Daphnia Genomics
26-30 March 2010
Leuven, Belgium

Organisers:

Draft Report

Summary

The Daphnia Genomics Consortium (DGC) is an international network of scientists with expertise in several fields of ecological genomics and evolutionary ecology. The goal of the DGC is to make the freshwater crustacean Daphnia a genomic model system in ecology, evolution and environmental sciences.

The Daphnia Genomics Consortium meeting 2010 gathered together researchers already belonging to the consortium as well as welcomed new researchers in the field of ecological genomics. This encounter resulted in a fruitful circulation of information among the consortium partners and boosted new collaborations with researchers working with Daphnia and other model organism.

The DGC 2010 was the first consortium meeting hosted by a European University. The conference was initiated by the Katholieke Universiteit in Leuven, co-organised by the Universities of Antwerpen and Gent, and co-funded by the European science Foundation (ESF) and the research Foundation Flanders (FWO).

A total of 116 participants from several European countries, the USA and Japan attended the five-day event that included a series of plenary sessions, followed by oral and poster presentations in several fields of ecological genomics. Time for plenary discussions as well as meetings among smaller groups of researchers took place throughout the meeting. Young investigators were given many opportunities for discussing their research by promoting a friendly atmosphere in which discussion flourished.

The evaluations and subsequent correspondence suggest that the Daphnia Genomics Consortium Meeting was an complete success. Participants found the scientific content of the conference sound and stimulating, and the atmosphere encouraging new collaborations and constructive discussion.

Scientific Content including assessment of the results & impact of the event on the future direction of the field

The Daphnia Genomics Consortium (DGC) meeting 2010 was held in Leuven, a medieval university town near Brussels, in the heart of Europe. The DGC represents a collaborative effort of several Universities spread across Europe and the USA to advance in the field of ecological genomics in Daphnia. Daphnia (Crustacea: Cladocera) is a recognised model organism in ecology, evolutionary biology and ecotoxicology, and has been intensively studied with respect to phenotypic plasticity towards a wide variety of stressors, including predators, parasites, and extreme or novel abiotic conditions (1-3). This is in part due to their ease of culture, convenient size, short generation time and cyclic parthenogenetic reproduction, which make them very suitable for laboratory and field experiments, experimental evolution, and quantitative genetic analyses in multiple environments. The DGC is attempting and largely succeeding in making Daphnia also a key model system in genomics. In this respect, the extensive knowledge on the ecology and physiology of the species represent a key asset for the fast development of the ecological genomics of this model organism.

The first edition of the DGC meeting was organised in 2002 by John Colbourne at Indiana University. During the first meeting, it was decided to initially focus most of the consortium efforts on the D. pulex complex. In a very short time we have seen the research on D. pulex flourishing in the field of ecological genomics, toxicogenomics and transcriptomics. Since 2002 the consortium has been joined by a number of outstanding researchers in the fields of genomics, ecology, toxicology and evolutionary biology. Finally, thanks to the sustained efforts of the DGC, Daphnia is also rapidly developing as invertebrate model organism in ecological genomics (3); http://www.nih.gov/science/models/daphnia/). The completed draft genome sequence assembly of D. pulex is publicly available since early 2007, with helpful bioinformatic resources (JGI Genome Portal; wFleaBase; (1, 2). Moreover, there is a steady stream of reports on the Daphnia research community’s discoveries from the consortium-wide manual annotation project (e.g. see http://www.biomedcentral.com/series/Daphnia). Complementary to this amazing development, we have advanced steadily in the research of D. magna, the European counterpart of D. pulex. D. magna respondsadaptivelytopollutants, climate change, and antagonistic interactions with predators and parasites (4-7). Building on this evidence, DGC researchers recently invested in the sequencing of the complete genome of D. magna, producing a wealth of data that pushed Daphnia in the ecogenomic world (https://projects.cgb.indiana.edu/display/grp/D.+magna+Genome).

The DGC 2010 was the ideal venue to present the state of art in the research of Daphnia. The first draft of the 22x coverage of the D. magna genome was presented for the first time. Based on this the complete genome annotation will be soon released. Meanwhile an increasing number of candidate genes underpinning responses to specific stressors are being identified, and recently, a number of Daphnia proteomics and microarray studies have been carried out. The DGC meeting was the hotspot for the presentation of such advances in the functional genomics of D. magna and D. pulex. Nearly 80 scientific presentations reported of achieved results in several fields of ecology, evolutionary biology and genomics, build on the availability of genomics and bioinformatics resources. Advanced research in several fields of ecological genomics made this meeting a concrete leap forward as compared to past meetings which mainly focused on the development of genomic tools. It goes without saying that without the previous meetings the actual state of art of the Daphnia genomics research would have strongly suffered.

