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A Guide to the PLAZA 3.0 Plant Comparative Genomic Database

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Plant Genomics Databases

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1533))

Abstract

PLAZA 3.0 is an online resource for comparative genomics and offers a versatile platform to study gene functions and gene families or to analyze genome organization and evolution in the green plant lineage. Starting from genome sequence information for over 35 plant species, precomputed comparative genomic data sets cover homologous gene families, multiple sequence alignments, phylogenetic trees, and genomic colinearity information within and between species. Complementary functional data sets, a Workbench, and interactive visualization tools are available through a user-friendly web interface, making PLAZA an excellent starting point to translate sequence or omics data sets into biological knowledge. PLAZA is available at http://bioinformatics.psb.ugent.be/plaza/.

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References

  1. Michael TP, Jackson S (2013) The first 50 plant genomes. Plant Genome 6. doi: 10.3835/plantgenome2013.3803.0001in

  2. Wegrzyn JL, Liechty JD, Stevens KA, Wu L-S, Loopstra CA, Vasquez-Gross HA, Dougherty WM, Lin BY, Zieve JJ, Martinez-Garcia PJ, Holt C, Yandell M, Zimin AV, Yorke JA, Crepeau MW, Puiu D, Salzberg SL, de Jong PJ, Mockaitis K, Main D, Langley CH, Neale DB (2014) Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. Genetics 196:891–909

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Vlad D, Kierzkowski D, Rast MI, Vuolo F, Dello Ioio R, Galinha C, Gan X, Hajheidari M, Hay A, Smith RS, Huijser P, Bailey CD, Tsiantis M (2014) Leaf shape evolution through duplication, regulatory diversification, and loss of a homeobox gene. Science 343:780–783

    Article  CAS  PubMed  Google Scholar 

  4. Choulet F, Alberti A, Theil S, Glover N, Barbe V, Daron J, Pingault L, Sourdille P, Couloux A, Paux E, Leroy P, Mangenot S, Guilhot N, Le Gouis J, Balfourier F, Alaux M, Jamilloux V, Poulain J, Durand C, Bellec A, Gaspin C, Safar J, Dolezel J, Rogers J, Vandepoele K, Aury J-M, Mayer K, Berges H, Quesneville H, Wincker P, Feuillet C (2014) Structural and functional partitioning of bread wheat chromosome 3B. Science 345:1249721

    Article  PubMed  Google Scholar 

  5. Hardison RC (2003) Comparative genomics. PLoS Biol 1:156–160

    Article  CAS  Google Scholar 

  6. Vandepoele K, Van de Peer Y (2005) Exploring the plant transcriptome through phylogenetic profiling. Plant Physiol 137:31–42

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Proost S, Van Bel M, Vaneechoutte D, Van de Peer Y, Inzé D, Mueller-Roeber B, Vandepoele K (2015) PLAZA 3.0: an access point for plant comparative genomics. Nucleic Acids Res 43:D974–D981

    Article  PubMed  Google Scholar 

  8. Vandepoele K, Van Bel M, Richard G, Van Landeghem S, Verhelst B, Moreau H, Van de Peer Y, Grimsley N, Piganeau G (2013) pico-PLAZA, a genome database of microbial photosynthetic eukaryotes. Environ Microbiol 15:2147–2153

    Article  CAS  PubMed  Google Scholar 

  9. Van Bel M, Proost S, Van Neste C, Deforce D, Van de Peer Y, Vandepoele K (2013) TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes. Genome Biol 14:R134

    Article  PubMed  PubMed Central  Google Scholar 

  10. Enright AJ, Van Dongen S, Ouzounis CA (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 30:1575–1584

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Li L, Stoeckert CJ Jr, Roos DS (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13:2178–2189

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Price MN, Dehal PS, Arkin AP (2010) FastTree 2 – approximately maximum-likelihood trees for large alignments. PLoS One 5:e9490

    Article  PubMed  PubMed Central  Google Scholar 

  13. Pérez-Rodríguez P, Riaño-Pachón DM, Corrêa LGG, Rensing SA, Kersten B, Mueller-Roeber B (2010) PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Res 38:D822–D827

    Article  PubMed  Google Scholar 

  14. Jin J, Zhang H, Kong L, Gao G, Luo J (2014) PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. Nucleic Acids Res 42:D1182–D1187

    Article  CAS  PubMed  Google Scholar 

  15. Nemhauser JL, Hong F, Chory J (2006) Different plant hormones regulate similar processes through largely nonoverlapping transcriptional responses. Cell 126:467–475

    Article  CAS  PubMed  Google Scholar 

  16. Jain M, Khurana JP (2009) Transcript profiling reveals diverse roles of auxin-responsive genes during reproductive development and abiotic stress in rice. FEBS J 276:3148–3162

    Article  CAS  PubMed  Google Scholar 

  17. Guilfoyle TJ, Hagen G (2007) Auxin response factors. Curr Opin Plant Biol 10:453–460

    Article  CAS  PubMed  Google Scholar 

  18. Fitch WM (1970) Distinguishing homologous from analogous proteins. Syst Biol 19:99–113

    CAS  Google Scholar 

  19. Van de Peer Y, Fawcett JA, Proost S, Sterck L, Vandepoele K (2009) The flowering world: a tale of duplications. Trends Plant Sci 14:680–688

    Article  PubMed  Google Scholar 

  20. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Chen F, Mackey AJ, Vermunt JK, Roos DS (2007) Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLoS One 2:e383

    Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

I thank Michiel Van Bel for excellent technical assistance and maintenance of the PLAZA platform, all long-term PLAZA users for their feedback and Annick Bleys for help in preparing the manuscript. This work was supported by the Multidisciplinary Research Partnership “Bioinformatics: From Nucleotides to Networks” Project (no 01MR0410W) of Ghent University.

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Authors and Affiliations

  1. Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium

    Klaas Vandepoele

  2. Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium

    Klaas Vandepoele

  3. Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, 9052, Ghent, Belgium

    Klaas Vandepoele

Authors
  1. Klaas Vandepoele
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Correspondence to Klaas Vandepoele .

Editor information

Editors and Affiliations

  1. PRI Bioscience, Biometris and Bioinformatics, Wageningen University & Research Wageningen, Wageningen, The Netherlands

    Aalt D.J van Dijk

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Vandepoele, K. (2017). A Guide to the PLAZA 3.0 Plant Comparative Genomic Database. In: van Dijk, A. (eds) Plant Genomics Databases. Methods in Molecular Biology, vol 1533. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6658-5_10

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  • DOI: https://doi.org/10.1007/978-1-4939-6658-5_10

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6656-1

  • Online ISBN: 978-1-4939-6658-5

  • eBook Packages: Springer Protocols

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