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Genome Analysis Suggests Elephant Sharks See Color

NEW YORK (GenomeWeb News) – A new genomic analysis suggests the elephant shark, which belongs to a group representing the oldest living jawed vertebrates, can see in color.

Researchers from Singapore and the UK searched the elephant shark genome photoreceptor genes, identifying three functional cone genes and one rod gene. Their results, published in this month's issue of Genome Research, suggest elephant shark color vision genes are functional but short wavelength shifted.

"It was unexpected that a 'primitive' vertebrate like the elephant shark had the potential for color vision like humans," co-senior author Byrappa Venkatesh, a molecular biologist at Singapore's Institute of Molecular and Cell Biology, said in a statement. "The discovery shows that it has acquired the traits for color vision during evolution in parallel with humans."

Along with related studies, including one revealing ultraconserved elements in the elephant shark genome, the research suggests the elephant shark has preserved many ancestral genome features and is a useful organism for understanding vertebrate evolution.

Elephant sharks are cartilaginous fish living in New Zealand and southern Australia. Its basal position in the jawed lineage, combined with its compact genome, has made the animal alluring from the research standpoint.

In early 2007, a team of researchers from the J. Craig Venter Institute and Singapore's Institute of Molecular and Cell Biology reported that they had sequenced the elephant shark genome to about 1.4 times coverage, generating sequence representing some 75 percent of the genome.

Since then, researchers have been mining the elephant shark genome for clues about vertebrate evolution. For instance, in a study appearing in the Proceedings of the National Academy of Sciences last spring, Venkatesh and his colleagues reported that the elephant shark genome has retained some protocadherin genes that have been lost in other jawed vertebrates.

"Interestingly, comparisons between the genomes of the elephant shark and other species have identified many unexpected features, such as the conservation of ancient non-coding elements, a high degree of synteny, and the presence of specific ancient genes that have been lost in subsequent teleost and tetrapod radiations," Venkatesh and his co-authors wrote.

For the latest study, Venkatesh and his colleagues used the TBlastn, Blastx, and 5'- and 3'-RACE to hunt for visual pigment genes in the elephant shark genome. Their search turned up three cone opsin pigment genes — Rh2, LWS1, and LWS2 — as well as one rod opsin pigment gene, Rh1. As in humans, the cone genes seem to have arisen through gene duplication.

The researchers didn't find genes for the short wavelength-sensitive cones found in other vertebrates. Even so, when they cloned and expressed Rh1, Rh2, LWS1, and LWS2 — middle and long wavelength-sensitive pigments — in vitro, the team found that all four pigments were short wavelength shifted.

Together, the results suggest elephant sharks possess a color vision system that's similar to but distinct from that used by primates. Based on their findings and comparisons with visual systems characterized in other fish, the researchers speculated that the modified color vision system found in elephant sharks may be adapted to dealing with light conditions between deep and shallow water, since elephant sharks live in both at some point in their lives.

Venkatesh said in a statement that the researchers plan to complete the entire elephant shark genome early next year. And down the road the researchers expect that the animal's genetic code will yield even more clues about vertebrate evolution and genetic elements shared by humans and the elephant shark.

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