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Daphnia: the companion papers for the genome sequence

This thematic series of companion papers constitutes the initial exploration of the genome biology of the waterflea (Daphnia) building on the first complete crustacean genome sequence. This series includes 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. Commentary

    Not just another genome

    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 ...

    Diethard Tautz

    BMC Biology 2011 9:8

    Published on: 4 February 2011

  2. Research article

    Simple sequence repeat variation in the Daphnia pulex genome

    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...

    Way Sung, Abraham Tucker, R Daniel Bergeron, Michael Lynch and W Kelley Thomas

    BMC Genomics 2010 11:691

    Published on: 3 December 2010

  3. Research article

    Conservation, loss, and redeployment of Wnt ligands in protostomes: implications for understanding the evolution of segment formation

    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...

    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

    BMC Evolutionary Biology 2010 10:374

    Published on: 1 December 2010

  4. Research article

    Unusual duplication of the insulin-like receptor in the crustacean Daphnia pulex

    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...

    Philippe Boucher, Delphine Ditlecadet, Caroline Dubé and France Dufresne

    BMC Evolutionary Biology 2010 10:305

    Published on: 12 October 2010

  5. Research article

    The first-generation Daphnia magna linkage map

    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...

    Jarkko Routtu, Bastiaan Jansen, Isabelle Colson, Luc De Meester and Dieter Ebert

    BMC Genomics 2010 11:508

    Published on: 22 September 2010

  6. Research article

    LTR retroelements in the genome of Daphnia pulex

    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...

    Mina Rho, Sarah Schaack, Xiang Gao, Sun Kim, Michael Lynch and Haixu Tang

    BMC Genomics 2010 11:425

    Published on: 9 July 2010

  7. Research article

    Predator-induced defences in Daphnia pulex: Selection and evaluation of internal reference genes for gene expression studies with real-time PCR

    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

    Katina I Spanier, Florian Leese, Christoph Mayer, John K Colbourne, Don Gilbert, Michael E Pfrender and Ralph Tollrian

    BMC Molecular Biology 2010 11:50

    Published on: 29 June 2010

  8. Research article

    Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach

    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...

    Ajna S Rivera, M Sabrina Pankey, David C Plachetzki, Carlos Villacorta, Anna E Syme, Jeanne M Serb, Angela R Omilian and Todd H Oakley

    BMC Evolutionary Biology 2010 10:123

    Published on: 30 April 2010

  9. Research article

    Gene up-regulation in response to predator kairomones in the water flea, Daphnia pulex

    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...

    Hitoshi Miyakawa, Maki Imai, Naoki Sugimoto, Yuki Ishikawa, Asano Ishikawa, Hidehiko Ishigaki, Yasukazu Okada, Satoshi Miyazaki, Shigeyuki Koshikawa, Richard Cornette and Toru Miura

    BMC Developmental Biology 2010 10:45

    Published on: 30 April 2010

  10. Research article

    Target gene approaches: Gene expression in Daphnia magna exposed to predator-borne kairomones or to microcystin-producing and microcystin-free Microcystis aeruginosa

    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 ...

    Anke Schwarzenberger, Cornelius Courts and Eric von Elert

    BMC Genomics 2009 10:527

    Published on: 16 November 2009

  11. Research article

    The genome sequence of the protostome Daphnia pulexencodes respective orthologues of a neurotrophin, a Trk and a p75NTR: Evolution of neurotrophin signaling components and related proteins in the bilateria

    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...

    Karen HS Wilson

    BMC Evolutionary Biology 2009 9:243

    Published on: 6 October 2009

  12. Research article

    Physiological responses of Daphnia pulex to acid stress

    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 ...

    Anna K Weber and Ralph Pirow

    BMC Physiology 2009 9:9

    Published on: 21 April 2009

  13. Research article

    Acclimatory responses of the Daphnia pulex proteome to environmental changes. I. Chronic exposure to hypoxia affects the oxygen transport system and carbohydrate metabolism

    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

    Bettina Zeis, Tobias Lamkemeyer, Rüdiger J Paul, Frank Nunes, Susanne Schwerin, Marita Koch, Wolfgang Schütz, Johannes Madlung, Claudia Fladerer and Ralph Pirow

    BMC Physiology 2009 9:7

    Published on: 21 April 2009

  14. Research article

    The cytochrome P450 (CYP) gene superfamily in Daphnia pulex

    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...

