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Surprises in sea anemone genome

The genome of one of Earth's oldest animal species shares genes, features with vertebrate genomes

By | July 5, 2007

The genome of the sea anemone, one of the oldest living animal species on Earth, shares a surprising degree of similarity with the genome of vertebrates, researchers report in this week's Science. The study also found that these similarities were absent from fruit fly and nematode genomes, contradicting the widely held belief that organisms become more complex through evolution. The findings suggest that the ancestral animal genome was quite complex, and fly and worm genomes lost some of that intricacy as they evolved. "What's exciting about this paper is that you're seeing the footprints of that ancient organization, reaching back perhaps 700 million years, which is an enormous expanse of evolution," said David Haussler of the University of California, Santa Cruz, who was not involved in the work. Led by Nicholas H. Putnam of the Department of Energy Joint Genome Institute (JGI) in Walnut Creek, Calif., the authors sequenced the genome of the starlet sea anemone Nematostella vectensis. They compared its DNA and protein sequence with those of other animals to reconstruct genome features of the ancestral eumetazoan -- the progenitor of all multicellular animals except sponges. The authors found that the sea anemone genome contains about 450 million base pairs and 18,000 protein-coding genes. They identified many gene families common to all sequenced animals. "We have this basic toolkit now for the whole animal kingdom," senior author Daniel S. Rokhsar of JGI and the University of California, Berkeley, told The Scientist. "It gives a kind of unity to all animals that I think is kind of surprising." They then compared the genomes of modern animals with that of the inferred ancestral eumetazoan, and found that about two-thirds of gene families in humans and sea anemones are derived from genes found in their common ancestor. Only about half of Drosophila and Caenorhabditis elegans gene families show such similarity to the common ancestor. Previous studies have shown gene loss in flies and worms, but this work shows that loss "was highly substantial, even more significant than we expected before," said Eugene V. Koonin of the National Center for Biotechnology Information (NCBI) in Bethesda, Md., who was not involved in the work. The researchers also discovered that exon-intron structure is very similar between modern vertebrates and sea anemones. Both have intron-rich genomes and about 80% of intron locations are conserved between humans and anemones. Fly and nematode genomes, on the other hand, have lost between 50 and 90% of the introns likely present in the animal ancestor. The anemone sequence also revealed that many blocks of linked genes in the ancestral genome remain together in the human and sea anemone genomes. Since these linkages "have remained together over this enormous evolutionary time period, [there may be] selective pressure against separating these genes," Haussler said. According to the study, about 80% of pan-eumetazoan genes have clearly recognizable homologs in fungi, plants, or other eukaryotes. The remaining 20% are specific to eumetazoan animals. These genes are involved in signal transduction, cell communication and adhesion, embryogenesis, and neural and muscular function. It's surprising to find such a "high level of genomic complexity in a supposedly primitive animal such as the sea anemone," Koonin told The Scientist. It implies that the ancestral animal "was already extremely highly complex, at least in terms of its genomic organization and regulatory and signal transduction circuits, if not necessarily morphologically." It's not yet possible to know exactly what that animal looked like or how it functioned, Rokhsar said, "but these kinds of genome projects help us to get at that." Melissa Lee Phillips mail@the-scientist.com Links within this article I. Ganguli, "Expanding the ranks of vertebrate genomes," The Scientist, September 2006. http://www.the-scientist.com/article/display/24470/ N.H. Putnam et al., "Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization," Science, July 6, 2007. http://www.sciencemag.org David Haussler http://www.cbse.ucsc.edu/staff/haussler.shtml M.L. Phillips, "Synaptic proteins in sea sponge," The Scientist, June 6, 2007. http://www.the-scientist.com/news/display/53271/ Daniel S. Rokhsar http://www.physics.berkeley.edu/people/directory.php?id=181 U. Technau et al., "Maintenance of ancestral complexity and non-metazoan genes in two basal cnidarians," Trends in Genetics, December 2005. http://www.the-scientist.com/pubmed/16226338 Eugene V. Koonin http://www.ncbi.nlm.nih.gov/CBBresearch/Koonin/ T.M. Powledge, "How many genomes are enough?" The Scientist, November 17, 2003. http://www.the-scientist.com/article/display/21809/
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Comments

July 22, 2007

I take issue with the statement, "The findings suggest that the ancestral animal genome was quite complex, and fly and worm genomes lost some of that intricacy as they evolved."\n\nWhile the findings certainly indicate that this ancestral animal genome was quite complex, fly and worm genomes are unquestionably not without complexity of their own. Surely it is as reasonable to suppose that fly and worm evolution replaced some of the ancestral intricacy with more streamlined, efficient, and successful (in the Darwinian sense) genomic organization? Could it be that the "intricacy" of a genome is best assessed at the level of expression? However, it is debatable as to which is the more intricate, a fly or an sea anemone.\n
Avatar of: Heresiarch

Heresiarch

Posts: 1

August 26, 2007

It seems to me that the capacity to sequence and analyze genomes gives scientists a great opportunity to test the theory of evolution, simply by making predictions about what sequencing and analysis will discover. But I don't see that happening. Might it be because the sequencing and analysis done so far has discovered several, if not many, instances of what, from a neoDarwinian perspective, can only be called genomic anomalies? \n\nC'mon evolutionists. Here's your chance to show up the intelligent design crowd and prove that your theory is on sound scientific footing: Make Predictions. Get it in the record. Then let the chips fall where they may. \n\nIf Thomas Kuhn was onto something, then we might see the day when so many sequencing and analysis anomalies pile up that the normal theory of evolution becomes untenable, implausible, and we witness a scientific revolution. \n\nOne way to account for the presence of "newer" genes in older organisms is to reposition phylogeny inside an overarching ontogeny. (All the genes in my body, even those not expressed until later in life, were present already when I was just a zygote.)This model better accounts for the genomic anomalies than does the normal model of evolution. \n\nSo, of what organism is our phylogeny a stage of ontogeny? Meet my candidate www.starlarvae.org

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