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Characterizing the Genome of Nicotiana tabacum

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The Tobacco Plant Genome

Part of the book series: Compendium of Plant Genomes ((CPG))

Abstract

The tobacco plant is an important crop and model organism, and there is a widespread interest in improving its agronomical properties. Unraveling its genome is necessary for understanding and predicting its biological properties and to ultimately contribute to breeding or engineering efforts for creating new varieties. Here, we discuss the key motivations behind the sequencing of its genome and the current state of genome sequencing efforts, as well as how it has been put to use. We finally speculate on what genomic trends relating to tobacco may be of interest in the near future.

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References

  • Bevan MW, Uauy C, Wulff BB, Zhou J, Krasileva K, Clark MD (2017) Genomic innovation for crop improvement. Nature 543:346–354

    Article  CAS  Google Scholar 

  • Bindler G, Plieske J, Bakaher N, Gunduz I, Ivanov N, van der Hoeven R, Ganal M, Donini P (2011) A high density genetic map of tobacco (Nicotiana tabacum L.) obtained from large scale microsatellite marker development. Theor Appl Genet 123:219–230

    Article  Google Scholar 

  • Bindler G, van der Hoeven R, Gunduz I, Plieske J, Ganal M, Rossi L, Gadani F, Donini P (2007) A microsatellite marker based linkage map of tobacco. Theor Appl Genet 114:341–349

    Article  CAS  Google Scholar 

  • Bland M, Matzinger D, Levings C (1985) Comparison of the mitochondrial genome of Nicotiana tabacum with its progenitor species. Theor Appl Genet 69:535–541

    Article  CAS  Google Scholar 

  • Bombarely A, Edwards KD, Sanchez-Tamburrino J, Mueller LA (2012) Deciphering the complex leaf transcriptome of the allotetraploid species Nicotiana tabacum: a phylogenomic perspective. BMC Genom 13:406

    Article  CAS  Google Scholar 

  • Chase MW, Knapp S, Cox AV, Clarkson JJ, Butsko Y, Joseph J, Savolainen V, Parokonny AS (2003) Molecular systematics, GISH and the origin of hybrid taxa in Nicotiana (Solanaceae). Ann Bot 92:107–127

    Article  CAS  Google Scholar 

  • Clarkson JJ, Knapp S, Garcia VF, Olmstead RG, Leitch AR, Chase MW (2004) Phylogenetic relationships in Nicotiana (Solanaceae) inferred from multiple plastid DNA regions. Mol Phylogenet Evol 33:75–90

    Article  CAS  Google Scholar 

  • Ding A, Marowa P, Kong Y (2016) Genome-wide identification of the expansin gene family in tobacco (Nicotiana tabacum). Mol Genet Genomics 291:1891–1907

    Article  CAS  Google Scholar 

  • Edwards KD, Fernandez-Pozo N, Drake-Stowe K, Humphry M, Evans AD, Bombarely A, Allen F, Hurst R, White B, Kernodle SP, Bromley JR, Sanchez-Tamburrino JP, Lewis RS, Mueller LA (2017) A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency. BMC Genom 18:448

    Article  CAS  Google Scholar 

  • Foerster H, Bombarely A, Battey JND, Sierro N, Ivanov NV, Mueller LA (2018) SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases. Database (Oxford)

    Google Scholar 

  • Gao J, Wang G, Ma S, Xie X, Wu X, Zhang X, Wu Y, Zhao P, Xia Q (2015) CRISPR/Cas9-mediated targeted mutagenesis in Nicotiana tabacum. Plant Mol Biol 87:99–110

    Article  CAS  Google Scholar 

  • Gao J, Zhang T, Xu B, Jia L, Xiao B, Liu H, Liu L, Yan H, Xia Q (2018) CRISPR/Cas9-mediated mutagenesis of carotenoid cleavage dioxygenase 8 (CCD8) in tobacco affects shoot and root architecture. Int J Mol Sci 19

    Google Scholar 

  • Gebhardt C (2016) The historical role of species from the Solanaceae plant family in genetic research. Theor Appl Genet 129:2281–2294

    Article  Google Scholar 

  • Hiatt A, Cafferkey R, Bowdish K (1989) Production of antibodies in transgenic plants. Nature 342:76–78

    Article  CAS  Google Scholar 

  • Jiao WB, Schneeberger K (2017) The impact of third generation genomic technologies on plant genome assembly. Curr Opin Plant Biol 36:64–70

