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Daphnia: the companion papers for the genome sequence

This thematic series of companion papers constituted the initial exploration of the genome biology of the waterflea (Daphnia), building on the first complete crustacean genome sequence. This series included contributions from members of the DaphniaGenomics Consortium. Daphnia is a versatile model system to investigate fundamental mechanisms of inheritance and development, cellular function, physiological systems, immunity response, disease, macromolecular structure/function relationships and the genetic basis of complex phenotypic traits. An extensive literature documenting physiological and ecological diversity make Daphnia an ideal model to study the genetic architecture of phenotypic variation in natural populations and the evolution of genome structure/function relationships in aquatic environments.

  1. Sequence analysis of the Daphnia pulex genome holds some surprises that could not have been anticipated from what was learned so far from other arthropod genomes. It establishes Daphnia as an eco-genetical model ...

    Authors: Diethard Tautz
    Citation: BMC Biology 2011 9:8
  2. Simple sequence repeats (SSRs) are highly variable features of all genomes. Their rapid evolution makes them useful for tracing the evolutionary history of populations and investigating patterns of selection a...

    Authors: Way Sung, Abraham Tucker, R Daniel Bergeron, Michael Lynch and W Kelley Thomas
    Citation: BMC Genomics 2010 11:691
  3. The Wnt genes encode secreted glycoprotein ligands that regulate a wide range of developmental processes, including axis elongation and segmentation. There are thirteen subfamilies of Wnt genes in metazoans and t...

    Authors: Ralf Janssen, Martine Le Gouar, Matthias Pechmann, Francis Poulin, Renata Bolognesi, Evelyn E Schwager, Corinna Hopfen, John K Colbourne, Graham E Budd, Susan J Brown, Nikola-Michael Prpic, Carolin Kosiol, Michel Vervoort, Wim GM Damen, Guillaume Balavoine and Alistair P McGregor
    Citation: BMC Evolutionary Biology 2010 10:374
  4. The insulin signaling pathway (ISP) has a key role in major physiological events like carbohydrate metabolism and growth regulation. The ISP has been well described in vertebrates and in a few invertebrate mod...

    Authors: Philippe Boucher, Delphine Ditlecadet, Caroline Dubé and France Dufresne
    Citation: BMC Evolutionary Biology 2010 10:305
  5. Daphnia magna is a well-established model species in ecotoxicology, ecology and evolution. Several new genomics tools are presently under development for this species; among them, a linkage map is a first require...

    Authors: Jarkko Routtu, Bastiaan Jansen, Isabelle Colson, Luc De Meester and Dieter Ebert
    Citation: BMC Genomics 2010 11:508
  6. Long terminal repeat (LTR) retroelements represent a successful group of transposable elements (TEs) that have played an important role in shaping the structure of many eukaryotic genomes. Here, we present a g...

    Authors: Mina Rho, Sarah Schaack, Xiang Gao, Sun Kim, Michael Lynch and Haixu Tang
    Citation: BMC Genomics 2010 11:425
  7. The planktonic microcrustacean Daphnia pulex is among the best-studied animals in ecological, toxicological and evolutionary research. One aspect that has sustained interest in the study system is the ability of

    Authors: Katina I Spanier, Florian Leese, Christoph Mayer, John K Colbourne, Don Gilbert, Michael E Pfrender and Ralph Tollrian
    Citation: BMC Molecular Biology 2010 11:50
  8. Duplication and divergence of genes and genetic networks is hypothesized to be a major driver of the evolution of complexity and novel features. Here, we examine the history of genes and genetic networks in th...

    Authors: Ajna S Rivera, M Sabrina Pankey, David C Plachetzki, Carlos Villacorta, Anna E Syme, Jeanne M Serb, Angela R Omilian and Todd H Oakley
    Citation: BMC Evolutionary Biology 2010 10:123
  9. Numerous cases of predator-induced polyphenisms, in which alternate phenotypes are produced in response to extrinsic stimuli, have been reported in aquatic taxa to date. The genus Daphnia (Branchiopoda, Cladocera...

