The Secrets of the Snake Genome

I kept snakes as pets for most of my graduate career. It started with a pair of ball pythons, but grew to include a Colombian rainbow boa and a Brazilian rainbow boa before I had to find new homes for all of them. Snakes are fascinatingly different from us, which makes them excellent company for a budding biologist (or, as it turns out, a budding science writer). Watching them eat is always a remarkable experience. I'm still amazed by their incredibly flexible skulls, and I never quite managed to dispel a sympathetic sense of suffocation during their seemingly interminable meals. Of course, the snakes themselves weren't suffering; their windpipe opens in the front of their mouth, so they can breathe while devouring prey, and even splitting apart your skull is pretty mundane if you've evolved to do it.

Of course, kinetic skulls and anterior tracheas aren't the only special tricks these creatures have evolved. Most snakes eat infrequently and consume prey that's quite large compared to their body. In the period between meals (which can stretch for months!), snakes decrease their metabolic rate, alter their physiology, and remodel some of their organs. Once they've eaten, everything gets fired up for the arduous task of digestion. The ensuing changes are some of the most extreme fluctations seen in any vertebrate. The heart, kidney, liver, and intestine all grow dramatically within just a few days; in Burmese pythons, the liver doubles in mass after a meal! Venomous snakes have evolved another handy device: an array of toxins which they use to incapacitate their prey. To learn about the basis of these extreme phenotypes, a team of researchers sequenced the genome of the Burmese python (Python molurus bivittatus) and King Cobra (Ophiophagus hannah); they also sequenced the transcriptome in the venom gland of the cobra and in the heart, kidneys, small intestine, and liver of the Burmese python before and after feeding. The team, which consisted of nearly 40 scientists from 17 institutions in four countries, published their findings in a pair of papers published in the journal PNAS.

Todd Castoe, lead author of the python study, started working on the project as a post-doc in the Pollock lab at the University of Colorado; he's now an assistant professor at The University of Texas. “One of the fundamental questions of evolutionary biology is how vertebrates with all the same genes display such vastly different characteristics. The Burmese python is a great way to study that because it is so extreme,” he said in a press release. “We’d like to know how the snake uses genes we all have to do things that no other vertebrates can do.” Castoe's study furnished a list of thousands of genes which changed their expression levels in the heart, liver, kidneys or intestine in the few days after the python ate. Many of these genes showed signs of selection when the team compared the python, cobra, and green anole lizard (Anolis carolinensis) genomes.

In the partner study, the researchers sequenced the King Cobra's and studied the expression of genes involved in producing toxins in the venom gland. Many of them, they discovered, came from the duplication of a gene that was normally active elsewhere in the body. The duplicate copy then gets switched on in the venom gland and mutates into a toxic protein. The team's findings support an old theory which has fallen out of favour — that the venom system evolved by co-option of proteins normally expressed in the pancreas. "Our results give a unique insight into the evolution of one of the world's most advanced natural bioweapons," said Freek Vonk, lead author of the cobra study.

These papers are an important step forward in our understanding of how snakes evolved. The list of genes that they've uncovered will form the basis for future studies into biology of these amazing creatures. Learning more about snakes' physiological and morphological tricks has more than just intrinsic value; as Castoe points out, we've got essentially the same genes, so knowing how snakes do what they do may help us figure out ways to manage our body's response to a variety of diseases, or even regrow damaged organs. Not bad for a symbol of medicine and healing.

References
Vonk FJ, et al. The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system. Proceedings of the Nationall Academy of Sciences USA 110:20651–20656. (2013)
Castoe TA, et al. The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. Proceedings of the Nationall Academy of Sciences USA 110:20645–20650. (2013)
Press release and video from UTA.

Image credit
The Indian Cobra picture (not a King Cobra) is by user Kamalnv via Wikimedia Commons.