That discovery is but one of many in a report this week in the prestigious journal Science by members of the Daphnia Genomics Consortium, an international group of scientists from Genome Project Solutions and dozens of other institutions, including the Center for Genomics and Bioinformatics (CGB) at Indiana University Bloomington and the U.S. Department of Energy's Joint Genome Institute (JGI). A bullet-point list of the Science paper's most important findings appears at the end of this release.
Daphnia Genomics Consortium projects are featured at http://daphnia.cgb.indiana.edu.
Further details can be found at http://www.genomeprojectsolutions.com/News_and_publications/News-Daphnia_genome.html
Scientists have studied Daphnia for centuries because of its importance in aquatic food webs and for its transformational responses to environmental stress. Predators signal some of the animals to produce exaggerated spines, neck-teeth or helmets in self-defense. And like the virgin nymph of Greek mythology that shares its name, Daphnia thrives in the absence of males, by clonal reproduction, until harsh environmental conditions favor the benefits of sex.
Arguably, more is known about the ecology and stress biology of the water flea than any other animal. The genome project was conceived with an expectation that many new gene functions would be uncovered when studied in light of the animal’s natural environment — not necessarily expecting to discover many more genes.
Yet, Daphnia's genome is no ordinary genome.
"Daphnia's high gene number is largely because its genes are multiplying, by creating copies at a higher rate than other species," said CGB genomics director John Colbourne, who is first author of the paper. "We estimate a rate that is three times greater than those of other invertebrates and 30 percent greater than that of human."
Don Gilbert, coauthor and scientist at IU Bloomington, added, "More than one-third of Daphnia's genes are undocumented in any other organism — in other words, are completely new to science."
Sequenced genomes often contain some fraction of genes with unknown functions, even among the most well-studied genetic model species for biomedical research, such as the fruit fly Drosophila. However, by using microarrays (containing millions of DNA strands affixed to microscope slides) that are made to measure the conditions under which these new genes are activated for producing their protein products, experiments that challenged Daphnia to environmental stressors point to these unknown genes having ecologically significant functions.
"If such large fractions of genomes evolved to cope with environmental challenges, information from traditional model species used only in laboratory studies may be insufficient to discover the roles for a considerable number of animal genes," Colbourne said.
In light of these findings, Daphnia emerges as a model organism for a new field —Environmental Genomics — which aims to better understand how the environment and genes interact. This includes building research tools for investigating the molecular underpinnings of key ecological and evolutionary problems.
All of this work has resulted in Daphnia being chosen by the National Institutes of Health as the 13th official model organism for biomedical research, designating its special status as being likely to offer key insights into human biology and the diagnosis and treatment of human disease. A requisite to reach model system status is a large research community that contributes to its growing body of knowledge and resources. Over the course of the project, the Daphnia Genomics Consortium has grown from a handful of founding members to over 450 investigators distributed around the globe. Nearly 200 scientists have contributed published work resulting from the genome study, many in open-source journals published as a thematic series by BioMedCentral. A list of these publications can be found at http://www.biomedcentral.com/series/Daphnia.
"An exciting consequence of our reaching-out, to involve as many people as possible to help interpret the genome sequence, is the establishment of a multidisciplinary research community that cooperates to now make excellent use of the data," said Igor Grigoriev, who is gene annotation group leader at the DOE Joint Genome Institute.
The end product is a better understanding of what genes matter for organisms to cope with environmental stress that includes pollutants and global warming, and the technologies necessary to understand how these genes function within an animal that is easily studied in water reservoirs around the globe.
The sequencing of the waterflea genome, identification of all genes, much of the gene expression studies, and many genome interpretations and comparisons were done at the DOE Joint Genome Institute (JGI). Jeffrey Boore, who led the work done at JGI and is now CEO of Genome Project Solutions, which also contributed to this study, said, “Crustaceans are the closest living relatives to insects, and Daphnia pulex is the first animal from this group to have its genome completely sequenced. The critical placement of Daphnia in the evolutionary tree allows many new and broad interpretations about the diversity of genome structures, not only for this animal, but also for the insect genomes being studied, such as those of the honeybee (Apis mellifera) and the fruit fly (Drosophila melanogaster).”
So why does Daphnia have so many genes compared to other animals? The co-authors of the Science paper begin addressing that issue as well as others related to the genomic architecture and evolution of the species.
"We don't yet have final answers," said Michael Pfrender, coauthor and associate professor of biology at the University of Notre Dame. "The sequenced isolate did originate from a naturally inbred population, which may contribute to some features of this genome — and Daphnia's partial asexuality may have a hand to play."
Another possibility, Colbourne said, is that "Since the majority of duplicated and unknown genes are sensitive to environmental conditions, their accumulation in the genome could account for Daphnia's flexible responses to environmental change."
This work received financial and material support from the Office of Science of the U.S. Department of Energy, the National Science Foundation, the Lilly Endowment, Inc., Roche NimbleGen Inc., the National Institutes of Health, the U.S. Department of Health and Human Services, and Indiana University.
To speak with senior author of this manuscript, Jeffrey L. Boore, please call 877-867-0146 or e-mail JLBoore@GenomeProjectSolutions.com.
Major Findings
• Largest inventory of genes ever recorded for a sequenced animal, packaged within a tiny genome of only 200 million bases.
• The genome is made compact by the reduction in size of spaces (introns) between the gene parts that code for proteins.
• First crustacean genome sequenced. Only 4.5 percent of genes are shared exclusively between Daphnia and insects, arthropods which shared a common ancestor some 500 MYA.
• First time an arthropod with a wholly aquatic life cycle has had its genome sequenced. Genes shared by Daphnia and unrelated aquatic vertebrates are identified, and are likely key for living life in water.
• Genes that have unknown functions -- because they are uniquely identified in Daphnia -- are involved in response to the environment.
• Of all sequenced genomes belonging to the animal group comprised of insects and crustaceans, Daphnia share the greatest number of genes with humans.
• The birth rates for genes can be high — duplications occur three times more in Daphnia pulex than in other invertebrates — and duplicated genes are more likely to be functionally related than not.
• Newly duplicated genes can rapidly acquire new functions, which are best identified by specific environmental conditions.
• Daphnia-specific gene families that have amplified to large numbers include hemoglobins (11 copies), and opsin (visual) genes (46 copies) — a very old and newly discovered expanded subfamily of opsins was lost in terrestrial animal lineages. • The overall data suggest an original hypothesis for how newly duplicated genes are retained in the genome, which depends on the condition-specific regulation of cooperatively evolving genes.
Citation:
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. 2011. The Ecoresponsive Genome of Daphnia pulex. Science 331, 555-561.