    Article  CAS  Google Scholar 

  • Kenton A, Parokonny AS, Gleba YY, Bennett MD (1993) Characterization of the Nicotiana tabacum L. genome by molecular cytogenetics. Mol Gen Genet 240:159–169

    Article  CAS  Google Scholar 

  • Kim JS, Lee J, Lee CH, Woo SY, Kang H, Seo SG, Kim SH (2015) Activation of pathogenesis-related genes by the Rhizobacterium, Bacillus sp. JS, which induces systemic resistance in tobacco plants. Plant Pathol J 31:195–201

    Article  CAS  Google Scholar 

  • Knief C (2014) Analysis of plant microbe interactions in the era of next generation sequencing technologies. Front Plant Sci 5:216–216

    Article  Google Scholar 

  • Kovarik A, Renny-Byfield S, Grandbastien M-A, Leitch A (2012) Evolutionary implications of genome and karyotype restructuring in Nicotiana tabacum L. In: Soltis PS, Soltis DE (eds) Polyploidy and genome evolution. Springer, Berlin, Heidelberg

    Google Scholar 

  • Lefeuvre P, Martin DP, Elena SF, Shepherd DN, Roumagnac P, Varsani A (2019) Evolution and ecology of plant viruses. Nat Rev Microbiol 1

    Google Scholar 

  • Leitch IJ, Hanson L, Lim KY, Kovarik A, Chase MW, Clarkson JJ, Leitch AR (2008) The ups and downs of genome size evolution in polyploid species of Nicotiana (Solanaceae). Ann Bot 101:805–814

    Article  CAS  Google Scholar 

  • Long N, Ren X, Xiang Z, Wan W, Dong Y (2016) Sequencing and characterization of leaf transcriptomes of six diploid Nicotiana species. J Biol Res Thessalon 23:6

    Article  Google Scholar 

  • Murad L, Lim KY, Christopodulou V, Matyasek R, Lichtenstein CP, Kovarik A, Leitch AR (2002) The origin of tobacco’s T genome is traced to a particular lineage within Nicotiana tomentosiformis (Solanaceae). Am J Bot 89:921–928

    Article  CAS  Google Scholar 

  • Nagata T, Hasewa S, Inzé D (eds) (2004) Tobacco BY-2 cells. Springer

    Google Scholar 

  • Narayan R (1987) Nuclear DNA changes, genome differentiation and evolution in Nicotiana (Solanaceae). Plant Syst Evol 157:161–180

    Article  CAS  Google Scholar 

  • News, NCSU (2008) NC State University maps tobacco genome [Online]. https://news.ncsu.edu/2008/06/nc-state-university-maps-tobacco-genome/. Accessed 19 Feb, 2019

  • Opperman CH, Lommel SA, Sosinski BR, Lakey N, Gadani F (2003) The tobacco genome initiative. In: CORESTA meeting, agronomy/phytopathology. Bucharest

    Google Scholar 

  • Petit M, Lim KY, Julio E, Poncet C, De Borne FD, Kovarik A, Leitch AR, Grandbastien MA, Mhiri C (2007 July 1) Differential impact of retrotransposon populations on the genome of allotetraploid tobacco (Nicotiana tabacum). Mol Genet Genomics 278(1):1–5

    Google Scholar 

  • Rabara RC, Tripathi P, Reese RN, Rushton DL, Alexander D, Timko MP, Shen QJ, Rushton PJ (2015) Tobacco drought stress responses reveal new targets for Solanaceae crop improvement. BMC Genom 16:484

    Article  Google Scholar 

  • Renny-Byfield S, Chester M, Kovarik A, le Comber SC, Grandbastien MA, Deloger M, Nichols RA, Macas J, Novak P, Chase MW, Leitch AR (2011) Next generation sequencing reveals genome downsizing in allotetraploid Nicotiana tabacum, predominantly through the elimination of paternally derived repetitive DNAs. Mol Biol Evol 28:2843–2854

    Article  CAS  Google Scholar 

  • Schachtsiek J, Stehle F (2019) Nicotine‐free, non‐transgenic tobacco (Nicotiana tabacum L.) Edited by CRISPR‐Cas9. Plant Biotechnol J

