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Genome Sequence Provides Peek at Visual Capabilities of Pacific Bluefin Tuna

NEW YORK (GenomeWeb News) – Patterns in the Pacific bluefin tuna genome suggest the fish may owe some of its predatory prowess to adaptations involving visual pigment genes.

As they reported in the early, online version of the Proceedings of the National Academy of Sciences, Japanese researchers used a combination of next-generation sequencing platforms to sequence and assemble a draft diploid genome for the Pacific bluefin tuna, Thunnus orientalis.

A dive into the newly sequenced genome — together with sequences from other sequenced fish — helped the team track down adaptations to sets of genes coding for various pigments. In particular, the bluefin genome appears to contain an extra green-sensitive RH2 gene, along with gene substitutions and/or duplications predicted to bolster the fish's ability to see blue-green contrast.

A better appreciation of the bluefin tuna's visual propensities is expected to prove useful for understanding the biology of wild tuna stocks, the study's authors noted. Beyond that though, they proposed that these and other genetic features could offer hints for matching bluefin tuna fish to suitable aquaculture environments.

"In tuna aquaculture … a high mortality due to wall collisions has been problematic," the Fisheries Research Agency's Kiyoshi Inouye, senior author on the study, and his colleagues wrote, "which can be considered as an adverse consequence of adaptation to the bluish pelagic environment."

"The findings we present here are thus applicable for design of tuna farms: perceptible and high-contrast coloring," they added. "In particular, because tuna is still difficult to culture and handle for experimental approaches, genomics strategy [are] widely expected to complement physiological studies on tuna."

Though much vaunted for its predatory capabilities in the ocean, tuna's position in the wild is precarious in some parts of the world, the team noted, owing to commercial demands on tuna stocks.

And while past studies have started to unravel physiological features behind tuna species' predatory success — offering clues to the fish's visual dexterity, for instance — the genetics and evolutionary history of important tuna traits remain more mysterious.

In an effort to more clearly characterize the ticket to tuna's success in the wild, the researchers put together a draft genome sequence for Pacific bluefin tuna, scouring it for information on the opsin genes that code for components of the fish's visual system.

Using Roche 454 GS FLX Titanium and Illumina GAIIx instruments, they sequenced genomic DNA from a wild male Pacific bluefin tuna from Amami, Japan.

From that shotgun sequence data, they assembled a draft assembly covering around 92.5 percent of the fish's genome, estimated at roughly 800 million base pairs in all.

The sequence housed 26,433 predicted protein-coding genes, according to the team's annotation efforts, which were helped along by RNA sequence data from 10 tuna tissues as well as existing sequence data for the Atlantic bluefin tuna.

That coding repertoire included 10 genes from opsin groups: five RH2 genes, which encode green-sensitive rhodopsin proteins; two SWS2 genes coding for blue-sensitive genes; and one copy apiece of red-sensitive opsin, UV light-sensitive opsin, and rhodopsin 1 genes (known as M/LWS, SWS1, and RH1, respectively).

The same sorts of visual pigments are found in other teleost fish, too, the researchers reported.

But their analysis indicated that the Pacific bluefin tuna genome has been home to amino acid substitutions, gene duplications, and/or gene duplication events that alter the so-called spectral tuning of certain opsin genes — adaptations to visual pigment genes that are predicted to make bluefin tuna especially adept at seeing blue-green contrasts.

"[M]olecular evolutionary changes in three opsin genes, RH1, RH2, and SWS2, may have occurred around the time when the ancestor of tuna appeared or diverged," Inouye and colleagues concluded.

"All of the changes are involved in blue-green light sensitivity," they wrote.

"In Pacific bluefin tuna, particularly, not only stepwise duplications of RH2 genes but also gene conversions in such multicopy genes (including SWS2) may have facilitated the functional diversification of spectral tuning to the offshore environment, which are useful for detecting bluish contrasts."