Taking advantage of extensive knowledge in the genomics of Daphnia, the DGC is also gearing up to develop strong genomics resources for other species of the group, including D. galeata, member of the subgenus Hyalodaphnia.

The first day's symposium on Ecological and Evolutionary Genomics saw several model organisms including Daphnia as main actors. The goal of this symposium was to compare several ecological genomics model organisms in an attempt to identify common ground for future research in this field in Europe. Luc De Meester (K.U.Leuven) and John Colbourne (U. Indiana) introduced the model system Daphnia, stressing the clear advantages of this species as an ecogenomic model organism as compared to other traditional invertebrate genetic model systems, such as Caenorhabditis elegans and Drosophila melanogaster. From an ecological and environmental point of view, Daphnia plays a pivotal role in the ecology of standing waters, are widely used in population studies and environmental risk assessments, and are supported by a large community of ecologists, evolutionary biologists and ecotoxicologists. A key asset of Daphnia is that quantifying trait variation and its link to fitness is relatively straightforward, as one can monitor changes in life history traits (8) and assess fitness in replicated competition experiments (6, 9). In addition, dormant egg banks in layered sediments allow historical reconstruction of evolutionary responses to stress through “resurrection ecology” (4, 7, 10) and paleogenetics (11). From a genomics point of view, the recent innovative tools developed for Daphnia will allow the study of the entire transcriptome at affordable prices. Moreover, the study of candidate gene polymorphism and gene expression profiles in natural populations will be routinely possible thanks to the development of SNP-chips and micro arrays developed purposely for Daphnia.

Other model organisms in the field of ecological genomics were the honeybee presented by Peter Verleyen (K.U.Leuven), the pea aphids presented by Denis Tagu and Jean-Christophe Simon (INRA, U. Rennes), Drosophila, presented by Stein Aerts (K.U.Leuven), and humans presented by Thierry Voet (K.U.Leuven). These presentations ranged from a more ecological approach (behavior in honey bees and life cycle studies in pea aphids) to hard core genetics (chromosome instability in human cleavage stage embryos), and genomics (gene regulatory networks in Drosophila).

This symposium stimulated interesting discussions and boosted future collaborations across model systems.

The next three days were dedicated to explore new advances in Daphnia research.

The meeting was organised in five symposia, including plenary lectures from keynote speakers with long term experience in their respective fields and presentations from young investigators.

In the Ecology and Evolutionary Genomics Symposium, advances in the study of natural selection, fitness and adaptation to environmental cues were presented. The two keynote speakers of this symposium were Dieter Ebert (U. Basel, CH) who presented the first linkage map of Daphnia magna and Abraham Tucker (U. Indiana) who focused on new finding in the population genomics of Daphnia pulex.

In the Gene Expression and Gene Function Symposium, studies showing the molecular basis of defenses from environmental treats were presented for both D. magna and D. pulex, along with preliminary results on the identification of candidate genes in D. magna. The keynote speakers of this symposium were Christian Laforsh (U. Münich), who debated on the molecular basis of inducible defenses in Daphnia, and Andrew Beckerman who presented data on changes in gene expression profiles associated with predators cues.

In the Toxicology and Environmental Genomics of Natural and Human Stressors Symposium, attention was given to the recent work investigating the genetic basis of human and natural induced stress. Among the human factors heavy metal pollution and land use intensity was considered. Among the natural factors, phytoplankton toxicity, parasitism and predation were analysed. The contribution of methylation to the adaptive response of Daphnia were also discussed. The keynote speakers of this symposium were Amanda Callaghan, who debated on the change in transcriptional factors in response to population dynamics and Joseph Shaw who presented results on the genetic basis of metal tolerance in D. pulex.

In the Genotype by Environment Interactions Symposium it was shown how selection and the adaptive responses to selection can be strongly altered by changing environmental conditions. The keynote speakers of this symposium were Michael Pfrender who gave an overview on the genome by environment interactions and the effect on the ecological genomics of invertebrates and Ralph Pirow who debated on the molecular and physiological responses to stress.

The last symposium of the conference was on Comparative Genomics and Development. In this symposium space was given to the recent technological advances in the field of genomics and hard core genetics. The keynote speakers of this symposium were Kelley Thomas who presented the recently developed SNP chip to study adaptive polymorphism in natural populations of Daphnia and John Manak who presented the cutting edge technology to annotate genomes.

