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New Genome Sequence Provides Clues About Vertebrate Evolution

NEW YORK (GenomeWeb News) – Scientists today reported that they have sequenced the genome of a small marine invertebrate — a feat that is providing a wealth of information about vertebrate evolution.
In a paper published online today in Nature, an international team of researchers report sequencing the genome of an amphioxus (also called lancelet) species called Branchiostoma floridae. The sequence provided them with information not only about relationships between chordate groups, but also about the characteristics of their shared common ancestor.
Three additional papers appearing online in Genome Research today include analyses of amphioxus sequence data to answer specific questions about vertebrate evolution.
Amphioxus are small, eel-like invertebrate chordates that live at the bottom of the ocean. Called cephalochordates, amphioxus share a common ancestor with vertebrates and urochordates, such as sea squirts. And, like other chordates, amphioxus have a segmented body plan, a hollow dorsal nerve tube and a notochord, a post-anal tail and gill slits.
“Amphioxus was selected because of its evolutionary relationship to vertebrates,” lead author Nicholas Putnam, a post-doctoral fellow affiliated with the US Department of Energy’s Joint Genome Institute and the University of California at Berkeley, told GenomeWeb Daily News. “It’s one of the living relatives to the vertebrate phylogenetically.”
The amphioxus genome sequence is helping to clarify relationships between the three chordate groups, he noted. At one time it was widely believed that amphioxus was a sister branch to vertebrates. But mounting evidence suggests that they are actually more distantly related than sea squirts and other urochordates.
Indeed, the amphioxus genome sequence supports the idea that amphioxus branched off from the chordate common ancestor before urochordates, diverging from vertebrates some 520 million years ago.
As such, the sequence shines new light on the relationships between living chordates. It also provides clues about the characteristics of their ancient common ancestor. “It gives sort of a starting point for changes that happened on the vertebrate stem,” Putnam said.
Putnam and his co-workers used whole-genome shotgun sequencing to sequence the roughly 520 megabase amphioxus genome, with collaborators at Japan’s RIKEN Genomic Sciences Center sequencing the BAC ends and ESTs.
The genome proved to be highly polymorphic — more so than that of any other organism reported so far — containing an estimated 21,900 protein-coding loci.
Using comparative genomics, the researchers identified genes that were conserved between amphioxus and vertebrates. They found another, somewhat surprising, similarity: non-coding sequences. “We weren’t expecting it, but we did find a number of conserved non-coding sequences,” Putnam said.
The researchers also found evidence that vertebrate genomes have undergone two rounds of whole-genome duplication. That’s consistent with the idea — first proposed by Susumu Ohno in 1970 — that genome duplication and vertebrate evolution go hand-in-hand.
In addition, the researchers wrote, it’s “tempting to speculate” that these genome duplications in ancestral jawed vertebrates paved the way for complex body plans and physiology. Consistent with this notion, they noted, genes linked to processes such as developmental signaling and gene regulation are often present in multiple copies in living vertebrates.
In a companion paper appearing in Genome Research, lead author Linda Holland, a marine biologist at Scripps Institution of Oceanography in La Jolla, and her colleagues delved more deeply into chordate evolutionary patterns by looking at specific genes, gene families, and conserved non-coding regions in amphioxus.
“[I]n many respects, amphioxus reflects the primitive pre-vertebrate condition, yet it also exhibits uniquely specialized features that arose in the half a billion years after its divergence from the rest of the chordate lineage,” Holland and her co-workers wrote.
In another Genome Research paper, a group of researchers from Sun Yat-sen University in Guangzhou, China, used the amphioxus genome sequence to help them study the evolution of innate immunity in vertebrates — the part of the immune system that responds directly to pathogens and other interlopers without adaptation. They found that “amphioxus, a species without vertebrate-type adaptive immunity, holds extraordinary innate complexity and diversity.”
In a third Genome Research paper, Marianne Bronner-Fraser, a biologist at the California Institute of Technology, led a team of researchers investigating the evolution of neural crest cells, cells involved in forming vertebrate heads and faces, as well as the peripheral nervous systems.
They found neural crest gene homologues in the amphioxus genome. But these genes aren’t used in quite the same way they are in vertebrates, suggesting that vertebrates may have usurped the genes for new purposes during evolution.
“I would say that this genome sequence is an example — along with the sea anemone and the sea urchin and hemichordate … of a dramatic increase in the sampling of animal diversity that is represented by whole-genome data sets,” Putnam said. In the future, he and others are interested in investigating the specific changes in both genome organization and gene families that are underlying this sort of major evolutionary transition.  

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