Abstract
This meeting report presents the cutting-edge research that is developing around the waterflea Daphnia, an emerging model system in environmental genomics. Daphnia has been a model species in ecology, toxicology and evolution for many years and is supported by a large community of ecologists, evolutionary biologists and ecotoxicologists. Thanks to new advances in genomics and transciptomics and to the sustained efforts of the Daphnia Genomics Consortium (DGC), Daphnia is also rapidly developing as a model system in environmental genomics. Advances in this emerging field were presented at the DGC 2010, held for the first time in a European University. During the meeting, a plethora of elegant studies were presented on the mechanisms of responses to environmental challenges using recently developed genomic tools. The DGC 2010 is a concrete example of the new trends in ecology and evolution. The times are mature for the application of innovative genomic and transcriptomic tools for studies of environmental genomics in non-model organisms.
Keywords: Daphnia magna, environmental genomics, transcriptomics
The 2010 Daphnia Genomics Consortium (DGC) meeting, the first held in Europe, in the city of Leuven (Belgium), was a pivotal point in the development of an emerging and powerful model system for environmental and ecological genomics. The waterflea Daphnia has been a key model organism in ecology, ecotoxicology and evolutionary biology for more than a century. Key assets of Daphnia are its ease of manipulation and culture, the possibility to work with clonal lineages and its sensitivity to environmental contaminants. Quantifying phenotypic trait variation and its link to fitness is relatively straightforward [1]. In addition, dormant egg banks in layered sediments allow historical reconstruction of evolutionary responses [2] and palaeogenetics. The extensive knowledge of the responses of Daphnia to environmental challenges represents an important asset for the fast development of this organism as a model in environmental genomics and transcriptomics [3].
The meeting yielded a powerful picture of the development of genomics resources and their application in the model Daphnia to unravel the mechanisms of responses to environmental challenges. The meeting provided a unique overview of the progress achieved with the Daphnia genome sequence and key innovations that are emerging from this research. Key features of the Daphnia genome are the high number of genes (greater than 30 000) and the large fraction of genes lacking homology to other arthropod genomes. The number of genes without ontology is probably the result of Daphnia's distant phylogenetic relationship to other arthropods with complete genome sequences, as well as its unique ecological context as the first fully aquatic arthropod sequenced. The recent assembly of the full transcriptome NimbleGen micro-array for Daphnia pulex will strongly boost gene function analysis. During the DGC meeting, a draft genome sequence of a second species, Daphnia magna, was presented, and strong momentum was generated for the development of full transcriptome micro-arrays for this species. Daphnia magna is the main Daphnia species used in European laboratories, and has been a pre-eminent model in studies of responses to a wide variety of stressors, including pollutants, predator risk, parasite exposure and climate change [4–6]. A recently developed single nucleotide polymorphism chip will guarantee fast progress in the study of adaptation to environmental stressors, natural or human-induced. This chip is able to capture polymorphisms in natural populations covering the entire genome of D. magna. It will be of key importance in identifying functional polymorphisms in the genome of Daphnia and its role in the adaptive processes.
Most inspiring, a plethora of elegant studies were presented on the mechanisms of responses to environmental challenges, which used recently developed genomic tools. These studies highlight the importance of a complete and well-annotated genome sequence in enabling evolutionary and ecologically relevant studies in natural populations. These included, among others, the genetic underpinning of inducible defences in Daphnia and changes in gene expression profiles associated with predator cues, quantitative trait locus analysis of parasite resistance, genomics of metal-induced stress responses, ecotoxicogenomics, methylome analysis and transcriptomics of responses to combined anthropogenic and natural stressors. The influence of environmental conditions on transcriptional responses was presented, along with an overview on recent insights in molecular and physiological responses to stress. These studies highlighted the great potential of Daphnia as model system in environmental genomics.
The growing interest in Daphnia as a model system in ecological genomics and the successful development of genomic infrastructure has gathered together a number of outstanding scientists ready to take advantage of the acquired tools and apply them in cutting-edge research. Some researchers of the DGC coordinated their efforts by joining a European network (EUROCORES funded project STRESSFLEA, 09-EuroEEFG-FP 040, 2010-2013). The DGC 2010 was the venue for announcing the starting of STRESSFLEA and to invite non-member groups to join the consortium as non-funded peripheral partners within the DGC. This will certainly enhance collaboration and communication within the consortium. The DGC 2010 was a concrete sign of the revolutionary development that is going on in biological and environmental science. In the last decade, new genomic resources from model organisms and advances in DNA-sequencing technologies have alleviated the limitations that researchers previously faced and opened new areas of research for studies of non-model organisms. Times are mature for the application of newly developed genomic resources for cutting-edge environmental genomic research on non-model organisms.
Acknowledgements
We thank the European Science Foundation (ESF) and the Research Fund, Flanders, Belgium (FWO) for funding the conference.
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