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One Stop Shop for Everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012

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Dictyostelium discoideum Protocols

Part of the book series: Methods in Molecular Biology ((MIMB,volume 983))

Abstract

dictyBase (http://dictybase.org), the model organism database for Dictyostelium discoideum, includes the complete genome sequence and expression data for this organism. Relevant literature is integrated into the database, and gene models and functional annotation are manually curated from experimental results and comparative multigenome analyses. dictyBase has recently expanded to include the genome sequences of three additional Dictyostelids and has added new software tools to facilitate multigenome comparisons. The Dicty Stock Center, a strain and plasmid repository for Dictyostelium research, has relocated to Northwestern University in 2009. This allowed us integrating all Dictyostelium resources to better serve the research community. In this chapter, we will describe how to navigate the Web site and highlight some of our newer improvements.

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References

  1. Chisholm RL, Gaudet P, Just EM, Pilcher KE, Fey P, Merchant SN, Kibbe WA (2006) dictyBase, the model organism database for Dictyostelium discoideum. Nucleic Acids Res 34:D423–D427

    Article  PubMed  CAS  Google Scholar 

  2. Gaudet P, Fey P, Basu S, Bushmanova YA, Dodson R, Sheppard KA, Just EM, Kibbe WA, Chisholm RL (2011) dictyBase update 2011: web 2.0 functionality and the initial steps towards a genome portal for the Amoebozoa. Nucleic Acids Res 39:D620–D624

    Article  PubMed  CAS  Google Scholar 

  3. Eichinger L, Pachebat JA, Glöckner G, Rajandream MA, Sucgang R, Berriman M, Song J, Olsen R, Szafranski K, Xu Q, Tunggal B, Kummerfeld S, Madera M, Konfortov BA, Rivero F, Bankier AT, Lehmann R, Hamlin N, Davies R, Gaudet P, Fey P, Pilcher K, Chen G, Saunders D, Sodergren E, Davis P, Kerhornou A, Nie X, Hall N, Anjard C, Hemphill L, Bason N, Farbrother P, Desany B, Just E, Morio T, Rost R, Churcher C, Cooper J, Haydock S, van Driessche N, Cronin A, Goodhead I, Muzny D, Mourier T, Pain A, Lu M, Harper D, Lindsay R, Hauser H, James K, Quiles M, Madan Babu M, Saito T, Buchrieser C, Wardroper A, Felder M, Thangavelu M, Johnson D, Knights A, Loulseged H, Mungall K, Oliver K, Price C, Quail MA, Urushihara H, Hernandez J, Rabbinowitsch E, Steffen D, Sanders M, Ma J, Kohara Y, Sharp S, Simmonds M, Spiegler S, Tivey A, Sugano S, White B, Walker D, Woodward J, Winckler T, Tanaka Y, Shaulsky G, Schleicher M, Weinstock G, Rosenthal A, Cox EC, Chisholm RL, Gibbs R, Loomis WF, Platzer M, Kay RR, Williams J, Dear PH, Noegel AA, Barrell B, Kuspa A (2005) The genome of the social amoeba Dictyostelium discoideum. Nature 435:43–57

    Article  PubMed  CAS  Google Scholar 

  4. Ogawa S, Yoshino R, Angata K, Iwamoto M, Pi M, Kuroe K, Matsuo K, Morio T, Urushihara H, Yanagisawa K, Tanaka Y (2000) The mitochondrial DNA of Dictyostelium discoideum: complete sequence, gene content and genome organization. Mol Gen Genet 263:514–519

    PubMed  CAS  Google Scholar 

  5. Sucgang R, Chen G, Liu W, Lindsay R, Lu J, Muzny D, Shaulsky G, Loomis W, Gibbs R, Kuspa A (2003) Sequence and structure of the extrachromosomal palindrome encoding the ribosomal RNA genes in Dictyostelium. Nucleic Acids Res 31:2361–2368

    Article  PubMed  CAS  Google Scholar 

  6. Urushihara H, Morio T, Saito T, Kohara Y, Koriki E, Ochiai H, Maeda M, Williams JG, Takeuchi I, Tanaka Y (2004) Analyses of cDNAs from growth and slug stages of Dictyostelium discoideum. Nucleic Acids Res 32:1647–1653

    Article  PubMed  CAS  Google Scholar 

  7. Morio T, Urushihara H, Saito T, Ugawa Y, Mizuno H, Yoshida M, Yoshino R, Mitra BN, Pi M, Sato T, Takemoto K, Yasukawa H, Williams J, Maeda M, Takeuchi I, Ochiai H, Tanaka Y (1998) The Dictyostelium Developmental cDNA Project: generation and analysis of expressed sequence tags from the first-finger stage of development. DNA Res 5:335–340