Ample space for discussion was also given to poster presentations. The authors of the posters could briefly present their poster to outline their main results. This encouraged the attendees to discuss more during the poster sessions.

Some of the key actors of this conference, including most of the keynote speakers are involved in a Eurocores EEFG-project ("How to Live in a Mosaic of Stressors: an Ecological Genomics Approach on the Waterflea Daphnia (STRESSFLEA). This project has been recently funded and aims at elucidating genomic and transcriptomic responses and the downstream mechanisms underlying morphological, behavioral, life history and physiological responses to stress factors in D. magna. The DGC meeting was the ideal venue for the first unofficial meeting for the Eurocore project that will officially start in the autumn 2010.

 In conclusion, the DGC Meeting 2010 brought together outstanding researchers in several fields of ecology, genomics, and evolution. This boosted collaborations among members of the consortium. More importantly, it enhanced collaborations among researchers that are not part of the consortium. This will result in a clear improvement of the coordination of groups working on complementary research and in the involvement of smaller groups in the ‘big loop’, giving them the chance to participate actively to cutting edge research.

References cited

1. Colbourne JK, Pfrender M, D. G, et al. (2009) Genome Biology of the Model Crustacean Daphnia pulex. submitted.
2. Colbourne JK, Singan VRa, & Gilbert D (2005) wFleaBase: the Daphnia genome database. BMC Bioinformatics 6:45.
3. Shaw JR, et al. (2008) Daphnia as an emerging model for toxicological genomics. Advances in experimental biology on toxicogenomics, eds Hogstrand C & Kille P (Elsevier Press), pp 165- 219.
4. Cousyn C, et al. (2001) Rapid, local adaptation of zooplankton behavior to changes in
predation pressure in the absence of neutral genetic changes. PNAS 98:6256-6260.
5. Meyer E, et al. (2009) Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. BMC genomics 10:219-236.
6. Van Doorslaer W, Stoks R, Duvivier C, Bednarska A, & De Meester L (2009) Population
dynamics determines genetic adaptation to temperature in Daphnia. Evolution in press.
7. Decaestecker E, et al. (2007) Host-parasite Red Queen dynamics archived in pond sediment. Nature 450:870-874.
8. Heckmann L-H, et al. (2007) Chronic toxicity of ibuprofen to Daphnia magna: effects on life history traits and population dynamics. Toxicol Lett 172:137-145.
9. Capaul M & Ebert D (2003) Parasite mediated selection in experimental populations of
Daphnia magna. Evolution 57:249-260.
10. Hairston JNG, et al. (1999) Rapid evolution revealed by dormant eggs. Nature 401:446.
11. Mergeay J, Vanoverbeke J, Verschuren D, & De Meester L (2007) Extinction, recolonization, and dispersal trough time in a planktonic crustacean Ecology 88(12):3032–3043

Programme

BioSCENTer Symposium:
Ecological and evolutionary genomics in model organisms
Friday March 26th

10.00-13.00: Registration
13.00-13.15: VICERECTOR KAREN MAEX & ORGANISERS
Welcome
13.15-13.35: LUC DE MEESTER
Introduction to the theme and the model system
13.35-14.30: JOHN COLBOURNE (invited)
The making of model species Daphnia for environmental genomics: shared efforts, shared rewards
14.30-15.00: Coffee break
15.00-15.30: THIERRY VOET (invited)
Single cell genomics reveals chromosome instability in human cleavage stage embryos
15.30-16.00: STEIN AERTS (invited)
Computational mapping of genregulatory networks in Drosophila
16.00-16.30: PETER VERLEYEN (invited)
From genome to behaviour: the honeybee model
16.30-17.00: DENIS TAGU (invited)
Analysis of phenotypic plasticity of the reproductive mode in the pea aphid, using genomic resources
17.00-17.30: JEAN-CHRISTOPHE SIMON (invited)
Population genomics of a terrestrial cyclical parthenogen
18.00-21.00: Reception & Registration

Ecology and Evolutionary Genomics
Saturday March 27th

8.00-8.45: Registration
8.45-9.00: Welcoming words
9.00-9.30: DIETER EBERT (invited)
Mapping phenotypic traits in the D. magna genome
9.30-10.00: ABRAHAM TUCKER (invited)
Population genomics of Daphnia pulex
10.00-10.20: CHRISTOPH R. HAAG
Genetic architecture of fitness in D. magna
10.20-10.50: Coffee break
10.50-11.10: PEPIJN LUIJCKX
Resistance of Daphnia magna to a bacterial pathogen is based on few loci with strong epistasis
11.10-11.30: BENJAMIN LANGE
Host range of a microsporidian parasite
11.30-11.50: LUISA ORSINI
Ecological genomics in space and time: the signature of natural selection in wild populations of the water flea Daphnia magna
11.50-12.10: JARKKO ROUTTU
Gene mapping of Daphnia magna parasite resistance
12.10-14.30: Lunch

