Genome Sequence and Analysis of<i>Nicotiana benthamiana</i>, the Model Plant for Interactions between Organisms
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- Ken-ichi Kurotani
- Bioscience and Biotechnology Center, Nagoya University , Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
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- Hideki Hirakawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute , 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
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- Kenta Shirasawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute , 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
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- Yasuhiro Tanizawa
- Research Organization of Information and Systems, National Institute of Genetics , Yata, Mishima, 411-8540 Japan
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- Yasukazu Nakamura
- Research Organization of Information and Systems, National Institute of Genetics , Yata, Mishima, 411-8540 Japan
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- Sachiko Isobe
- Department of Frontier Research and Development, Kazusa DNA Research Institute , 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
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- Michitaka Notaguchi
- Bioscience and Biotechnology Center, Nagoya University , Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
説明
<jats:title>Abstract</jats:title><jats:p>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.</jats:p>
収録刊行物
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- Plant and Cell Physiology
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Plant and Cell Physiology 64 (2), 248-257, 2023-02-01
Oxford University Press (OUP)