    Article  PubMed  CAS  Google Scholar 

  8. Sucgang R, Kuo A, Tian X, Salerno W, Parikh A, Feasley CL, Dalin E, Tu H, Huang E, Barry K, Lindquist E, Shapiro H, Bruce D, Schmutz J, Salamov A, Fey P, Gaudet P, Anjard C, Babu MM, Basu S, Bushmanova Y, van der Wel H, Katoh-Kurasawa M, Dinh C, Coutinho PM, Saito T, Elias M, Schaap P, Kay RR, Henrissat B, Eichinger L, Rivero F, Putnam NH, West CM, Loomis WF, Chisholm RL, Shaulsky G, Strassmann JE, Queller DC, Kuspa A, Grigoriev IV (2011) Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum. Genome Biol 12:R20

    Article  PubMed  CAS  Google Scholar 

  9. Heidel AJ, Lawal HM, Felder M, Schilde C, Helps NR, Tunggal B, Rivero F, John U, Schleicher M, Eichinger L, Platzer M, Noegel AA, Schaap P, Glöckner G (2011) Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication. Genome Res 21:1882–1891

    Article  PubMed  CAS  Google Scholar 

  10. Benson DA, Karsch-Mizrachi I, Clark K, Lipman DJ, Ostell J, Sayers EW (2012) GenBank. Nucleic Acids Res 40:D48–D53

    Article  PubMed  CAS  Google Scholar 

  11. Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C (2009) InterPro: the integrative protein signature database. Nucleic Acids Res 37:D211–D215

    Article  PubMed  CAS  Google Scholar 

  12. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD (2012) The Pfam protein families database. Nucleic Acids Res 40:D290–D301

    Article  PubMed  CAS  Google Scholar 

  13. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25–29

    Article  PubMed  CAS  Google Scholar 

  14. Drew K, Winters P, Butterfoss GL, Berstis V, Uplinger K, Armstrong J, Riffle M, Schweighofer E, Bovermann B, Goodlett DR, Davis TN, Shasha D, Malmström L, Bonneau R (2011) The Proteome Folding Project: proteome-scale prediction of structure and function. Genome Res 21:1981–1994

    Article  PubMed  CAS  Google Scholar 

  15. du Plessis L, Skunca N, Dessimoz C (2011) The what, where, how and why of gene ontology–a primer for bioinformaticians. Brief Bioinform 12:723–735

    Article  PubMed  Google Scholar 

  16. Masseroli M, Pinciroli F (2006) Using Gene Ontology and genomic controlled vocabularies to analyze high-throughput gene lists: three tool comparison. Comput Biol Med 36:731–747

    Article  PubMed  CAS  Google Scholar 

  17. Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S, AmiGO Hub, Web Presence Working Group (2009) AmiGO: online access to ontology and annotation data. Bioinformatics 25:288–289

    Article  PubMed  CAS  Google Scholar 

  18. Ostlund G, Schmitt T, Forslund K, Köstler T, Messina DN, Roopra S, Frings O, Sonnhammer ELL (2010) InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res 38:D196–D203

    Article  PubMed  Google Scholar 

  19. Chen F (2006) OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res 34:D363–D368

    Article  PubMed  CAS  Google Scholar 

  20. Kersey PJ, Lawson D, Birney E, Derwent PS, Haimel M, Herrero J, Keenan S, Kerhornou A, Koscielny G, Kahari A, Kinsella RJ, Kulesha E, Maheswari U, Megy K, Nuhn M, Proctor G, Staines D, Valentin F, Vilella AJ, Yates A (2009) Ensembl Genomes: extending Ensembl across the taxonomic space. Nucleic Acids Res 38:D563–D569

    Article  PubMed  Google Scholar 

  21. Gaudet P, Williams JG, Fey P, Chisholm RL (2008) An anatomy ontology to represent biological knowledge in Dictyostelium discoideum. BMC Genomics 9:130

    Article  PubMed  Google Scholar 

  22. Fey P, Gaudet P, Curk T, Zupan B, Just EM, Basu S, Merchant SN, Bushmanova YA, Shaulsky G, Kibbe WA, Chisholm RL (2009) dictyBase–a Dictyostelium bioinformatics resource update. Nucleic Acids Res 37:D515–D519

    Article  PubMed  CAS  Google Scholar 

  23. Rot G, Parikh A, Curk T, Kuspa A, Shaulsky G, Zupan B (2009) dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface. BMC Bioinformatics 10:265

