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Fifty + published Daphnia Genome Project manuscripts

Foundation Paper:

Colbourne, J.K., M.E. Pfrender, D. Gilbert, W.K. Thomas, A. Tucker, T.H. Oakley, S. Tokishita, A. Aerts, G.J. Arnold, M. Kumar Basu, D.J. Bauer, C.E. Cáceres, L. Carmel, C. Casola, J.-H. Choi, C. Detter, Q. Dong, S. Dusheyko, B.D. Eads, T. Fröhlich, K.A. Geiler-Samerotte, D. Gerlach, P. Hatcher, S. Jogdeo, J. Krijgsveld, E.V. Kriventseva, D. Kültz, C. Laforsch, E. Lindquist, J. Lopez, J.R. Manak, J. Muller, J. Pangilinan, R.P. Patwardhan, S. Pitluck, E.J. Pritham, A. Rechtsteiner, M. Rho, I.B. Rogozin, O. Sakarya, A. Salamov, S. Schaack, H. Shapiro, Y. Shiga, C. Skalitzky, Z. Smith, A. Souvorov, W. Sung, Z. Tang, D. Tsuchiya, H. Tu, H. Vos, M. Wang, Y.I. Wolf, H. Yamagata, T. Yamada, Y. Ye, J.R. Shaw, J. Andrews, T.J. Crease, H. Tang, S.M. Lucas, H.M. Robertson, P. Bork, E.V. Koonin, E.M. Zdobnov, I. Grigoriev, M. Lynch and J.L. Boore. 2010. The ecoresponsive genome of Daphnia pulex. Science 331: 555-561.

CONTRIBUTIONS

Acknowledgements - We thank Marvin Frazer, then head of U.S. DOE Life Sciences, for the inspiration and commitment to pursue the sequencing of this first crustacean genome. We thank Peter Cherbas, who directs the Center for Genomics and Bioinformatics (CGB), for his support and leadership in creating this new genomic model system. We thank Gregory Werner and his group at JGI for support of gene annotation tools. We also thank Roland Green, Tsetska Takova and their groups at Roche NimbleGen Inc. for providing early access and technical expertise to custom microarray technologies enabling the functional annotation of the genome sequence. The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231, and in collaboration with the Daphnia Genomics Consortium (DGC). This project was also supported by the NSF Biocompolexity grant 0221837 to Joshua Hamilton (and Celia Chen, Carol Folt, Joseph Shaw, Michael Lynch and John Colbourne), and FIBR grant 0328516 to Michael Lynch (and John Colbourne, Justen Andrews, Curtis Lively, Elizabeth Housworth, Miriam Zolan, Jeffrey Boore, Carla Cáceres, Thomas Little and W. Kelley Thomas). NIH support IR24GM07827401A1 was granted to Michael Pfrender (and John Colbourne, Donald Gilbert, Dieter Ebert and W. Kelley Thomas). Euro Cores/EuroEEFG grant support (through DFG) grant LA 2159/6-1 was provided to Christian Laforsch, Georg Arnold and Thomas Frohlich, in partnership with Luc De Meester (PI; and Luisa Orsini, Ellen Decaestecker, Colin Janssen, Karel De Schamphelaere, Dieter Ebert, Cristoph Haag, Adam Petrusek, Mikko Frilander, John Colbourne, Andrew Beckerman, Thomas Little). Malay Kumar Basu, Liran Carmel, Eugene Koonin, Igor Rogozin, and Yuri Wolf were supported by Intramural funds of the US Department of Health and Human Services (NIH, National Library of Medicine). Todd Oakley was supported by NSF grant DEB 1027279. Dietmar Kültz was supported by NSF grant IOS0542755 and NIH grant P42ES004699. Thanks to Keithanne Mockaitis and the CGB sequencing team (Jade Carter, James Ford, Zach Smith) for access to an early draft assembly of the Daphnia magna genome sequence. Sequencing infrastructure at the CGB was provided by a major grant from the the Lilly Endowment, Inc. Thanks to Matthew Hahn (Indiana University) for providing critical suggestions. The following people contributed DNA and RNA samples for this research: Jim Haney (University of New Hampshire), Rebecca Klaper (University of Wisconsin-Milwaukee), Thomas Little (University of Edinburgh), Norman Yan (York University), Jarkko Routtu and Dieter Ebert (University of Basel). Analyses, data curation and data distribution are primarily attributed to wFleaBase, developed at the Genome Informatics Lab of Indiana University with support to Don Gilbert from the National Science Foundation and the National Institutes of Health. Specialized shared databases were also created by Mark Blaxter (University of Edinburgh) and Hajime Watanabe (Okazaki National Research Institutes). Coordination infrastructure for the DGC is provided by The Center for Genomics and Bioinformatics at Indiana University, which is supported in part by the METACyt Initiative of Indiana University, funded in part through a major grant from the Lilly Endowment, Inc. Computer support was provided by an allocation TG-MCB060059N through the TeraGrid Advanced Support, by the University Information Technology Services (UITS) and by The Center for Genomics and Bioinformatics computing group. We thank the computing group leaders Phillip Steinbachs (CGB), Craig Stewart and Richard Repasky (UITS). Ann Miracle advised on the successful timing for the initial submission of the White Paper proposal to the JGI. Our work benefits from, and contributes to the Daphnia Genomics Consortium. http://daphnia.cgb.indiana.edu

