Acorn worm genome reveals evolution of human pharynx

HudsonAlpha researchers assemble two acorn worm genomes

Photo credit: Chris Lowe, Stanford University

Marine invertebrates like the acorn worm could help researchers better understand human evolution. Photo credit: Chris Lowe, Stanford University

Jeremy Schmutz, a faculty investigator at the HudsonAlpha Institute for Biotechnology in Huntsville, Ala., had never seen an acorn worm until he was asked to assemble the genome of one species of the marine invertebrate. But the results of Schmutz’s work helped researchers understand more about the 570 million year evolution of gills into the human pharynx and jaw. Those conclusions were published online Nov. 18 in Nature.

“We were asked to join the project because of our expertise and experience with genome assembly,” said Schmutz, who is also the co-director of the Genome Sequencing Center (GSC) at HudsonAlpha. “We were able to improve the contiguity of the sequence, and we’re pleased that the research team could use the genome to learn more about evolutionary development.”

Jerry Jenkins, PhD, the genome analysis group leader in the GSC, worked with Schmutz on piecing together the Saccoglossus kowalevskii genome, and he is one of the co-authors for the paper.

“Acorn worms are hard to raise in captivity, making them difficult to observe or study,” Jenkins said. “It was challenging for us to assemble and produce the acorn worm genome, and overall we were very satisfied with the results.”

Schmutz and Jenkins collaborated with Kim Worley, PhD, and her team at the Baylor College of Medicine, who sequenced and performed a preliminary assembly for the acorn worm.

“The GSC team crafted a high quality assembly that allowed us to study the conserved gene linkages between this worm and other species,” said Dan Rokhsar, PhD, who was one of the leaders for the sequencing effort. Rokhsar is the chief informatics officer and eukaryote super program head at the Department of Energy Joint Genome Institute. He is also a professor at UC Berkeley.

First hemichordate genome sequencing

The research team sequenced two acorn worm genomes for the project. The two genomes are the first to be sequenced for hemichordates, which are the ancestors of chordates. Chordates are animals with backbones and hollow nerve cords that include such seemingly different creatures as humans and sea squirts.

The marine worms — named for the acorn-like “nose” at the front of their bodies — burrow in ocean sediment and can be found along the shoreline as well as nearly two miles below the surface on the ocean floor.

“It’s an ugly beast,” John Gerhart, PhD, said. Gerhart is the senior author of the report and a professor at UC Berkeley. “Acorn worms look very different from chordates, which makes it especially surprising that they and chordates, like humans, are so similar on the genomic, developmental and cell biological levels.”–D3MeA

Acorn worm pharyngeal slits related to human pharynx

Gerhart and other scientists are interested in acorn worms and other hemichordates because their place in the evolutionary tree is close to the point where vertebrates branched off from invertebrates.

And the newly assembled acorn worm genomes made that connection even clearer, especially regarding pharyngeal slits. For an acorn worm to feed, seawater pumps through dozens of openings located just beneath the acorn cap on the worm, allowing the animal to capture nutrients, algae and bacterial prey. Those openings — called pharyngeal slits — evolved into gill slits in fish and other marine vertebrates and became specialized to extract oxygen from water, losing their filter feeding role.

The gill slits later evolved into today’s human upper and lower jaw and pharynx, which includes the thyroid gland, tongue, voice box and glands and muscles between the mouth and the throat. Early in embryonic development, humans and other vertebrates still develop vestigial gill slits near the throat; the slits never actually become gills, however.

“The presence of these slits in acorn worms and vertebrates tells us that our last common ancestor also had them, and was likely a filter feeder like acorn worms today,” Rokhsar said. “Acorn worms are marine invertebrates that, despite their decidedly non-vertebrate form, are nevertheless among our closest invertebrate relatives.”

When they compared the new acorn worm genome sequences to the genomes of other animals, the research team found clusters of genes on human chromosomes that were also clustered together on the acorn worm genome. Sometimes even the structure of the cluster was the same, although the two genomes diverged 570 million years ago.

“I hope these new sequences will encourage more people to study acorn worms,” Gerhart said.

The research group included 61 scientists from UC Berkeley; the Okinawa Institute of Science and Technology (OIST) Graduate University in Onna, Okinawa, Japan; Stanford University’s Hopkins Marine Station; the Baylor College of Medicine in Texas; the HudsonAlpha Institute for Biotechnology in Huntsville, Alabama; and the University of Oxford in the United Kingdom.

Rokhsar, who heads OIST’s Molecular Genetics Unit as a visiting professor, and Nori Satoh, head of OIST’s Marine Genomics Unit, co-led the project with Gerhart. Oleg Simakov of OIST and Takeshi Kawashima of the University of Heidelberg in Germany are first authors of the paper.