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Tobacco Resources in the Sol Genomics Network and Nicotiana Metabolic Databases

  • Hartmut FoersterEmail author
  • Lukas A. Mueller
Chapter
  • 39 Downloads
Part of the Compendium of Plant Genomes book series (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.

References

  1. Ashburner M, Ball CA, Blake JA et al (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25–29CrossRefPubMedPubMedCentralGoogle Scholar
  2. Baldwin IT (2001) An ecologically motivated analysis of plant-herbivore interactions in native tobacco. Plant Physiol 127:1449–1458CrossRefPubMedPubMedCentralGoogle Scholar
  3. Ball CA, Cherry JM (2001) Genome comparisons highlight similarity and diversity within the eukaryotic kingdoms. Curr Opin Chem Biol 5:86–89CrossRefPubMedPubMedCentralGoogle Scholar
  4. Bally J, Jung H, Mortimer C et al (2018) The rise and rise of Nicotiana benthamiana: a plant for all reasons. Annu Rev Phytopathol 56:405–426CrossRefPubMedPubMedCentralGoogle Scholar
  5. Baulcombe DC (1999) Fast forward genetics based on virus-induced gene silencing. Curr Opin Plant Biol 2:109–113CrossRefPubMedPubMedCentralGoogle Scholar
  6. Baxevanis AD, Bateman A (2015) The importance of biological databases in biological discovery. Curr Protoc Bioinforma 50(1):1–8Google Scholar
  7. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2010) GenBank. Nucleic Acids Res 38:D46–D51CrossRefPubMedPubMedCentralGoogle Scholar
  8. Bombarely A, Menda N, Tecle IY et al (2011) The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. Nucleic Acids Res 39:D1149–D1155CrossRefPubMedPubMedCentralGoogle Scholar
  9. 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 25:1523–1530CrossRefPubMedPubMedCentralGoogle Scholar
  10. Caspi R, Dreher K, Karp PD (2013) The challenge of constructing, classifying, and representing metabolic pathways. FEMS Microbiol Lett 345:85–93CrossRefPubMedPubMedCentralGoogle Scholar
  11. 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–D480CrossRefPubMedPubMedCentralGoogle Scholar
  12. Dreher K (2014) Putting The Plant Metabolic Network pathway databases to work: going offline to gain new capabilities. Methods Mol Biol Clifton NJ 1083:151–171CrossRefGoogle Scholar
  13. 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 18:448CrossRefGoogle Scholar
  14. 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–D1041CrossRefPubMedPubMedCentralGoogle Scholar
  15. Fernie AR, Aharoni A, Willmitzer L et al (2011) Recommendations for reporting metabolic data. Plant Cell 23:2477–2482CrossRefPubMedPubMedCentralGoogle Scholar
  16. 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 CurationGoogle Scholar
  17. 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:e0184839CrossRefPubMedPubMedCentralGoogle Scholar
  18. Gerjets T, Sandmann M, Zhu C, Sandmann G (2007) Metabolic engineering of ketocarotenoid biosynthesis in leaves and flowers of tobacco species. Biotechnol J 2:1263–1269CrossRefPubMedPubMedCentralGoogle Scholar
  19. 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 33:895–904CrossRefPubMedPubMedCentralGoogle Scholar
  20. 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–D463CrossRefPubMedPubMedCentralGoogle Scholar
  21. 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 30:565–583CrossRefPubMedPubMedCentralGoogle Scholar
  22. Karp PD, Caspi R (2011) A survey of metabolic databases emphasizing the MetaCyc family. Arch Toxicol 85:1015–1033CrossRefPubMedPubMedCentralGoogle Scholar
  23. 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 11:40–79CrossRefPubMedPubMedCentralGoogle Scholar
  24. Karp PD, Paley S, Altman T (2013) Data mining in the MetaCyc family of pathway databases. Methods Mol Biol Clifton NJ 939:183–200CrossRefGoogle Scholar
  25. Kessler A, Baldwin IT (2001) Defensive function of herbivore-induced plant volatile emissions in nature. Science 291:2141–2144CrossRefPubMedPubMedCentralGoogle Scholar
  26. Kim S, Thiessen PA, Bolton EE et al (2016) PubChem substance and compound databases. Nucleic Acids Res 44:D1202–D1213CrossRefPubMedPubMedCentralGoogle Scholar
  27. Latendresse M, Karp PD (2011) Web-based metabolic network visualization with a zooming user interface. BMC Bioinform 12:176CrossRefGoogle Scholar