    Authors: Hitoshi Miyakawa, Maki Imai, Naoki Sugimoto, Yuki Ishikawa, Asano Ishikawa, Hidehiko Ishigaki, Yasukazu Okada, Satoshi Miyazaki, Shigeyuki Koshikawa, Richard Cornette and Toru Miura
    Citation: BMC Developmental Biology 2010 10:45
  10. Two major biological stressors of freshwater zooplankton of the genus Daphnia are predation and fluctuations in food quality. Here we use kairomones released from a planktivorous fish (Leucaspius delineatus) and ...

    Authors: Anke Schwarzenberger, Cornelius Courts and Eric von Elert
    Citation: BMC Genomics 2009 10:527
  11. The nuclear receptor superfamily currently consists of seven gene subfamilies that encompass over 80 distinct receptor proteins. These transcription factors typically share a common five-domain structure with ...

    Authors: Susanne A Thomson, William S Baldwin, Ying H Wang, Gwijun Kwon and Gerald A LeBlanc
    Citation: BMC Genomics 2009 10:500
  12. Neurotrophins and their Trk and p75NTR receptors play an important role in the nervous system. To date, neurotrophins, Trk and p75NTR have only been found concomitantly in deuterostomes. In protostomes, homolo...

    Authors: Karen HS Wilson
    Citation: BMC Evolutionary Biology 2009 9:243
  13. Branchiopod crustaceans in the genus Daphnia are key model organisms for investigating interactions between genes and the environment. One major theme of research on Daphnia species has been the evolution of resi...

    Authors: Seanna J McTaggart, Claire Conlon, John K Colbourne, Mark L Blaxter and Tom J Little
    Citation: BMC Genomics 2009 10:175
  14. EST sequencing projects are increasing in scale and scope as the genome sequencing technologies migrate from core sequencing centers to individual research laboratories. Effectively, generating EST data is no ...

    Authors: Zuojian Tang, Jeong-Hyeon Choi, Chris Hemmerich, Ankita Sarangi, John K Colbourne and Qunfeng Dong
    Citation: BMC Genomics 2009 10:174
  15. Shotgun sequences of DNA extracts from whole organisms allow a comprehensive assessment of possible symbionts. The current project makes use of four shotgun datasets from three species of the planktonic freshw...

    Authors: Weihong Qi, Guang Nong, James F Preston, Frida Ben-Ami and Dieter Ebert
    Citation: BMC Genomics 2009 10:172
  16. Daphniids, commonly known as waterfleas, serve as important model systems for ecology, evolution and the environmental sciences. The sequencing and annotation of the Daphnia pulex genome both open future avenues ...

    Authors: Thomas Fröhlich, Georg J Arnold, Rainer Fritsch, Tobias Mayr and Christian Laforsch
    Citation: BMC Genomics 2009 10:171
  17. The large gene superfamily of ABC (ATP-binding cassette) transporters encodes membrane proteins involved in trafficking processes across biological membranes and further essential cell biological functions. AB...

    Authors: Armin Sturm, Phil Cunningham and Michael Dean
    Citation: BMC Genomics 2009 10:170
  18. Cytochrome P450s (CYPs) in animals fall into two categories: those that synthesize or metabolize endogenous molecules and those that interact with exogenous chemicals from the diet or the environment. The latt...

    Authors: William S Baldwin, Peter B Marko and David R Nelson
    Citation: BMC Genomics 2009 10:169
  19. Acidity exerts a determining influence on the composition and diversity of freshwater faunas. While the physiological implications of freshwater acidification have been intensively studied in teleost fish and ...

    Authors: Anna K Weber and Ralph Pirow
    Citation: BMC Physiology 2009 9:9
  20. Temperature affects essentially every aspect of the biology of poikilothermic animals including the energy and mass budgets, activity, growth, and reproduction. While thermal effects in ecologically important ...

