The genome of a prehistoric fish once thought to be extinct has been sequenced. What technical challenges were involved? Find out...
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04/18/2013 Rachael Moeller Gorman
In 2002, a lone coelacanth—a prehistoric fish once thought to be extinct—was caught off the coast of Africa. And now that sample has provided researchers with just enough DNA to sequence its genome, a feat that fills a major gap in our understanding of how water vertebrates came up onto land
Analysis of the sequence pinpoints genes important for thriving on dry land and helps explain why Latimeria chalumnae, the so-called “living fossil”, looks so similar to its 300 million year old fossilized ancestors. But assembling the genome wasn’t easy.
“The coelacanth is endangered, and it is rightfully very difficult to obtain samples,” said Jessica Alföldi, a researcher at the Massachusetts Institute of Technology (MIT) and Harvard’s Broad Institute who coordinated the team of 90 researchers from 33 institutions for this project and authored a paper published this week in Nature reporting the team’s findings (1).
“Once we had them, we were worried that we wouldn't have enough DNA to sequence using the old Sanger technology, so we waited for the next-gen technologies to come up to speed. Then we waited even more, because we just had one shot, so we didn't want to screw this up.”
Even after all the waiting, there was still not as much high molecular weight DNA as the team would have liked. Unlike other genomes that can be run mostly automatically through the ALLPATHS-LG short read genome assembler, the small amount of available coelacanthDNA required the team to spend several months manually improving the assembly.
The researchers wanted to sequence the fish’s DNA to ascertain whether its genome has actually evolved as little as its outward prehistoric appearance—complete with limb-like lobed fins—would suggest.
The modern fish looks eerily similar to its fossil; the team found that the coelacanth’s protein-coding genes are evolving significantly more slowly than those in tetrapods (four-limbed vertebrates), while the rest of the genome is changing at a normal rate. The scientists suggest this could be because the fish lives hundreds of feet below the ocean surface, where conditions have remained constant over the intervening millennia and where few predators prowl.
Due to its inaccessible habitat, the coelacanth had been presumed extinct for 70 million years until a South African trawler dredged one up in its net in 1938.
In addition, when comparing RNA sequence data from West African lungfish, they found that the coelacanth is not the closest living relative of tetrapods; it actually appears to be the lungfish, although the lungfish genome remains unsequenced because of its relatively large 50-100 Gb size.
The researchers also pinpointed genes and regulatory elements involved in the adaptation of animals to dry land. Genes involved in fin development, for example, were lost, while those coding for the urea cycle were altered. In water, animals can excrete pure ammonia because it is diluted before reaching toxic levels, but on land less toxic urea or uric acid is produced.
“Now, there is a lot of evolutionary research that can be done—to try to understand further why the coelacanth genes are slow-evolving, and to follow up on our efforts to understand how fins became limbs when fish first came up onto land,“ said Alföldi.
- Amemiya, C. T., J. Alföldi, A. P. Lee, S. Fan, H. Philippe, I. MacCallum, I. Braasch, T. Manousaki, I. Schneider, N. Rohner, et al. 2013. The african coelacanth genome provides insights into tetrapod evolution. Nature 496(7445):311-316