09.20.08

‘Simple’ Animal’s Genome Proves Unexpectedly Complex

Posted in Evolution at 6:13 pm by nemo

Rescued from the clutches of the ID gang at UD, speaks for itself sans ID?
Science 22 August 2008:
Vol. 321. no. 5892, pp. 1028 – 1029
DOI: 10.1126/science.321.5892.1028b
GENOMICS: ‘Simple’ Animal’s Genome Proves Unexpectedly Complex
Elizabeth Pennisi
Aptly named “sticky hairy plate,” Trichoplax adhaerens barely qualifies as an animal. About 1 millimeter long and covered with cilia, this flat marine organism lacks a stomach, muscles, nerves, and gonads, even a head. It glides along like an amoeba, its lower layer of cells releasing enzymes that digest algae beneath its ever-changing body, and it reproduces by splitting or budding off progeny. Yet this animal’s genome looks surprisingly like ours, says Daniel Rokhsar, an evolutionary biologist at the University of California, Berkeley (UCB) and the U.S. Department of Energy Joint Genome Institute in Walnut Creek, California. Its 98 million DNA base pairs include many of the genes responsible for guiding the development of other animals’ complex shapes and organs, he and his colleagues report in the 21 August issue of Nature.

Biologists had once assumed that complicated body plans and complex genomes went hand in hand. But T. adhaerens’s genome, following on the heels of the discovery of a similarly sophisticated genome in a sea anemone (Science, 6 July 2007, p. 86), “highlights a disconnect between molecular and morphological complexity,” says Mark Martindale, an experimental embryologist at the University of Hawaii, Honolulu. Adds Casey Dunn, an evolutionary biologist at Brown University, “It is now completely clear that genomic complexity was present very early on” in animal evolution.

Ever since German zoologist Franz Eilhard Schulze first found Trichoplax more than a century ago in a saltwater aquarium, this disc-shaped animal has stirred debate. It has just four apparent types of cells, prompting Schulze and others to consider it a holdover from the earliest animals. They eventually assigned it to its own phylum, Placozoa.

But not everyone agrees which branch of the animal tree of life is oldest: sponges, comb jellies, or placozoans. And a few researchers have dismissively argued that placozoans are just larvae of cnidarians–jellyfish, sea anemones, and the like–or else a streamlined version of a cnidarian ancestor.

Rokhsar, his graduate student Mansi Srivastava, and their colleagues sequenced a Trichoplax from the Red Sea, finding an estimated 11,514 protein-coding genes. After comparing the sequences of 104 Trichoplax genes with their counterparts in other organisms, they concluded that placozoans aren’t the oldest animals; they branched off after sponges but before cnidaria. Placing Trichoplax on the tree “will now allow us to understand how to interpret its biology in the context of animals as a whole,” says Dunn.

The sequence is also clarifying what ancient genomes looked like. Trichoplax genes have comparable numbers of introns, noncoding regions interspersed between the coding regions, as vertebrates and as the sea anemone. And many of the same genes were linked on the chromosomes of vertebrates, Trichoplax, and sea anemones, the researchers report. This was not the case with the fruit fly and nematode genomes, whose genes have fewer introns and have moved about quite a bit.

Despite being developmentally simple–with no organs or many specialized cells–the placozoan has counterparts of the transcription factors that more complex organisms need to make their many body parts and tissues. It also has genes for many of the proteins, such as membrane proteins, needed for specialized cells to coordinate their function. “Many genes viewed as having particular ‘functions’ in bilaterians or mammals turn out to have much deeper evolutionary history than expected, raising questions about why they evolved,” says Douglas Erwin, an evolutionary biologist at the Smithsonian National Museum of Natural History (NMNH) in Washington, D.C.

Trichoplax could yet be more complex than observed, perhaps having subtle differences in cell types. Or, the amoeboid form may be just one phase of a complex life cycle that’s still undiscovered, says Rokhsar.

The surprises in the Trichoplax genome emphasize the importance of sequencing other early-arising species, such as comb jellies or different kinds of sponges, says evolutionary biologist Allen Collins of the National Marine Fisheries Service and NMNH. “The more taxa we fill in,” says Collins, “the clearer our picture will be for how the entire suite of these molecules evolved over the critical time early in metazoan history.”

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