First Genome Sequence of a Crustacean Has Extreme Features
Hercules, California — Of the many animals now with complete
genome sequences, the one with the most genes is the near-microscopic,
freshwater crustacean Daphnia pulex, sometimes referred to as the
water flea. Daphnia is the first crustacean to have its genome
sequenced, and it contains more than 31,000 genes. By comparison, humans
have only about 23,000 genes.
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 US DOE Joint Genome Institute (JGI). A bullet-point
list of the Science paper's most important findings appears here.
Daphnia Genomics Consortium projects are featured at http://daphnia.cgb.indiana.edu.
Scientists have studied Daphnia for centuries because of its importance
in aquatic food webs and for its 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, 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 prerequisite 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
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
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
"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."
To speak with senior author of this manuscript, Jeffrey L. Boore, please
call 877-867-0146 or e-mail JLBoore@GenomeProjectSolutions.com.
Further details can be found here.
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