  28. Mann V, Harker M, Pecker I, Hirschberg J (2000) Metabolic engineering of astaxanthin production in tobacco flowers. Nat Biotechnol 18:888–892CrossRefPubMedPubMedCentralGoogle Scholar
  29. Mueller LA, Zhang P, Rhee SY (2003) AraCyc: a biochemical pathway database for Arabidopsis. Plant Physiol 132:453–460CrossRefPubMedPubMedCentralGoogle Scholar
  30. Mueller LA, Solow TH, Taylor N et al (2005) The SOL genomics network: a comparative resource for Solanaceae biology and beyond. Plant Physiol 138:1310–1317CrossRefPubMedPubMedCentralGoogle Scholar
  31. NCBI Resource Coordinators (2018) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 46:D8–D13CrossRefGoogle Scholar
  32. Owen C, Patron NJ, Huang A, Osbourn A (2017) Harnessing plant metabolic diversity. Curr Opin Chem Biol 40:24–30CrossRefPubMedPubMedCentralGoogle Scholar
  33. Paley SM, Karp PD (2006) The Pathway Tools cellular overview diagram and Omics Viewer. Nucleic Acids Res 34:3771–3778CrossRefPubMedPubMedCentralGoogle Scholar
  34. Paley S, O’Maille PE, Weaver D, Karp PD (2016) Pathway collages: personalized multi-pathway diagrams. BMC Bioinformatics 17:529CrossRefPubMedPubMedCentralGoogle Scholar
  35. 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):12113–12124CrossRefPubMedPubMedCentralGoogle Scholar
  36. Pearson WR (2015) Protein function prediction: problems and pitfalls. Curr Protoc Bioinforma 51(1):4–12Google Scholar
  37. Pence HE, Williams A (2010) ChemSpider: an online chemical information resource. J Chem Educ 87:1123–1124CrossRefGoogle Scholar
  38. 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 23:716–729CrossRefPubMedPubMedCentralGoogle Scholar
  39. Rhee SY, Crosby B (2005) Biological databases for plant research. Plant Physiol 138:1–3CrossRefPubMedPubMedCentralGoogle Scholar
  40. Rushton PJ, Bokowiec MT, Laudeman TW, Brannock JF, Chen X, Timko MP (2008) TOBFAC: the database of tobacco transcription factors. BMC Bioinform 9:53CrossRefGoogle Scholar
  41. Sierro N, Battey JND, Ouadi S et al (2013) Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis. Genome Biol 14:R60CrossRefPubMedPubMedCentralGoogle Scholar
  42. Sierro N, Battey JND, Ouadi S et al (2014) The tobacco genome sequence and its comparison with those of tomato and potato. Nat Commun 5:3833CrossRefPubMedPubMedCentralGoogle Scholar
  43. Sussex IM (2008) The scientific roots of modern plant biotechnology. Plant Cell 20:1189–1198CrossRefPubMedPubMedCentralGoogle Scholar
  44. The Gene Ontology Consortium (2017) Expansion of the Gene Ontology knowledgebase and resources. Nucleic Acids Res 45:D331–D338CrossRefGoogle Scholar
  45. The UniProt Consortium (2017) UniProt: the universal protein knowledgebase. Nucleic Acids Res 45:D158–D169CrossRefGoogle Scholar
  46. Toya Y, Kono N, Arakawa K, Tomita M (2011) Metabolic flux analysis and visualization. J Proteome Res 10:3313–3323CrossRefPubMedPubMedCentralGoogle Scholar
  47. Travers M, Paley SM, Shrager J, Holland TA, Karp PD (2013) Groups: knowledge spreadsheets for symbolic biocomputing. Database J Biol Databases Curation 2013:bat061Google Scholar
  48. 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 10:129CrossRefPubMedPubMedCentralGoogle Scholar
  49. Whitelaw CA, Barbazuk WB, Pertea G et al (2003) Enrichment of gene-coding sequences in maize by genome filtration. Science 302:2118–2120CrossRefPubMedPubMedCentralGoogle Scholar
  50. Xu S, Brockmöller T, Navarro-Quezada A et al (2017) Wild tobacco genomes reveal the evolution of nicotine biosynthesis. Proc Natl Acad Sci USA 114:6133–6138CrossRefPubMedPubMedCentralGoogle Scholar
  51. Zadran S, Levine RD (2013) Perspectives in metabolic engineering: understanding cellular regulation towards the control of metabolic routes. Appl Biochem Biotechnol 169:55–65CrossRefPubMedPubMedCentralGoogle Scholar
  52. Zhang P, Foerster H, Tissier CP et al (2005) MetaCyc and AraCyc. Metabolic pathway databases for plant research. Plant Physiol 138:27–37CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2020

Authors and Affiliations

  1. 1.Boyce Thompson Institute, Cornell UniversityIthacaUSA

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