Associated Papers:

  1. Baldwin, W.S., P.B. Marko and D.R. Nelson. 2009. The cytochrome P450 (CYP) gene superfamily in Daphnia pulex. BMC Genomics 2009, 10:169 (21 April 2009).
  2. Bauer, D.J. 2007. The Daphnia Genomics Consortium Meeting: the genome biology of the model crustacean Daphnia. Expert Rev Proteomics 4:601-2.
  3. Boucher, P., D. Ditlecadet, C. Dubé, F. Dufresne. 2010. Unusual duplication of the insulin-like receptor in the crustacean Daphnia pulex. BMC Evolutionary Biology 2010, 10:305 (12 October 2010).
  4. Colbourne, J.K., V.R. Singan and D.G. Gilbert. 2005. wFleaBase: the Daphnia genome database. BMC Bioinformatics 2005, 6:45 (7 March 2005)
  5. Colbourne, J.K., B.D. Eads, J. Shaw, E. Bohuski, D.J. Bauer and J. Andrews. 2007. Sampling Daphnia's expressed genes: preservation, expansion and invention of crustacean genes with reference to insect genomes. BMC Genomics 2007, 8:217 (6 July 2007).
  6. Colson, I., L. Du Pasquier and D. Ebert. 2009. Intragenic tandem repeats in Daphnia magna: structure, function and distribution. BMC Research Notes 2009, 2:206 (6 October 2009).
  7. Cristescu, M.E.A., J.K. Colbourne, J. Radivojac and M. Lynch. 2006. A microsatellite-based genetic linkage map of the waterflea, Daphnia pulex: On the prospect of crustacean genomics. Genomics 88:415-430.
  8. Cristescu, M.E., D.J. Innes, J.H. Stillman and T.J. Crease. 2008. D- and L-lactate dehydrogenases during invertebrate evolution. BMC Evolutionary Biology 2008, 8:268 (1 October 2008)
  9. Denslow, N.D., J.K. Colbourne, D. Dix, J. Freedman, C. Helbing, S. Kennedy and P. Williams. Selection of surrogate animal species for comparative toxicogenomics. 2007. In: Genomic Approaches for Cross-Species Extrapolation in Toxicology. eds. W.H. Benson and R.T. Di Giulio. CRC Press. pp. 33-75 (invited paper).
  10. Eads, B.D., J. Andrews and J.K. Colbourne. 2007. Ecological genomics in Daphnia: stress responses and environmental sex determination. Heredity (23 May 2007) (invited paper).
  11. Eads, B.D., J.K. Colbourne, E. Bohuski and J. Andrews. 2007. Profiling sex-biased gene expression during parthenogenetic reproduction in Daphnia pulex. BMC Genomics 2007, 8:464 (18 December 2007).
  12. Fröhlich, T., G.J. Arnold, R. Fritsch, T. Mayr and C. Laforsch. 2009. LC-MS/MS-based proteome profiling in Daphnia pulex and Daphnia longicephala: the Daphnia pulex genome database as a key for high throughput proteomics in Daphnia. BMC Genomics 2009, 10:171 (21 April 2009).
  13. Gard, A.L., P.H. Lenz, J.R. Shaw, A.E. Christie. 2009. Identification of putative peptide paracrines/hormones in the water flea Daphnia pulex (Crustacea; Branchiopoda; Cladocera) using transcriptomics and immunohistochemistry. General and Comparative Endocrinology 160:271-287.
  14. Heckmann, L.-H., R.M. Sibly, R. Connon, H.L. Hooper, T.H. Hutchinson, S.J. Maund, C.J. Hill, A. Bouetard and A. Callaghan. 2008. Systems biology meets stress ecology: linking molecular and organismal stress responses in Daphnia magna. Genome Biology 2008, 9:R40 (21 February 2008).
