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UC Berkeley, JGI Collaboration Sequences Trichoplax Genome

NEW YORK (GenomeWeb News) – An international research team led by scientists at the University of California at Berkeley and the US Department of Energy’s Joint Genome Institute has completed the draft genome of an organism representing one of the earliest forms of animal life.
The Trichoplax adhaerens genome, published online today in Nature, reveals the genetics behind a group of animals called placozoans — tiny, disc-shaped creatures with just four or five documented cell types. The work is helping to clarify the phylogeny of placozoans and also revealing the surprising complexity housed in the compact Trichoplax genome — information that is expected to shed light on early stages in animal evolution.
“With the genome in hand, renewed interest in this ‘simple’ animal with a complex genome will add to our appreciation of animal diversity and perhaps yield fundamental insights into early animal evolution,” the authors concluded.
“People are really interested in how Trichoplax relates to other animals,” lead author Mansi Srivastava, a graduate student in Daniel Rokhsar’s lab at the University of California at Berkeley, told GenomeWeb Daily News.
Trichoplax is composed of two epithelial layers flanking core fibre cells that contain more than one nucleus. Although Trichoplax is a “simple critter with just a few different cell types,” Srivastava said, many have hypothesized that it actually represents the earliest form of animal life. Even so, Trichoplax’s phylogenetic placement with respect to other animals has been hotly debated.
In an effort to get to the bottom of Trichoplax biology and evolution, the researchers used whole-genome shotgun sequencing to sequence the roughly 98 million base pairs of the Trichoplax genome to about eight-fold coverage. They then assembled and analyzed this sequence data to get a handle on Trichoplax function and phylogeny.
By comparing about a hundred nuclear genes between Trichoplax and other animals, Srivastava explained, the researchers were able to shift placozoan placement in the animal tree. In contrast to mitochondrial DNA sequence analyses that put placozoans at the base of this tree, branching before other animals, the latest data suggests placozoans diverged in the Precambrian period before both cnidarians, such as anemones and jellyfish, and animals with bilateral symmetry but after some sponges.
The researchers also gained a better appreciation for the genetic complexity of this seemingly straightforward organism. “It is a really simple looking organism,” Srivastava said.
Still, she emphasized, the small Trichoplax genome contains sequences coding for many of the major transcription factors, signaling proteins, and pathways found in humans and other animals, including some involved in neuron development. “Even though Trichoplax doesn’t have a neuron, it has many of the genes that we use to make a neuron,” she said.
The organism’s genome also retained some conserved introns that are found in the human genome but which have been lost from the genomes of fruit flies, sea squirts, and other animals. “The observation of blocks of conserved synteny is consistent with a relatively low rate of local rearrangement in Trichoplax,” the authors wrote.
That, in turn, suggests that these genes were present in the last shared common ancestor between humans and Trichoplax, some 600 million years ago. “We still retain some of the signatures of how genes were organized in the common ancestor,” Srivastava explained.
Overall, the research provides new information about basal animal relationships. Still, Srivastava noted, only by sequencing additional genomes will researchers be able to resolve the details of these relationships. To that end, she said that the team is currently unraveling the genome of a sponge called Amphimedon queenslandica.

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