The simple sponge can reveal much about life on Earth. Researchers who have
sequenced the genome of one Down Under inhabitant are learning just how common
those roots are.
In a paper published online in the journalNature, Rice University's
Nicholas Putnam is among a group of scientists who have established a draft
genome sequence for Amphimedon
queenslandica, a sponge found off the coast of Australia. The genome is helping
evolutionary biologists connect the dots as they look for DNA sequences shared
by metazoans, or multicelled animals.
Sponges are an ancient group, with fossils dating back at least 650 million
years. They are thought to have been the first group of animals to branch from
all the others. Therefore, genes shared by sponges and other animals must have
been present in the common ancestor of all metazoans. This ancestor would have
evolved mechanisms to coordinate cell division, growth, specialization,
adhesion, and death; this suggests that early sponges already had a
developmental set of tools similar to those in metazoans today, said Putnam, an
assistant professor of ecology and evolutionary biology.
"What's exciting is the new things we're learning about animal
evolution," said Putnam, who got involved with the project while working
at the Department of Energy's Joint
Genome Institute in 2006. "For example, sponges have embryos, and
having the genome helps us look at how they develop and make specific
connections to developmental pathways in other animals.”
"It's the kind of thing that will lead to a much clearer understanding
of what the very first metazoans looked like," he said.
That distant ancestor may well have looked like a sponge. For the paper,
Putnam helped compare Amphimedon's draft genome with 13 other complete animal
genomes, including a selection of invertebrates, as well as a choanoflagellate. The
researchers wrote of a "striking conservation of gene structure and genome
organization" that is common to all. "We can now say that the
large-scale patterns of genome organization we've seen conserved in other
animal groups come from the very root of the animal tree," Putnam said.
The challenge ahead is learning what they do. "The focus of my research
is to understand whether patterns that have been around for a billion years have
some particular functions—or if they're hanging around because not enough time
has gone by to erase them."
What's missing is also interesting, he said. The ancestral patterns of
genome organization common to other creatures is absent from certain arthropods
and nematodes. "If the missing pattern is neutral, you'd say that
somewhere along the history of those groups, the rate of (evolutionary) change
sped up enough to break the connection," Putnam said. "If it's
functional, then somehow those groups overcame whatever constraint is on it in
other lineages."
Also puzzling is that while Amphimedon shares key developmental genes with a
diverse set of metazoans, its basic structure hasn't changed in 600 million
years. Given the same roots, researchers wonder why it didn't evolve more
radically, and they are working to identify the differences that gave rise to,
say, nerve cells in other creatures but not sponges.
Unlocking the basic mechanisms of multicellularity may also help researchers
understand what happens when those mechanisms go wrong and lead to cancer and
autoimmune disorders.
The paper's senior authors are Daniel Rokhsar of the University
of California, Berkeley,
and Bernard Degnan of the University
of Queensland in Australia.
The work was funded by the Australian Research Council, the Department of
Energy Joint Genome Institute, Harvey Karp, the National Science Foundation, the
National Institutes of Health/National Human Genome Research Institute, the
University of Queensland Postdoctoral Fellowship, the Sars International Center
for Marine Molecular Biology, Deutsche Forschungsgemeinschaft, Agricultural and
Natural Resources/University of California, the French National Center for
Scientific Research, the Gordon and Betty Moore Foundation and Richard Melmon.
Read the paper here: http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html
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