  15. Heckmann, L.-H., R.M. Sibly, M.J.T.N. Timmermans and A. Callaghan. 2008. Outlining eicosanoid biosynthesis in the crustacean Daphnia. Frontiers in Zoology 2008, 5:11 (14 July 2008).
  16. Janssen, R., M. Le Gouar, M. Pechmann, F. Poulin, R. Bolognesi, E.E. Schwager, C. Hopfen, J.K. Colbourne, G.E. Budd, S.J. Brown, N.-M. Prpic, C. Kosiol, M. Vervoort, W.G.M. Damen, G. Balavoine and A.P. McGregor. 2010. Conservation, loss, and redeployment of Wnt ligands in protostomes: implications for understanding the evolution of segment formation. BMC Evolutionary Biology 2010, 10:374 (1 December 2010).
  17. Jeyasingh, P.D., A. Ragavendran, S. Paland, J.A. Lopez, R.W. Sterner and J.K. Colbourne. 2010. How do consumers deal with stoichiometric constraints? Lessons from functional genomics using Daphnia pulex. Molecular Ecology, In Press.
  18. Kato, Y., K. Kobayashi, H. Watanabe, T. Iguchi. 2010. Introduction of foreign DNA into the water flea, Daphnia magna, by electroporation. Ecotoxicology 19:589-592.
  19. Li, W., A.E. Tucker, W. Sung, W.K. Thomas and M. Lynch. 2009. Extensive, recent intron gains in Daphnia populations. Science 326(5957): 1260-1262.
  20. Lopez, J.A. and J.K. Colbourne. 2010. Dual-Labeled Expression Microarray Protocol for High-Throughput Genomic Investigations: Laboratory handbook for Environmental Genomics courses at Mount Desert Island Biological Laboratory and at Indiana University. CGB Technical Report 2010-01. doi:10.2506/cgbtr-201001.
  21. Lopez, J.A. and J.K. Colbourne. 2010. Dual-Labeled Expression-Tiling Microarray Protocol for Empirical Annotation of Genome Sequences. CGB Technical Report 2010-02. doi:10.2506/cgbtr-201002.
  22. Lynch, M., A. Seyfert, B. Eads, E. Williams. 2008. Localization of the genetic determinants of meiosis suppression in Daphnia pulex. Genetics 180:317-327.
  23. Mayer, C., F. Leese and R. Tollrian. 2010. Genome-wide analysis of tandem repeats in Daphnia pulex - a comparative approach. BMC Genomics 2010, 11:277 (30 April 2010).
  24. McClintock, T.S. and C.D. Derby. 2006. Shelling out for genomics. Genome Biology 2006, 7:312 (20 April 2006).
  25. McTaggart, S.J., C. Conlon, J.K. Colbourne, M.L. Blaxter and T.J. Little. 2009. The components of the Daphnia pulex immune system as revealed by complete genome sequencing. BMC Genomics 2009, 10:175 (22 April 2009).
  26. Miyakawa, H., M. Imai, N. Sugimoto, Y. Ishikawa, A. Ishikawa, H. Ishigaki, Y. Okada, S. Miyazaki, S. Koshikawa, R. Cornette and T. Miura. 2010. Gene up-regulation in response to predator kairomones in the water flea, Daphnia pulex. BMC Developmental Biology 2010, 10:45 (30 April 2010).
  27. Odronitz, F., S. Becker and M. Kollmar. 2009. Reconstructing the phylogeny of 21 completely sequenced arthropod species based on their motor proteins. BMC Genomics 2009, 10:173 (21 April 2009).
  28. Omilian, A.R., M. Lynch. 2009. Patterns of intraspecific DNA variation in the Daphnia nuclear genome. Genetics 182:325-336.
  29. Orsini, L., E. Decaestecker, L. De Meester, M.E. Pfrender and J.K. Colbourne. 2010. Genomics in the ecological arena. Biology Letters doi: 10.1098/rsbl.2010.0629.