Poster Presentations
Saturday March 27th

14.00-14.30: Registration continues
14.30-15.30: ECOLOGY AND EVOLUTIONARY GENOMICS & GENE EXPRESSION AND GENE FUNCTION
Aurora Geerts: The genomics underpinning adaptive responses to global warming.
Pia Kreuzer: Grubbing in mud - Has Global warming already left traces in Daphnia's genome?
Julia Reger: Mapping the geography and genetics of fear - a case study with predators and prey
Sarah Rousseaux: Association between species diversity and genetic diversity in a zooplankton metacommunity
Isa Schön: Putative ancient asexual Darwinulidae (Crustacea,Ostracoda) gogenomics
Alexander Wacker: Essential resources in Daphnia - evolutionary aspects?
Joost Van overbeke: Clonal selection and genetic drift in cyclical parthenogens – the interplay between neutral and selective processes
Mathilde Cordelier: Differential gene expression profiles in response to temperature changes in a large lake Cladocera species, Daphnia galeata.
Florian Leese: Predator-induced defences in Daphnia pulex: Selection and evaluation of interna lreference genes for gene expression studies with real-time PCR
Yasuhiko Kato: Sequence divergence and expression of a transformer gene in the branchiopod crustacean, Daphnia magna
Hitoshi Miyakawa: Chaoborus-induced polyphenism is regulated by the juvenile hormone pathway in Daphnia pulex
Kevin Pauwels: Unraveling mechanisms underlying antipredator responses in Daphnia magna: a proteomic approach
Johannes Strauss: A novel pigment-dispersing hormone in multiple interneurons of the Daphnia brain and visual ganglia, some displaying circadian rhythmicity
Tokishita Shin-ichi:Temporal and spatial expression of Boule homologs during embryogenesis and gameto genesis in Daphnia magna.
Isabel Van overberghe:The development of transgenic Daphnia in the Daphnia-Pasteuria interaction
Evelyne Van vlasselaer: Trapped in diapause? Can we resurrect old dormant eggs of the waterflea Daphnia magna
Linda Weiss: The Neurohormone Dopamine influences Life-History Traits and inducible morphological Defense Structures against Chaoborusspec. in Daphnia pulex
Gang Wu: Plant LEA-like genes activated in post-diapause embryo of Artemia franciscana against water stress

15.30-16.00: Coffee break
16.00-17.00:TOXICOLOGY AND ENVIRONMENTAL GENOMICS OF NATURAL AND HUMAN STRESSORS, GENOTYPE BY ENVIRONMENT
INTERACTIONS & COMPARATIVE GENOMICS AND DEVELOPMENT
Jana Asselman: Metallothionein expression in Daphnia pulex unde rstress: functional characterization of a gene with high ecotoxicological relevance
Dörthe Becker: Reactive oxygen species (ROS) and redox buffers as an interface between stresssensing, signaling and physiological responses in Daphnia magna
Anke Cielen: Gene-expression patterns of combined stressors in Daphnia magna
Jo Devrieze: Putting evolutionary principles into ecotoxicology:at which concentration of cadmium can we expect natural selection in anatural Daphnia magna population?
Nathalie Dom: Toxicogenomics used as a biology-based alternative method to investigate themodeof action of structural analogues
Taisen Iguchi: Molecular impact of juvenile hormone agonists onneonatal Daphniamagna
Benjamin Nota: Gene expression analysis reveals agene setdiscriminatory to different metalsin soil
Marlies Messiaen: Do natural and human stressors explain the observed genetic variation of Cd tolerance within and between Daphnia magna populations
Gessica Gorbi: Effects of crowding and food limitation in two different clones of Daphnia magna
Yann Reydelet: Proteomic analysis of short-term heat stress response in two Daphnia pulex clones
Torrance C. Hanley:The interaction of food quality, predation, and genotypic variation: the effects of ribosomal DNA intergenic spacer length on Daphnia life history response
Kan Liu: Analysis and comparison of a set of expressed sequence tags of the parthogenetic waterflea Daphnia carinata
Kuchi Srikeerthana: Comparative inter-genome analysis using ESTs to identify new immune genes in Daphnia pulex
Way Sung: Synteny between D.pulex and D.magna physical maps
Hangxiao Zhang: A comparative analysis of the Artemia mitochondrial genomes

