer. (B) Coverage of regions of high homology with N. sylvestris and N. tomentosiformis on N. benthamiana and N. tabacum. Circles indicate the coverage of N. sylvestris (blue) and N. tomentosiformis (red) from inner to outer. The center of the image represents the linkage of SSRs. Blue and red lines indicate SSRs on N. sylvestris and N. tomentosiformis, respectively. S010–S210 represent the 21 longest scaffolds of N. benthamiana, and Nt1–Nt24 represent the 24 chromosomes of N. tabacum.