  30. Peñalva-Arana, D.C., M. Lynch and H.M. Robertson. 2009. The chemoreceptor genes of the waterflea Daphnia pulex: many Grs but no Ors. BMC Evolutionary Biology 2009, 9:79 (21 April 2009).
  31. Qi, W., G. Nong, J.F. Preston, F. Ben-Ami and D. Ebert. 2009. Comparative metagenomics of Daphnia symbionts. BMC Genomics 2009, 10:172 (21 April 2009).
  32. Rewitz, K.F. and L.I. Gilbert. 2008. Daphnia Halloween genes that encode cytochrome P450s mediating the synthesis of the arthropod molting hormone: Evolutionary implications. BMC Evolutionary Biology 2008, 8:60 (25 February 2008).
  33. Rho, M.N., H.X. Tang. 2009. MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes. Nucleic Acids Research 37: Art. No. e143 NOV 2009.
  34. Rho, M., S. Schaack, X. Gao, S. Kim, M. Lynch and H. Tang. 2010. LTR retroelements in the genome of Daphnia pulex. BMC Genomics 2010, 11:425 (9 July 2010).
  35. Rivera, A.S., M.S. Pankey, D.C. Plachetzki, C. Villacorta, A.E. Syme, J.M. Serb, A.R. Omilian and T.H. Oakley. 2010. Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach. BMC Evolutionary Biology 2010, 10:123 (30 April 2010).
  36. Routtu, J., B. Jansen, I. Colson, L. De Meester and D. Ebert. 2010. The first-generation Daphnia magna linkage map. BMC Genomics 2010, 11:508 (22 September 2010).
  37. Schaack, S., E. Choi, M. Lynch and E.J. Pritham. 2010. DNA transposons and the role of recombination in mutation accumulation in Daphnia pulex. Genome Biology 2010, 11:R46 (30 April 2010).
  38. Schaack, S., E.J. Pritham, A. Wolf, M. Lynch. 2010. DNA transposon dynamics in populations of Daphnia pulex with and without sex. Proceedings of the Royal Society B-BIOLOGICAL SCIENCES 277:2381-2387.
  39. Schaack, S. 2008. Daphnia comes of age: an ecological model in the genomic era. Molecular Ecology 17:1634-1635.
  40. Schwerin, S., B. Zeis, T. Lamkemeyer, R.J. Paul, M. Koch, J. Madlung, C. Fladerer and R. Pirow. 2009. Acclimatory responses of the Daphnia pulex proteome to environmental changes. II. Chronic exposure to different temperatures (10 and 20°C) mainly affects protein metabolism. BMC Physiology 2009, 9:8 (21 April 2009).
  41. Schurko, A.M., J.M. Logsdon Jr. and B.D. Eads. 2009. Meiosis genes in Daphnia pulex and the role of parthenogenesis in genome evolution. BMC Evolutionary Biology 2009, 9:78 (21 April 2009).
  42. Schwarzenberger, A., C. Courts and E. von Elert. 2009. Target gene approaches: Gene expression in Daphnia magna exposed to predator-borne kairomones or to microcystin-producing and microcystin-free Microcystis aeruginosa. BMC Genomics 2009, 10:527 (16 November 2009).
  43. Scoville, A. G. and M. E. Pfrender. 2010. Phenotypic plasticity facilitates rapid parallel adaptation to an introduced predator. PNAS 107:4260-4263 (02 March 2010)
  44. Seetharam, A., Y. Bai and G.W. Stuart. 2010. A survey of well conserved families of C2H2 zinc-finger genes in Daphnia. BMC Genomics 2010, 11:276 (30 April 2010).
  45. Simon, J.-C., D. Tagu, M. Pfrender, R. Tollrian and J.K. Colbourne. 2010. Genomics of environmentally-induced phenotypes in two extremely plastic arthropods. J. Heredity. In Press (invited paper).
