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Researchers Sequence Sponge Genome

By Andrea Anderson

NEW YORK (GenomeWeb News) – An international research team reported online today in Nature that they have sequenced and started analyzing the genome of the sponge Amphimedon queenslandica.

The researchers used Sanger sequencing to tackle the genome of A. queenslandica — a demosponge species found around Australia's Great Barrier Reef. When they compared the draft genome with genomes of other animals, the team found that the sponge harbors a large collection of genes found in more complex multicellular organisms — including genes that go awry in some human cancers.

"Comparing the genome of sponges to those of other animals will tell us a lot more about the common ancestor of all animals," lead author Mansi Srivastava told GenomeWeb Daily News. "Our ultimate goal with having the genome sequence is actually to enable experimental work, which will give us more precise answers on the functions of these genes in sponges."

Srivastava participated in the sponge sequencing project as a graduate student in Daniel Rokhsar's UC Berkeley lab. She is currently a post-doctoral researcher in Peter Reddien's lab at the Whitehead Institute for Biomedical Research.

Sponges, some of the earliest branching animals, are multicellular but lack a nervous system, gut, and some other organ systems found in most animals, the researchers explained. And fossil evidence going back more than 600 million years suggests sponge ancestors appeared remarkably similar to sponges living today.

In an effort to learn more about early multicellularity and animal evolution, the team decided to sequence the genome of A. queenslandica, a sponge species studied in co-author Bernard Degnan's lab at the University of Queensland for several years, Srivastava explained.

"Although the diversity of sponges and their uncertain phylogeny make it doubtful that any single species can reveal the intricacies of early animal evolution, comparison of the A. queenslandica draft genome with sequences from other species can provide a conservative estimate of the genome of the common ancestor of all animals and the timing and nature of the genomic events that led to the origin and early evolution of animal lineages," the researchers wrote.

The researchers did whole-genome shotgun sequencing on genomic DNA extracted from A. queenslandica embryos and larvae from an adult sponge, using the Sanger approach to generate sequence covering about 167 million bases of the genome to roughly nine times coverage. In the process, the team also garnered sequence representing the genome of a commensal microbe found in sponge embryos.

Based on their analyses of sponge genome sequence and previously generated EST data, the team estimates that the sea sponge genome contains as many as 30,000 genes. They subsequently found homologues for 18,693 of these genes in other animal species.

Moreover, the team noted, the sponge genome shows conserved gene structure and genome organization when compared with other animal genomes.

Among the gene families detected in the sponge were several associated with multicellular functions, including genes involved in cell cycle control, cell adhesion, embryonic development, and more. The finding suggests genes in these families belong to what the team calls a "toolkit" of ancestral animal genes.

"Even though sponges don't have specialized cell types like neurons or muscles, they do have many of the genes that operate in those cell types in humans or fruit flies," Srivastava noted, though the function of these genes in sponges is still unclear.

The researchers also found many genes implicated in human cancers in the sponge genome, consistent with the notion that some of the same genes that evolved to support multicellular processes can cause cancer in humans when their activity is disrupted.

"When cells are growing in a multicellular context, they have to regulate each other's division," Srivastava explained. "When the genes that regulate growth and division lose their functions is when a disease like cancer arises."

When they looked at how the number of genes within each gene family correlates with complexity in multicellular animals, the researchers found that the transition from unicellular to multicellular animals appears to have coincided with expansions to specific gene families.

And by comparing the sponge genome with the genomes of 18 other animals, the researchers were also able to learn more about the phylogenetic relationships between animals. "We do find that [sponges belong to] the earliest branching lineage — it's kind of confirming what we expected," Srivastava said.

Now, she added, researchers can begin using the newly sequenced sponge genome to further explore when specific genes originated in animals and how their functions differ between lineages over the course of animal evolution.