How is the dna of a mouse different from the dna of a snake?

By Lori Garrett-Hatfield

With the discovery of the structure of deoxyribonucleic acid, and the technology to sequence the genomes of both humans and animals, it is no surprise to find that we have a lot in common with our animal friends. How much humans have in common with animals may come as a bit of a shock. While it is understandable that we share DNA with our cousins the apes, we also share DNA with other, less simian animals.

Humans are most closely related to the great apes of the family Hominidae. This family includes orangutans, chimpanzees, gorillas, and bonobos. Of the great apes, humans share 98.8 percent of their DNA with bonobos and chimpanzees. Humans and gorillas share 98.4 percent of their DNA. Once the apes are not native to Africa however, the differences in DNA increase. Humans and orangutans share 96.9 percent of their DNA. Humans and monkeys share approximately 93 percent.

Humans and mice share nearly 90 percent of human DNA. This is important because mice have been used in laboratories as experimental animals for research into human disease processes for years. Mice are currently used in genetic research to test gene replacement, and gene therapy because they have similar gene types to those of humans and will have similar reactions to diseases and disease processes.

Humans and dogs share 84 percent of their DNA, which again, makes them useful animals to study human disease processes. Researchers are particularly interested in specific diseases that affect both dogs and humans. Retinal disease, cataracts, and retinitis pigmentosa blind both humans and their canine friends, and scientists study and research treatments of the disease in dogs in the hope that the same treatments will be beneficial to humans. Dogs are also being studied and treated for cancer, epilepsy, and allergies, to find more successful treatment for humans.

Of course, humans, dogs, mice and apes are going to have DNA in common. They are all mammals. Humans and birds are a different matter. Yet they, too, share a lot of DNA -- 65 percent. Understanding the similarities and differences between human and avian DNA is important. First, because chickens make proteins, such as interferon, that are helpful to human immunity, and need to be further studied. Second, because viruses like the ones that cause the flu cross between birds and humans and need to be studied so that vaccines can be invented and improved.

The ancestors of today's slithery snakes once sported full-fledged arms and legs, but genetic mutations caused the reptiles to lose all four of their limbs about 150 million years ago, according to two new studies.

The findings are welcome news to herpetologists, who have long wondered what genetic changes caused snakes to lose their arms and legs, the researchers said.

Both studies showed that mutations in a stretch of snake DNA called ZRS (the Zone of Polarizing Activity Regulatory Sequence) were responsible for the limb-altering change. But the two research teams used different techniques to arrive at their findings. [Image Gallery: Snakes of the World]

According to one study, published online today (Oct. 20) in the journal Cell, the snake's ZRS anomalies became apparent to researchers after they took several mouse embryos, removed the mice's ZRS DNA and replaced it with the ZRS section from snakes.

The swap had severe consequences for the mice. Instead of developing regular limbs, the mice barely grew any limbs at all, indicating that ZRS is crucial for the development of limbs, the researchers said.

"This is one of many components of the DNA instructions needed for making limbs in humans and, essentially, all other legged vertebrates. In snakes, it's broken," the study's senior author Axel Visel, a geneticist at the Lawrence Berkeley National Laboratory in California, said in a statement.

Pinpointing ZRS

Visel and his colleagues began looking at the genomes of "early" snakes that were closer to the base of the snake family tree — such as the boa and python — that have vestigial legs, or tiny bones buried within their muscles. The scientists also studied "advanced" snakes, including the viper and cobra, which do not have any limb structures.

During their investigation, the researchers focused on a gene called sonic hedgehog, which is key in embryonic development, including limb formation. Sonic hedgehog's regulators, located in the ZRS sequence of DNA, had mutated, they found.

However, the researchers needed proof that the ZRS mutations were responsible for limb loss. To find out, they used a DNA-editing technique called CRISPR (short for "clustered regularly interspaced short palindromic repeats") to cut out the ZRS stretch in mice embryos and replace it with the ZRS section from other animals, including snakes.

When the mice had ZRS DNA from other animals, including humans and fish, they developed limbs just like any regular mouse would. But when the researchers inserted the python and cobra ZRS into the mice, the mice's limbs barely developed, the researchers found.

Next, the researchers took an in-depth look at the snakes' ZRS, and found that a deletion of 17 base pairs (that is, paired DNA "letters") within the snakes' DNA appeared to be the cause of the limb loss, they said. When they painstakingly "fixed" the mutations in the snake ZRS and inserted it into mice embryos, the mice grew normal legs, they found. [Photos: Weird 4-Legged Snake Was Transitional Creature]

However, creatures usually have redundant DNA that protects against mutations such as these, so it's likely that multiple evolutionary events led to limb loss in snakes, Visel said.

"There's likely some redundancy built in the mouse ZRS," he said. "A few of the other mutations in the snake ZRS probably also played a role in its loss of function during evolution."

Snake femurs

Adult snakes don't have limbs, but extremely young snake embryos do, according to the other study, published online today in the journal Current Biology.