    Article  PubMed  Google Scholar 

  24. Gaudet P, Lane L, Fey P, Bridge A, Poux S, Auchincloss A, Axelsen K, Braconi Quintaje S, Boutet E, Brown P, Coudert E, Datta RS, de Lima WC, de Oliveira Lima T, Duvaud S, Farriol-Mathis N, Ferro RS, Feuermann M, Gateau A, Hinz U, Hulo C, James J, Jimenez S, Jungo F, Keller G, Lemercier P, Lieberherr D, Moinat M, Nikolskaya A, Pedruzzi I, Rivoire C, Roechert B, Schneider M, Stanley E, Tognolli M, Sjölander K, Bougueleret L, Chisholm RL, Bairoch A (2009) Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase. Database (Oxford) 2009:bap016

    Article  Google Scholar 

  25. Magrane M, Consortium U (2011) UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford) 2011:bar009

    Article  Google Scholar 

  26. Leinonen R, Akhtar R, Birney E, Bower L, Cerdeno-Tárraga A, Cheng Y, Cleland I, Faruque N, Goodgame N, Gibson R, Hoad G, Jang M, Pakseresht N, Plaister S, Radhakrishnan R, Reddy K, Sobhany S, Ten Hoopen P, Vaughan R, Zalunin V, Cochrane G (2011) The European Nucleotide Archive. Nucleic Acids Res 39:D28–D31

    Article  PubMed  CAS  Google Scholar 

  27. Parikh A, Miranda ER, Katoh-Kurasawa M, Fuller D, Rot G, Zagar L, Curk T, Sucgang R, Chen R, Zupan B, Loomis WF, Kuspa A, Shaulsky G (2010) Conserved developmental transcriptomes in evolutionarily divergent species. Genome Biol 11:R35

    Article  PubMed  Google Scholar 

  28. 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  PubMed  CAS  Google Scholar 

  29. Müller H-M, Kenny EE, Sternberg PW (2004) Textpresso: an ontology-based information retrieval and extraction system for biological literature. PLoS Biol 2:e309

    Article  PubMed  Google Scholar 

  30. Sawai S, Guan X-J, Kuspa A, Cox EC (2007) High-throughput analysis of spatio-temporal dynamics in Dictyostelium. Genome Biol 8:R144

    Article  PubMed  Google Scholar 

  31. Maeda M, Sakamoto H, Iranfar N, Fuller D, Maruo T, Ogihara S, Morio T, Urushihara H, Tanaka Y, Loomis WF (2003) Changing patterns of gene expression in Dictyostelium prestalk cell subtypes recognized by in situ hybridization with genes from microarray analyses. Eukaryot Cell 2:627–637

    Article  PubMed  CAS  Google Scholar 

  32. Maruo T, Sakamoto H, Iranfar N, Fuller D, Morio T, Urushihara H, Tanaka Y, Maeda M, Loomis WF (2004) Control of cell type proportioning in Dictyostelium discoideum by differentiation-inducing factor as determined by in situ hybridization. Eukaryot Cell 3:1241–1248

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

We thank Kerry Sheppard for her expert technical work at the Dicty Stock Center, Yulia Bushmanova for her contributions to the new gene page layout and the gene model curation tool, and Pascale Gaudet for her many years as a curator of dictyBase. dictyBase and the Dicty Stock Center are funded by National Institutes of Health GM64426, GM087371, and HG0022.s

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Authors and Affiliations

  1. dictyBase and the Dicty Stock Center, Center for Genetic Medicine, Northwestern University, Chicago, IL, USA

    Petra Fey, Robert J. Dodson, Siddhartha Basu & Rex L. Chisholm

Authors
  1. Petra Fey
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  2. Robert J. Dodson
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  3. Siddhartha Basu
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  4. Rex L. Chisholm
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Corresponding author

Correspondence to Petra Fey .

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Editors and Affiliations

  1. , Centre for Biochemistry, University of Cologne, Joseph-Stelzmann-Str. 52, Köln, 50931, Nordrhein-Westfalen, Germany

    Ludwig Eichinger

  2. , Centre for Biomedical Research, University of Hull, Hull, HU6 7RX, Montserrat

    Francisco Rivero

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Fey, P., Dodson, R.J., Basu, S., Chisholm, R.L. (2013). One Stop Shop for Everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012. In: Eichinger, L., Rivero, F. (eds) Dictyostelium discoideum Protocols. Methods in Molecular Biology, vol 983. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-302-2_4

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  • DOI: https://doi.org/10.1007/978-1-62703-302-2_4

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-301-5

  • Online ISBN: 978-1-62703-302-2

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