  46. Spanier, K., F. Leese, C. Mayer, J.K. Colbourne, D. Gilbert, M.E. Pfrender and R. Tollrian. 2010. Predator-induced defences in Daphnia pulex: Selection and evaluation of internal reference genes for gene expression studies with real-time PCR. BMC Molecular Biology 2010, 11:50 (29 June 2010).
  47. Shaw, J.R., M.E. Pfrender, B.D. Eads, R. Klaper, A. Callaghan, I. Colson, B. Jansen, D. Gilbert and J.K. Colbourne. 2007. Daphnia as an emerging model for toxicological genomics. In: Advances in experimental biology on toxicogenomics. eds. C. Hogstrand and P. Kille. Elsevier Press. Volume 2:165-219 (invited paper).
  48. Shaw, J.R., J.K. Colbourne, J.C. Davey, S.P. Glaholt, T.H. Hampton, C.Y. Chen, C.L. Folt and J.W. Hamilton. 2007. Gene response profiles for Daphnia pulex exposed to the environmental stressor cadmium reveals novel crustacean metallothioneins. BMC Genomics 2007, 8:477 (21 December 2007).
  49. Stillman, J.H., J.K. Colbourne, C.E. Lee, N.H. Patel, M.R. Phillips, D.W. Towle, R.P. Henry, E.A. Johnson, M.E. Pfrender and N.B. Terwilliger. 2008. Recent Advances in Crustacean Genomics. Integrative and Comparative Biology 48:852-868.
  50. Sturm, A., P. Cunningham and M. Dean. 2009. The ABC transporter gene family of Daphnia pulex. BMC Genomics 2009, 10:170 (21 April 2009).
  51. Sung, W., A. Tucker, R.D. Bergeron, M. Lynch and W.K. Thomas. 2010. Simple sequence repeat variation in the Daphnia pulex genome. BMC Genomics 2010, 11:691 (3 December 2010).
  52. Tang, Z., J.-H. Choi, C. Hemmerich, A. Sarangi, J.K. Colbourne and Q. Dong. 2009. ESTPiper - a web-based analysis pipeline for expressed sequence tags. BMC Genomics 2009, 10:174 (21 April 2009).
  53. Thomson, S.A., W.S. Baldwin, Y.H. Wang, G. Kwon and G.A. LeBlanc. 2009. Annotation, phylogenetics, and expression of the nuclear receptors in Daphnia pulex. BMC Genomics 2009, 10:500 (28 October 2009).
  54. Tollrian, R. and F. Leese. 2010. Ecological genomics: steps towards unraveling the genetic basis of inducible defenses in Daphnia. BMC Biology 2010, 8:51 (7 May 2010).
  55. Weber, A.K. and R. Pirow. 2009. Physiological responses of Daphnia pulex to acid stress. BMC Physiology 2009, 9:9 (21 April 2009).
  56. Wilson, K.H.S. 2009. The genome sequence of the protostome Daphnia pulex encodes respective orthologues of a neurotrophin, a Trk and a p75NTR: Evolution of neurotrophin signaling components and related proteins in the bilateria. BMC Evolutionary Biology 2009, 9:243 (6 October 2009).
  57. Yasuhiko, K., K. Kobayashi, S. Oda, J.K. Colbourne, N. Tatarazako, H. Watanabe and T. Iguchi. 2007. Molecular cloning and sexually dimorphic expression of DM-domain genes in Daphnia magna. Genomics 91:94-101.
  58. Zeis, B., T. Lamkemeyer, R.J. Paul, F. Nunes, S. Schwerin, M. Koch, W. Schütz, J. Madlung, C. Fladerer and R. Pirow. 2009. Acclimatory responses of the Daphnia pulex proteome to environmental changes. I. Chronic exposure to hypoxia affects the oxygen transport system and carbohydrate metabolism. BMC Physiology 2009, 9:7 (21 April 2009).

Associated Book:

Daphnia: Development of a Model Organism in Ecology and Evolution

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