    William S Baldwin, Peter B Marko and David R Nelson

    BMC Genomics 2009 10:169

    Published on: 21 April 2009

  15. Research article

    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

    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 ...

    Thomas Fröhlich, Georg J Arnold, Rainer Fritsch, Tobias Mayr and Christian Laforsch

    BMC Genomics 2009 10:171

    Published on: 21 April 2009

  16. Research article

    Acclimatory responses of the Daphnia pulex proteome to environmental changes. II. Chronic exposure to different temperatures (10 and 20°C) mainly affects protein metabolism

    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 ...

    Susanne Schwerin, Bettina Zeis, Tobias Lamkemeyer, Rüdiger J Paul, Marita Koch, Johannes Madlung, Claudia Fladerer and Ralph Pirow

    BMC Physiology 2009 9:8

    Published on: 21 April 2009

  17. Research article

    Comparative metagenomics of Daphnia symbionts

    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...

    Weihong Qi, Guang Nong, James F Preston, Frida Ben-Ami and Dieter Ebert

    BMC Genomics 2009 10:172

    Published on: 21 April 2009

  18. Research article

    The ABC transporter gene family of Daphnia pulex

    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...

    Armin Sturm, Phil Cunningham and Michael Dean

    BMC Genomics 2009 10:170

    Published on: 21 April 2009

  19. Research article

    The chemoreceptor genes of the waterflea Daphnia pulex: many Grs but no Ors

    Chemoreception is vitally important for all animals, yet little is known about the genetics of chemoreception in aquatic organisms. The keystone species Daphnia pulex, a well known crustacean, is the first aquati...

    D Carolina Peñalva-Arana, Michael Lynch and Hugh M Robertson

    BMC Evolutionary Biology 2009 9:79

    Published on: 21 April 2009

  20. Software

    ESTPiper – a web-based analysis pipeline for expressed sequence tags

    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 ...

    Zuojian Tang, Jeong-Hyeon Choi, Chris Hemmerich, Ankita Sarangi, John K Colbourne and Qunfeng Dong

    BMC Genomics 2009 10:174

    Published on: 21 April 2009

  21. Research article

    D- and L-lactate dehydrogenases during invertebrate evolution

    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...

    Melania E Cristescu, David J Innes, Jonathon H Stillman and Teresa J Crease

    BMC Evolutionary Biology 2008 8:268

    Published on: 1 October 2008

  22. Research

    Outlining eicosanoid biosynthesis in the crustacean Daphnia

    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...

    Lars-Henrik Heckmann, Richard M Sibly, Martijn JTN Timmermans and Amanda Callaghan

    Frontiers in Zoology 2008 5:11

    Published on: 14 July 2008

  23. Research

    Systems biology meets stress ecology: linking molecular and organismal stress responses in Daphnia magna

    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...

    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

    Genome Biology 2008 9:R40

    Published on: 21 February 2008

  24. Research article

    Gene response profiles for Daphnia pulex exposed to the environmental stressor cadmium reveals novel crustacean metallothioneins

    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...

    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

    BMC Genomics 2007 8:477

    Published on: 21 December 2007

  25. Research article

    Sampling Daphnia's expressed genes: preservation, expansion and invention of crustacean genes with reference to insect genomes

    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 ...

    John K Colbourne, Brian D Eads, Joseph Shaw, Elizabeth Bohuski, Darren J Bauer and Justen Andrews

    BMC Genomics 2007 8:217

    Published on: 6 July 2007

  26. Meeting report

    Shelling out for genomics

    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.

    Timothy S McClintock and Charles D Derby

    Genome Biology 2006 7:312

    Published on: 20 April 2006

  27. Database

    wFleaBase: the Daphnia genome database

    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...

    John K Colbourne, Vasanth R Singan and Don G Gilbert

    BMC Bioinformatics 2005 6:45

    Published on: 7 March 2005