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New Genome Puts Comb Jelly in Sister Lineage to Other Animals

NEW YORK (GenomeWeb News) – A genome sequencing study of the comb jelly Mnemiopsis leidyi is prompting a new look at the events that occurred early in animal evolution.

As they reported in today's issue of Science, researchers from the National Institutes of Health and elsewhere sequenced and assembled the genome of M. leidyi, which belongs to a group of animals known as the ctenophores, commonly called comb jellies, sea walnuts, or sea gooseberries.

"Having genomic data from the ctenophores is crucial from a comparative genomics perspective, since it allows us to determine what physical and structural features were present in animals early on," senior author Andreas Baxevanis, a genome technology researcher with NHGRI, said in a statement.

"These data also provide us an invaluable window for determining the order of events that led to the incredible diversity that we see in the animal kingdom," Baxevanis said.

By annotating the sequence and comparing it to those from other animals, for instance, he and his team found phylogenetic evidence that the comb jelly lineage branched off from that leading to other animals early in the evolutionary process — earlier, even, than the lineage leading to seemingly simpler animals such as sponges.

The researchers' placement of the comb jelly in a sister group to other animals conflicts with past analyses putting sponges in early branches of the animal tree, but is consistent with at least a few phylogenetic studies done with limited sequence sets. Notably, the placement, together with features in the M. leidyi genome, point to the possibility that some animal systems may have evolved more than once in the animal tree.

"With our whole-genome sequencing data in hand, it is now clear that the cell types that make up muscles and nervous systems were either lost in some animal lineages or that, despite the complexity of these cells, they very well may have evolved multiple times," first author Joseph Ryan said in a statement.

Ryan was a post-doctoral researcher with the National Human Genome Research Institute's genome technology branch when the research was performed. He is now based at the University of Bergen Sars International Center for Marine Molecular Biology.

Representatives from most other animal lineages have already had their genomes sequenced, Baxevanis, Ryan, and their co-authors noted. But a lack of whole-genome sequences for the comb jelly made it tricky to tease apart evolutionary events at the root of the animal tree, particularly amongst so-called non-bilaterian branches that include animals without bilateral symmetry.

For the current study, the researchers used Roche 454 and Illumina instruments to sequence genomic DNA from embryos of self-fertilized M. leidyi individuals from Woods Hole.

Using that sequence, they put together a 150 million base genome assembly containing an estimated 16,548 protein-coding genes, including some that appear to be tucked away within other genes.

The team's analysis of the comb jelly's gene set indicated that the animal is missing some of the nervous system genes found in both sponges, which lack an organized nervous system, and in jellyfish from the cnidarian lineage, which have types of nerve net-based nervous systems that are distinct from that used by M. leidyi.

But other genes important to the M. leidyi nervous system are present in both the comb jelly and sponge lineages, researchers reported. Those patterns, together with comb jelly muscle cell features, seemed to support the notion that some complex animal systems and characteristics either evolved more than once or appeared in a shared ancestor to all animals before being lost or extensively modified in later-branching lineages.

When the researchers looked at M. leidyi's position in the animal tree using either amino acid or gene repertoire profiles, the investigators saw that both types of data put the comb jelly in a lineage that branched off prior to branching by the other non-bilaterian and bilaterian lineages.

"With a ctenophore genome in hand, we show that gene content data support Ctenophora as the sister group to all other animals and statistically reject competing hypotheses," the study's authors wrote, though they noted that "[i]t will be important to test this result once more genomic data are available from other ctenophores, sponges, and other relevant groups."

In a related perspectives article appearing in Science, Vanderbilt University researcher Antonis Rokas discussed the latest genomic findings in light of what was previously known about animal evolution.

"The advent of the ctenophore genome suggests that simplification and loss of genes, pathways, and even cell types, and perhaps also their independent evolution, are an integral part of the fabric of animal origins," Rokas wrote.