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Acorn Worm Genome Sequencing Provides Insight Into Ancestral Animal Group

NEW YORK (GenomeWeb) – By sequencing the genomes of two sea worms, an international research team has uncovered new clues about the common ancestor of deuterostomes — an animal superphylum that includes vertebrates and other chordates; echinoderms such as starfish; and hemichordates.

The researchers, led by investigators at the University of California at Berkeley, the US Department of Energy Joint Genome Institute, and the Okinawa Institute of Science and Technology (OIST), generated draft genome assemblies for two marine hemichordates: the acorn worms Saccoglossus kowalevskii and Ptychodera flava, which belong to lineages that diverged from one another an estimated 370 million years ago.

Through comparisons with gene, pathways, and transcripts from other deuterostome and non-deuterostome animals, the team got a glimpse at genomic features that were presumably present in the common ancestor of hemichordate, chordate, and echinoderm animals. The study appeared online today in Nature.

"Comparative analysis reveals numerous deuterostome-specific gene novelties," the study's authors noted, "including genes found in deuterostomes and marine microbes, but not other animals."

Acorn worms have developmental and physical features that resemble animals in both the echinoderm and chordate phyla, the team noted. The deep sea worms use gill-like slits that separate their mouths and esophagi to filter food from water, for example, pointing to early origins of such gills and related pharyngeal structures in deuterostome animals.

"These structures were ancestral deuterostome characters elaborated upon the bilaterian ancestral body plan," they wrote, "but the gill slits were subsequently lost in extant echinoderms and amniotes."

To gain further insights about ancestral deuterostome genome features, the team set out to sequence representatives from the hemichordate phylum so that they could be compared to chordates, echninoderms, and other animals.

Using Sanger, Roche 454, and/or Illumina MiSeq sequencing, the researchers tackled genomic DNA from sperm samples collected for outbred, diploid S. kowalevskii and P. flava worms in the Atlantic and Pacific Oceans, respectively.

The team's annotation of the genomes, helped along by transcriptome sequences generated by Roche 454 sequencing on acorn worm adult and developmental tissues, revealed some 19,270 predicted protein-coding genes in the S. kowalevskii genome and an estimated 18,556 coding genes in the genome of the P. flava.

The new genomes fleshed out the team's comparisons between deuterostome and non-deuterostome animals, offering a look at gene families that arose and/or expanded as the superphylum appeared.

Meanwhile, when they compared the acorn worm gene repertoires with those found in other deuterostomes — from the sea urchin and amphioxus to humans — the researchers encountered more than 8,700 homologous gene families in animals from the hemichordate, chordate, and echinoderm phyla.

The gene families include some 14,000 genes found in the genomes of humans and other modern-day deuterostome animals, the team noted, suggesting they belong to gene families that stretch back to the common deuterostome ancestor.

Similarly, the researchers scrutinized conserved splice sites, non-coding regulatory elements, and gene linkage patterns for clues to the ancestral deuterostome state, uncovering examples of gene clusters that continue to work together in animals from the deuterostome lineage.

In particular, their results pointed to a cluster of half a dozen pharyngeal genes and four transcription factors that appear to have contributed to pharynx-related structure formation since the advent of deuterostome animals.

"The presence of this cluster in the crown-of-thorns sea star, an echinoderm that lacks gill pores, and in amniote vertebrates that lack gill slits, suggest that the cluster's ancestral role was in pharyngeal apparatus patterning as a whole … and the cluster is retained in these cases because of its continuing contribution to pharynx development," the study's authors wrote.

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