    Google Scholar 

  • Sierro N, Battey JN, Ouadi S, Bakaher N, Bovet L, Willig A, Goepfert S, Peitsch MC, Ivanov NV (2014) The tobacco genome sequence and its comparison with those of tomato and potato. Nat Commun 5:3833

    Article  CAS  Google Scholar 

  • Sierro N, Battey JN, Ouadi S, Bovet L, Goepfert S, Bakaher N, Peitsch MC, Ivanov NV (2013a) Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis. Genome Biol 14:R60

    Article  Google Scholar 

  • Sierro N, van Oeveren J, van Eijk MJ, Martin F, Stormo KE, Peitsch MC, Ivanov NV (2013b) Whole genome profiling physical map and ancestral annotation of tobacco Hicks Broadleaf. Plant J 75:880–889

    Article  CAS  Google Scholar 

  • Skalicka K, Lim K, Matyasek R, Matzke M, Leitch A, Kovarik A (2005) Preferential elimination of repeated DNA sequences from the paternal, Nicotiana tomentosiformis genome donor of a synthetic, allotetraploid tobacco. New Phytol 166:291–303

    Article  CAS  Google Scholar 

  • Song Z, Pan F, Lou X, Wang D, Yang C, Zhang B, Zhang H (2019) Genome-wide identification and characterization of Hsp70 gene family in Nicotiana tabacum. Mol Biol Rep

    Google Scholar 

  • Tong Z, Xiao B, Jiao F, Fang D, Zeng J, Wu X, Chen X, Yang J, Li Y (2016) Large-scale development of SSR markers in tobacco and construction of a linkage map in flue-cured tobacco. Breed Sci 66:381–390

    Article  Google Scholar 

  • Tong Z, Yang Z, Chen X, Jiao F, Li X, Wu X, Gao Y, Xiao B, Wu W (2012) Large-scale development of microsatellite markers in Nicotiana tabacum and construction of a genetic map of flue-cured tobacco. Plant Breed 131:674–680

    Article  CAS  Google Scholar 

  • Tyson JR, O’Neil NJ, Jain M, Olsen HE, Hieter P, Snutch TP (2018) MinION-based long-read sequencing and assembly extends the Caenorhabditis elegans reference genome. Genome Res 28:266–274

    Article  CAS  Google Scholar 

  • Wei C, Chen J, Kuang H (2016) Dramatic number variation of R genes in Solanaceae species accounted for by a few R gene subfamilies. PLoS ONE 11:e0148708

    Article  Google Scholar 

  • Yuan XL, Cao M, Liu XM, Du YM, Shen GM, Zhang ZF, Li JH, Zhang P (2018) Composition and genetic diversity of the Nicotiana tabacum microbiome in different topographic areas and growth periods. Int J Mol Sci 19

    Google Scholar 

  • Yukawa M, Tsudzuki T, Sugiura M (2006) The chloroplast genome of Nicotiana sylvestris and Nicotiana tomentosiformis: complete sequencing confirms that the Nicotiana sylvestris progenitor is the maternal genome donor of Nicotiana tabacum. Mol Genet Genomics 275:367–373

    Article  CAS  Google Scholar 

  • Zhou XM, Zhao P, Wang W, Zou J, Cheng TH, Peng XB, Sun MX (2015) A comprehensive, genome-wide analysis of autophagy-related genes identified in tobacco suggests a central role of autophagy in plant response to various environmental cues. DNA Res 22:245–257

    Article  CAS  Google Scholar 

  • Zimmerman JL, Goldberg RB (1977) DNA sequence organization in the genome of Nicotiana tabacum. Chromosoma 59:227–252

    Article  CAS  Google Scholar 

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Author information

Authors and Affiliations

  1. PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, Neuchâtel, 2000, Switzerland

    James N. D. Battey, Nicolas Sierro & Nikolai V. Ivanov

Authors
  1. James N. D. Battey
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  2. Nicolas Sierro
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  3. Nikolai V. Ivanov
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Corresponding author

Correspondence to James N. D. Battey .

Editor information

Editors and Affiliations

  1. PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland

    Nikolai V. Ivanov

  2. PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland

    Nicolas Sierro

  3. PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland

    Manuel C. Peitsch

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Battey, J.N.D., Sierro, N., Ivanov, N.V. (2020). Characterizing the Genome of Nicotiana tabacum. In: Ivanov, N.V., Sierro, N., Peitsch, M.C. (eds) The Tobacco Plant Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-030-29493-9_4

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