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Tobacco Resources in the Sol Genomics Network and Nicotiana Metabolic Databases

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Book cover The Tobacco Plant Genome

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

Abstract

Genomic databases provide essential information to scientists worldwide, including genome sequences, gene annotations, genetic markers, and phenotypic information. In addition to collecting and disseminating information, many databases also actively curate their data using a number of approaches, to ensure the data represent current knowledge and correspond to accepted quality standards. In this chapter, we review genome databases for the Nicotiana clade, and survey databases designed to further understand the metabolism of members of this clade. Although Nicotiana tabacum and its relatives, such as Nicotiana benthamiana, have been used widely in plant research over the last few decades, relatively few online Nicotiana resources exist, especially when compared with Solanaceae model systems such as tomato (Solanum lycopersicum). Tobacco plants are a major component of databases such as the Sol Genomics Network (https://solgenomics.net/) and the SolCyc metabolic databases, on which we will largely focus in this chapter.

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References

  • Ashburner M, Ball CA, Blake JA et al (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25–29

    CAS  PubMed  PubMed Central  Google Scholar 

  • Baldwin IT (2001) An ecologically motivated analysis of plant-herbivore interactions in native tobacco. Plant Physiol 127:1449–1458

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ball CA, Cherry JM (2001) Genome comparisons highlight similarity and diversity within the eukaryotic kingdoms. Curr Opin Chem Biol 5:86–89

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bally J, Jung H, Mortimer C et al (2018) The rise and rise of Nicotiana benthamiana: a plant for all reasons. Annu Rev Phytopathol 56:405–426

    CAS  PubMed  Google Scholar 

  • Baulcombe DC (1999) Fast forward genetics based on virus-induced gene silencing. Curr Opin Plant Biol 2:109–113

    CAS  PubMed  Google Scholar 

  • Baxevanis AD, Bateman A (2015) The importance of biological databases in biological discovery. Curr Protoc Bioinforma 50(1):1–8

    Google Scholar 

  • Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2010) GenBank. Nucleic Acids Res 38:D46–D51

    CAS  PubMed  Google Scholar 

  • Bombarely A, Menda N, Tecle IY et al (2011) The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. Nucleic Acids Res 39:D1149–D1155

    CAS  PubMed  Google Scholar 

  • Bombarely A, Rosli HG, Vrebalov J, Moffett P, Mueller LA, Martin GB (2012) A draft genome sequence of Nicotiana benthamiana to enhance molecular plant-microbe biology research. Mol Plant-Microbe Interact MPMI 25:1523–1530

    CAS  PubMed  Google Scholar 

  • Caspi R, Dreher K, Karp PD (2013) The challenge of constructing, classifying, and representing metabolic pathways. FEMS Microbiol Lett 345:85–93

    CAS  PubMed  Google Scholar 

  • Caspi R, Billington R, Ferrer L et al (2016) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 44:D471–D480

    CAS  PubMed  Google Scholar 

  • Dreher K (2014) Putting The Plant Metabolic Network pathway databases to work: going offline to gain new capabilities. Methods Mol Biol Clifton NJ 1083:151–171

    CAS  Google Scholar 

  • Edwards KD, Fernandez-Pozo N, Drake-Stowe K et al (2017) A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency. BMC Genom 18:448

    CAS  Google Scholar 

  • Fernandez-Pozo N, Menda N, Edwards JD et al (2015) The Sol Genomics Network (SGN)–from genotype to phenotype to breeding. Nucleic Acids Res 43:D1036–D1041

    CAS  PubMed  Google Scholar 

  • Fernie AR, Aharoni A, Willmitzer L et al (2011) Recommendations for reporting metabolic data. Plant Cell 23:2477–2482

    CAS  PubMed  PubMed Central  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 J Biol Databases Curation

    Google Scholar 

  • Fresquet-Corrales S, Roque E, Sarrión-Perdigones A et al (2017) Metabolic engineering to simultaneously activate anthocyanin and proanthocyanidin biosynthetic pathways in Nicotiana spp. PLoS ONE 12:e0184839

    PubMed  PubMed Central  Google Scholar 

  • Gerjets T, Sandmann M, Zhu C, Sandmann G (2007) Metabolic engineering of ketocarotenoid biosynthesis in leaves and flowers of tobacco species. Biotechnol J 2:1263–1269

    CAS  PubMed  Google Scholar 

  • Hasan MM, Kim H-S, Jeon J-H et al (2014) Metabolic engineering of Nicotiana benthamiana for the increased production of taxadiene. Plant Cell Rep 33:895–904

    CAS  PubMed  Google Scholar 

  • Hastings J, de Matos P, Dekker A et al (2013) The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res 41:D456–D463

    CAS  PubMed  Google Scholar 

  • Hur M, Campbell AA, Almeida-de-Macedo M et al (2013) A global approach to analysis and interpretation of metabolic data for plant natural product discovery. Nat Prod Rep 30:565–583

    CAS  PubMed  PubMed Central  Google Scholar 

  • Karp PD, Caspi R (2011) A survey of metabolic databases emphasizing the MetaCyc family. Arch Toxicol 85:1015–1033

    CAS  PubMed  PubMed Central  Google Scholar 

  • Karp PD, Paley SM, Krummenacker M et al (2010) Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief Bioinform 11:40–79

    CAS  PubMed  Google Scholar 

  • Karp PD, Paley S, Altman T (2013) Data mining in the MetaCyc family of pathway databases. Methods Mol Biol Clifton NJ 939:183–200

    CAS  Google Scholar 

  • Kessler A, Baldwin IT (2001) Defensive function of herbivore-induced plant volatile emissions in nature. Science 291:2141–2144