Like the researchers of the Cell study, the scientists found that snake ZRS had disabling mutations that prevented limb development. However, they also found that during the first 24 hours of their existence, python embryos have a "pulse of sonic hedgehog transcription [the first step of gene expression] in just a few limb bud cells," said the study's senior author Martin Cohn, a professor of molecular genetics and microbiology at the University of Florida College of Medicine.

But that transcription switches off within a day of the egg being laid, meaning that the snake cannot fully develop legs, Cohn and his co-author Francisca Leal, a doctoral student in Cohn's lab, found.

"Python ZRS proved to be very inefficient, turning on transcription for a short time in a few cells," Cohn said.

However, even during that short time, python embryos managed to begin development for leg bones such as a femur, tibia and fibula, the researchers found. "[But] those distal structures degenerate before they fully differentiate into cartilage, and python hatchlings are left with just a rudimentary femur and a claw," Cohn said. He added, "the results tell us that pythons have retained a lot more of the leg than we appreciated, but the structures are transitory and are found only at embryonic stages."

Cohn called the Cell study, "a tour de force" and "absolutely thrilling."

"The two groups took very different approaches to the question of limb loss in snakes," Cohn said. "Axel [Visel]'s group started with genomics, and we started with developmental biology, and the two groups converged on exactly the same discovery."

Original article on Live Science.

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King Cobra (Ophiophagus hannah; top) and Burmese Python (Python bivittatus; bottom), the two snake species whose genomes were fully sequenced in 2013

One year ago today, the first snake genomes ever sequenced hit the newsstands. OK, so two papers in Proceedings of the National Academy of Sciences isn't exactly the cover of Time magazine to most people, but it was big enough news that it was covered by The Huffington Post and the two most prominent interdisciplinary scientific journals, Science and Nature, the former devoting a special section to the event. One year later, dear reader, welcome to the Life is Short, but Snakes are Long coverage of the snake genome project. So just what is the big deal about these snake genomes anyway, and what's changed in snake biology in the year that they've been available?

In one way, sequencing a snake genome means that snakes finally join the illustrious ranks of lab animals like the mouse, rat, guinea pig, fruit fly, and amoeba, all of whom have already had their genomes sequenced. By now the genomes of several hundred species have been sequenced, starting with a virus in the 1970s, and the first archaeon, bacterium, and eukaryote within one year of one another in 1995-96. The first animal genome sequenced was that of the model nematode Caenorhabditis elegans in 1998, and the first vertebrate was a pufferfish, so chosen because its genome is so small, in 2002 (although an incomplete first draft of the human genome preceded that by a year). As of 2014, we're now up to just over 100 vertebrate species, about 60 of which have been annotated and formally published, as well as numerous other animals, plants, fungi, protists, and prokaryotes. Last week, Science highlighted drafts of 38 new bird and 3 new crocodilian genomes, the largest single release of vertebrate genomes to date. But we are still a long way from sequencing the genomes of all known species. Why have we chosen the species we have? What does it mean to sequence a genome, exactly, and why do we do it?

We use the word genome to refer to all the DNA within a single organism. Confusingly, this is not quite the same thing as saying all the genes in an organism, because we usually only call sections of DNA "genes" if we know what they do. You've probably heard that 98% of the human genome is "junk", or non-coding, DNA, which is just another way of saying that we haven't figured out what it does yet. Actually, we now know lots of things that non-coding DNA is good for, but we still usually don't call most of that DNA "genes" because we use that word specifically to mean sections of DNA that are read out via RNA and translated (usually) into proteins, which then have obvious effects on cells and the body. Non-coding DNA can also have effects on the body, often by regulating other genes, but it works in a more complicated way that we don't yet fully understand, so we tend make over-generalizations about it or dismiss it as unimportant.

Avian tree of life based on whole-genome sequences. We're still several years away from a tree like this for squamate reptiles. From Jarvis et al. 2014

Understanding the genes controlling variation among individuals of the same species, like the color morphs of these Groundsnakes (Sonora semiannulata), must await population genomics and a better understanding of gene expression regulation

• Snake genomes are about half the size of the human genome (although an organism's complexity is not directly proportional to its genome size; for example, some salamander genomes are more than 60 times larger than the human genome).
• The proportion of repetitive elements (the most common form of "junk DNA") in snake genomes is about the same as that in humans (~60%).
• Snakes have a faster baseline rate of evolution than other reptiles, birds, or mammals, as evidenced by their larger accumulation of neutral substitutions. And colubroid snakes have rates even faster than that of snakes at large.
• Adaptive evolution (as evidenced by functional, non-neutral, changes to genes) in snakes has happened to over 500 genes, especially those involved in the development of the limbs, spine, skull, and eye, and those regulating the function of the cardiovascular system, lipid and protein metabolism, and cell birth and death. We already knew that all of these systems in snakes were highly modified relative to other vertebrates, and now we know that the genes that underlie them are too.
• Some groups of genes have grown or shrank in snakes - for example, snakes have a lot more genes coding for vomeronasal receptors, and a lot fewer genes coding for opsins, which are light-sensitive proteins in the eye. This makes sense given what we know about snake sensory systems.
• Changes to gene expression that happen after a snake feeds involve thousands of genes that control rapid changes in organ size—but genes that control cell division change in the kidney, liver, and spleen, organs that grow by cell division, but not in the heart, which grows when individual existing cells get larger.
• Snake genomes contain endogenous viral elements from three families of viruses that have recurrently infiltrated their DNA over the past 50 million years. This is actually not rare, although it is bizarre and awesome that the 'fossils' of these ancient viral genomes can be identified in their host genomes even after tens of millions of years, and it can help us better understand both the biology of viruses and that of their snake hosts, including how viruses have contributed functions to the genetic repertoires of their hosts.

