The tiny water flea Daphnia has the most genes of any animal, some 31,000. Credit: Paul Hebert, University of Guelph |
Scientists
have discovered that the animal with the most genes–about 31,000–is
the near-microscopic freshwater crustacean Daphnia pulex, or water flea.
By comparison, humans have about 23,000 genes. Daphnia is the first crustacean to have its genome sequenced.
The
water flea’s genome is described in a Science paper published this week
by members of the Daphnia Genomics Consortium, an international network
of scientists led by the Center for Genomics and Bioinformatics (CGB)
at Indiana University (IU) Bloomington and the U.S. Department of
Energy’s Joint Genome Institute.
“Daphnia’s
high gene number is largely because its genes are multiplying, creating
copies at a higher rate than other species,” said project leader and
CGB genomics director John Colbourne. “We estimate a rate that is three
times greater than those of other invertebrates and 30 percent greater
than that of humans.”
“This
analysis of the Daphnia genome significantly advances our understanding
of how an organism’s genome interacts with its environment both to
influence genome structure and to confer ecological and evolutionary
success,” says Saran Twombly, program director in the National Science
Foundation (NSF)’s Division of Environmental Biology, which funded the
research.
“This
gene-environment interplay has, to date, been studied in model
organisms under artificial, laboratory conditions,” says Twombly.
“Because
the ecology of Daphnia pulex is well-known, and the organism occurs
abundantly in the wild, this analysis provides unprecedented insights
into the feedback between genes and environment in a real and
ever-changing environment.”
Daphnia’s genome is no ordinary genome.
What reasons might Daphnia have so many genes compared to other animals?
A
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.”
Scientists
have studied Daphnia for centuries because of its importance in aquatic
food webs and for its transformational responses to environmental
stress.
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.
“More
than one-third of Daphnia’s genes are undocumented in any other
organism–in other words, they are completely new to science,” says Don
Gilbert, paper co-author and scientist at IU Bloomington.
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.
By
using microarrays (containing millions of DNA strands affixed to
microscope slides), experiments that subjected 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.
Daphnia
is emerging as a model organism for a new field of
science–environmental genomics–that aims to better understand how the
environment and genes interact.
This
includes a practical need to apply scientific developments from this
field to managing our water resources and protecting human health from
chemical pollutants in the environment.
James
Klaunig, a scientist at IU Bloomington, predicts that the work will
yield a more realistic and scientifically-based risk evaluation.
“Genome
research on the responses of animals to stress has important
implications for assessing environmental risks to humans,” Klaunig said.
“Daphnia is an exquisite aquatic sensor, a potential high-tech and
modern version of the mineshaft canary.”
“With
knowledge of its genome, and using both field sampling and laboratory
studies, the possible effects of environmental agents on cellular and
molecular processes can be resolved and linked to similar processes in
humans.”
The scientists learned that of all sequenced invertebrate genomes so far, Daphnia shares the most genes with humans.
Daphnia’s gene expression patterns change depending on its environment, and the patterns indicate what state its cells are in.
A
water flea bobbing in water containing a chemical pollutant will
tune-up or tune-down a suite of genes differently than its sisters
accustomed to water without the pollutant, for example.
The
health effects of most industrially produced compounds in the
environment are unknown, because current testing procedures are too
slow, too costly, and unable to indicate the causes for their effects on
animals, including humans.
Over
the course of the project, the Daphnia Genomics Consortium has grown
from a handful of founding members to more than 450 investigators around
the globe.
“Assembling
so many experts around a shared research goal is no small feat,” said
Peter Cherbas, director of the CGB. “The genome project signals the
coming-of-age of Daphnia as a research tool for investigating the
molecular underpinnings of key ecological and environmental problems.”
Colbourne
agreed, adding, “New model systems rarely arrive on the scene with such
clear and important roles to play in advancing a new field of science.”
The
work also received support from the U.S. Department of Energy, Lilly
Endowment Inc., Roche NimbleGen Inc., the U.S. National Institutes of
Health, the U.S. Department of Health and Human Services, and Indiana
University.