    Authors: Susanne Schwerin, Bettina Zeis, Tobias Lamkemeyer, Rüdiger J Paul, Marita Koch, Johannes Madlung, Claudia Fladerer and Ralph Pirow
    Citation: BMC Physiology 2009 9:8
  21. Freshwater planktonic crustaceans of the genus Daphnia show a remarkable plasticity to cope with environmental changes in oxygen concentration and temperature. One of the key proteins of adaptive gene control in

    Authors: Bettina Zeis, Tobias Lamkemeyer, Rüdiger J Paul, Frank Nunes, Susanne Schwerin, Marita Koch, Wolfgang Schütz, Johannes Madlung, Claudia Fladerer and Ralph Pirow
    Citation: BMC Physiology 2009 9:7
  22. The L-lactate and D-lactate dehydrogenases, which are involved in the reduction of pyruvate to L(-)-lactate and D(+)-lactate, belong to evolutionarily unrelated enzyme families. The genes encoding L-LDH have b...

    Authors: Melania E Cristescu, David J Innes, Jonathon H Stillman and Teresa J Crease
    Citation: BMC Evolutionary Biology 2008 8:268
  23. Eicosanoids are biologically active, oxygenated metabolites of three C20 polyunsaturated fatty acids. They act as signalling molecules within the autocrine or paracrine system in both vertebrates and invertebr...

    Authors: Lars-Henrik Heckmann, Richard M Sibly, Martijn JTN Timmermans and Amanda Callaghan
    Citation: Frontiers in Zoology 2008 5:11
  24. In crustaceans and insects, development and reproduction are controlled by the steroid hormone, 20-hydroxyecdysone (20E). Like other steroids, 20E, is synthesized from cholesterol through reactions involving c...

    Authors: Kim F Rewitz and Lawrence I Gilbert
    Citation: BMC Evolutionary Biology 2008 8:60
  25. Ibuprofen and other nonsteroidal anti-inflammatory drugs have been designed to interrupt eicosanoid metabolism in mammals, but little is known of how they affect nontarget organisms. Here we report a systems b...

    Authors: Lars-Henrik Heckmann, Richard M Sibly, Richard Connon, Helen L Hooper, Thomas H Hutchinson, Steve J Maund, Christopher J Hill, Anthony Bouetard and Amanda Callaghan
    Citation: Genome Biology 2008 9:R40
  26. Genomic research tools such as microarrays are proving to be important resources to study the complex regulation of genes that respond to environmental perturbations. A first generation cDNA microarray was dev...

    Authors: Joseph R Shaw, John K Colbourne, Jennifer C Davey, Stephen P Glaholt, Thomas H Hampton, Celia Y Chen, Carol L Folt and Joshua W Hamilton
    Citation: BMC Genomics 2007 8:477
  27. Sexual reproduction is a core biological function that is conserved throughout eukaryotic evolution, yet breeding systems are extremely variable. Genome-wide comparative studies can be effectively used to iden...

    Authors: Brian D Eads, John K Colbourne, Elizabeth Bohuski and Justen Andrews
    Citation: BMC Genomics 2007 8:464
  28. Functional and comparative studies of insect genomes have shed light on the complement of genes, which in part, account for shared morphologies, developmental programs and life-histories. Contrasting the gene ...

    Authors: John K Colbourne, Brian D Eads, Joseph Shaw, Elizabeth Bohuski, Darren J Bauer and Justen Andrews
    Citation: BMC Genomics 2007 8:217
  29. A report on the symposium 'Genomic and Proteomic Approaches to Crustacean Biology' held as part of the Society for Integrative and Comparative Biology 2006 Annual Meeting, Orlando, USA, 4-8 January 2006.

    Authors: Timothy S McClintock and Charles D Derby
    Citation: Genome Biology 2006 7:312
  30. wFleaBase is a database with the necessary infrastructure to curate, archive and share genetic, molecular and functional genomic data and protocols for an emerging model organism, the microcrustacean Daphnia. Com...

    Authors: John K Colbourne, Vasanth R Singan and Don G Gilbert
    Citation: BMC Bioinformatics 2005 6:45