17.00-18.00: Posters discussion

Gene expression and Gene function
Sunday March 28th

9.00-9.30: CHRISTIAN LAFORSCH (invited)
Molecular basis of inducible defenses in Daphnia.
9.30-10.00: ANDREW BECKERMAN (invited)
Predator induced gene expression in developmental hormone pathways
10.00-10.20: D. CAROLINA PEÑALVA-ARANA
Extrachromosomal DNA transformations with multigenerational stability in eyeless clones of Daphnia pulex
10.20-10.50: Coffee break
10.50-11.10: HEINRICH DIRCKSEN
Genomics, transcriptomics and peptidomics reveal Daphnia pulex neuropeptides and protein hormones closer related to insect than to decapod
11.10-11.30: ANKE SCHWARZENBERGER
Gene expression in Daphnia: response to cyanobacterial protease inhibitors
11.30-11.50: ELLEN DECAESTECKER
Candidate immunity gene expression in the ecological genetics model Daphnia
11.50-12.10: FEI LIU
Diapause associated gene regulation networks of Artemia franciscana

12.10-15.00: Lunch & Excursion

Toxicology and Environmental Genomics of Natural and Human Stressors
Sunday March 28th

15.00-15.30: AMANDA CALLAGHAN (invited)
Linking transcriptomic profiles to population effects in Daphnia magna.
15.30-16.00: JOSEPH R. SHAW (invited)
Genomic basis for evolved metal tolerance in Daphnia pulex
16.00-16.20: WILLIAM S. BALDWIN
Annotation and phylogenetics of the nuclear receptors and cytochromeP450s
16.20-16.40: Coffee break
16.40-17.00: DARREN J. BAUER
Use of RNA-seq to identify Daphnia genes involved in resistance to toxic Microcystis aeruginosa
17.00-17.20: BETTINA ZEIS
Acclimatory responses of the Daphnia pulex proteome to changes of oxygen and temperature conditions
17.20-17.40: MIEKE JANSEN
Gene-expression profiles in response to three different stressors
17.40-18.00: MICHIEL B. VANDEGEHUCHTE
DNA methylation and transgenerational effects of exposure in Daphnia magna
18.00-18.20: NADINE TAYLOR
Discriminating the modes of action of toxicants via changes in the daphnid metabolome

Genotype by environment interactions
Monday March 29th

9.00-9.30: MICHAEL PFRENDER (invited)
A Functional Ecological Genomic Perspective on Genome by Environment Interaction
9.30-10.00: RALPH PIROW (invited)
Molecular and physiological responses of Daphnia pulex to acid stress
10.00-10.20: JUSTYNA WOLINSKA
Genotype-environment interactions can alter selection in a host-parasite system
10.20-10.40: Coffee break
10.40-11.00: STUART R. DENNIS
Phenotypic convergence under predation risk
11.00-11.20: JEFFRY L. DUDYCHA
Differential gene expression and adaptation to resource environment
11.20-11.40: JOACHIM MERGEAY
Priority effects in Daphnia: consequences for genomic approaches
11.40-12.00: KATRIN P. LAMPERT
A test of genetic differences for overwintering strategies in Daphnia pulex

12.00-14.00: Lunch

Comparative Genomics and Development
Monday March 29th

14.00-14.30: W. KELLEY THOMAS (invited)
Heterozygousity in the Xinb31 X Iinb1 cross: the Daphnia magna mating panel
14.30-15.00: JOHN MANAK (invited)
The use of cutting-edge genomics technologies to annotate and characterize genomes: Lessons from water fleas, sea squirts, flies and beetles
15.00-15.20: CHRISTOPH MAYER
Genome-wide analysis of tandem repeats in Daphnia pulex -a comparative approach
15.20-15.40: Coffee break
15.40-16.00: YASHIRO SHIGA
Co-option of a conserved gene regulatory module during the evolution of wings, carapace and other flat outgrowths
16.00-16.20: FRANCE DUFRESNE
Unusual duplications of the insulin receptor in Daphnia pulex
16.20-16.40: PETRA UNGERER
Neurogenesis in the water flea Daphnia magna (Crustacea, Branchiopoda)
16.40-17.00: JING SUN
Role of mitochondria in post-diapause reactivation of Artemia encysted embryos

17.00-18.00: Posters discussion
20.00-onward: Social dinner & Party