    CAS  PubMed  Google Scholar 

  • Kim S, Thiessen PA, Bolton EE et al (2016) PubChem substance and compound databases. Nucleic Acids Res 44:D1202–D1213

    CAS  PubMed  Google Scholar 

  • Latendresse M, Karp PD (2011) Web-based metabolic network visualization with a zooming user interface. BMC Bioinform 12:176

    Google Scholar 

  • Mann V, Harker M, Pecker I, Hirschberg J (2000) Metabolic engineering of astaxanthin production in tobacco flowers. Nat Biotechnol 18:888–892

    CAS  PubMed  Google Scholar 

  • Mueller LA, Zhang P, Rhee SY (2003) AraCyc: a biochemical pathway database for Arabidopsis. Plant Physiol 132:453–460

    CAS  PubMed  PubMed Central  Google Scholar 

  • Mueller LA, Solow TH, Taylor N et al (2005) The SOL genomics network: a comparative resource for Solanaceae biology and beyond. Plant Physiol 138:1310–1317

    CAS  PubMed  PubMed Central  Google Scholar 

  • NCBI Resource Coordinators (2018) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 46:D8–D13

    Google Scholar 

  • Owen C, Patron NJ, Huang A, Osbourn A (2017) Harnessing plant metabolic diversity. Curr Opin Chem Biol 40:24–30

    CAS  PubMed  PubMed Central  Google Scholar 

  • Paley SM, Karp PD (2006) The Pathway Tools cellular overview diagram and Omics Viewer. Nucleic Acids Res 34:3771–3778

    CAS  PubMed  PubMed Central  Google Scholar 

  • Paley S, O’Maille PE, Weaver D, Karp PD (2016) Pathway collages: personalized multi-pathway diagrams. BMC Bioinformatics 17:529

    PubMed  PubMed Central  Google Scholar 

  • Paley S, Parker K, Spaulding A, Tomb JF, O’Maille P, Karp PD (2017) The Omics Dashboard for interactive exploration of gene-expression data. Nucleic Acids Res 45(21):12113–12124

    CAS  PubMed  PubMed Central  Google Scholar 

  • Pearson WR (2015) Protein function prediction: problems and pitfalls. Curr Protoc Bioinforma 51(1):4–12

    Google Scholar 

  • Pence HE, Williams A (2010) ChemSpider: an online chemical information resource. J Chem Educ 87:1123–1124

    CAS  Google Scholar 

  • Pfalz M, Mikkelsen MD, Bednarek P, Olsen CE, Halkier BA, Kroymann J (2011) Metabolic engineering in Nicotiana benthamiana reveals key enzyme functions in Arabidopsis indole glucosinolate modification. Plant Cell 23:716–729

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rhee SY, Crosby B (2005) Biological databases for plant research. Plant Physiol 138:1–3

    PubMed  PubMed Central  Google Scholar 

  • Rushton PJ, Bokowiec MT, Laudeman TW, Brannock JF, Chen X, Timko MP (2008) TOBFAC: the database of tobacco transcription factors. BMC Bioinform 9:53

    Google Scholar 

  • Sierro N, Battey JND, Ouadi S et al (2013) Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis. Genome Biol 14:R60

    PubMed  PubMed Central  Google Scholar 

  • Sierro N, Battey JND, Ouadi S et al (2014) The tobacco genome sequence and its comparison with those of tomato and potato. Nat Commun 5:3833

    CAS  PubMed  Google Scholar 

  • Sussex IM (2008) The scientific roots of modern plant biotechnology. Plant Cell 20:1189–1198

    CAS  PubMed  PubMed Central  Google Scholar 

  • The Gene Ontology Consortium (2017) Expansion of the Gene Ontology knowledgebase and resources. Nucleic Acids Res 45:D331–D338

    Google Scholar 

  • The UniProt Consortium (2017) UniProt: the universal protein knowledgebase. Nucleic Acids Res 45:D158–D169

    Google Scholar 

  • Toya Y, Kono N, Arakawa K, Tomita M (2011) Metabolic flux analysis and visualization. J Proteome Res 10:3313–3323

    CAS  PubMed  Google Scholar 

  • Travers M, Paley SM, Shrager J, Holland TA, Karp PD (2013) Groups: knowledge spreadsheets for symbolic biocomputing. Database J Biol Databases Curation 2013:bat061

    Google Scholar 

  • Walsh JR, Schaeffer ML, Zhang P, Rhee SY, Dickerson JA, Sen TZ (2016) The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize. BMC Syst Biol 10:129

    PubMed  PubMed Central  Google Scholar 

  • Whitelaw CA, Barbazuk WB, Pertea G et al (2003) Enrichment of gene-coding sequences in maize by genome filtration. Science 302:2118–2120

    PubMed  Google Scholar 

  • Xu S, Brockmöller T, Navarro-Quezada A et al (2017) Wild tobacco genomes reveal the evolution of nicotine biosynthesis. Proc Natl Acad Sci USA 114:6133–6138

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zadran S, Levine RD (2013) Perspectives in metabolic engineering: understanding cellular regulation towards the control of metabolic routes. Appl Biochem Biotechnol 169:55–65

    CAS  PubMed  Google Scholar 

  • Zhang P, Foerster H, Tissier CP et al (2005) MetaCyc and AraCyc. Metabolic pathway databases for plant research. Plant Physiol 138:27–37

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Boyce Thompson Institute, Cornell University, Ithaca, NY, USA

    Hartmut Foerster & Lukas A. Mueller

Authors
  1. Hartmut Foerster
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  2. Lukas A. Mueller
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Corresponding author

Correspondence to Hartmut Foerster .

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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Foerster, H., Mueller, L.A. (2020). Tobacco Resources in the Sol Genomics Network and Nicotiana Metabolic Databases. 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_5

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