1. A snake has a gene that makes a protein somewhere in its body, including possibly in its salivary or venom gland5
2. The gene for that protein is duplicated by accident during routine DNA replication or repair, resulting in a new, spare copy of the gene
3. The effects of selection are relaxed on the duplicate gene, which gives it opportunities to mutate (because, if it does, no harm is done; the original copy continues to perform its original function)
4. Mutations to transcription-factor binding sites change the signal for where the duplicate gene should be expressed, causing the new protein to be made only in the venom gland
5. If the new protein helps the snake catch more prey, it improves fitness and causes natural selection
6. Because the old protein is still being made, the new gene and protein are free to evolve to become more toxic or to take on some new function
7. The new copy of the gene may become duplicated again, and subsequent new copies may mutate further, leading to diversification within a gene/toxin family6

The King Cobra venom gland, with expression profiles of the venom (left) and accessory gland (right). From Vonk et al. 2013

The cobra genome by itself does not answer these questions, even with help from that of the python. In order to fully understand the evolution of snake venoms (with major implications for public health, particularly in developing countries, not to mention the potential of venoms to be used as drugs), we'll need genomic, transcriptomic, and proteomic data from numerous snake species.

Characterization of genomic biodiversity has the potential to change our understanding of evolution in fundamental ways. From explaining how snakes are capable of physiological feats to helping us understand how new genes appear, what "junk DNA" does, and what the tree of life looks like, genome sequencing is one of the most exciting current frontiers in biology. As in many things, snakes are (one of) the last groups of vertebrates to the party (although it's worth noting that there aren't any fully annotated salamander or caecilian genomes yet). A snake genome doesn't add a whole lot to the picture of the vertebrate tree of life, because the Green Anole genome, sequenced in 2011, represents squamates on the tree, and no one is arguing that snakes aren't squamates. But, within squamates there are a number of puzzling unresolved relationships, including such fundamental questions as the origin of snakes and the placement of iguanians. In the interest of helping to shed light on these, and on the aforementioned complexity of snake venom evolution, another 10 or so snake genomes are likely to come out within the next couple of years, including those of the:

• Texas Blindsnake (Rena dulcis)
• Reticulate Wormsnake (Amerotyphlops reticulatus)
• Red Pipesnake (Anilius scytale)
• Mexican Burrowing Python (Loxocemus bicolor)
• Round Island Splitjaw Snake (or "boa"; Casarea dussumieri)
• Boa Constrictor (Boa constrictor)
• Western Diamond-backed Rattlesnake (Crotalus atrox)
• Speckled Rattlesnake (Crotalus mitchelli)
• Copperhead (Agkistrodon contortrix)
• Eastern Coralsnake (Micrurus fulvius)
• Cloudy Snail-eating Snake (Sibon nebulatus)
• Common Gartersnake (Thamnophis sirtalis)

As you can probably see if you know your snake taxonomy, these species represent a scattering of well-known snakes from each of the major branches of the snake tree. They have been strategically chosen to enable snake biologists to use them to put together a well-supported skeleton of the snake tree of life. However, several branches (such as the dwarf pipesnakes, acrochordids, and lamprophiids) are still missing.7 In particular, an atractaspidid genome would be useful in building a better understanding of the role of convergence in snake venom evolution - resolving the debate between proponents of a single ancient origin for venom and those of several more recent, independent origins. Genomes of scolecophidian blindsnakes and toxicoferan lizards such as Gila monsters will also help resolve this question. Hopefully, these genomes and others will continue to illuminate evolutionary biology for us in ways Darwin could have scarcely imagined.

1 Because genome sequences contain so much data, they are stored electronically and require a large amount of computing power and storage capacity. The computing power is actually more limiting than the biochemistry right now. A human genome contains about 6 billion base pairs (one for each person on Earth in 1999), which take up a couple of gigabytes. If that doesn't sound that impressive, imagine all that information stored in every one of your cells, then compare the size of a cell with that of a microchip here.↩


2 This is not to say that (as has been presumed by many) molecular data are inherently superior to morphological data, especially in the case of extinct fossil taxa, from which we cannot garner much molecular information (although that generalization too has been challenged).↩

3 How are the individuals whose genomes are sequenced chosen? The unsatisfying answer is that the scientists involved typically use whatever individuals are convenient. Specifically, the cobra and python genomes seem to have been taken from animals from the pet trade. We may not know the true geographic origin of these individuals, or even whether they might be the offspring of animals from two or more different parts of the species' range. Why is this important? If we sequence the genome of a cobra from Indonesia, but cobras in India have evolved different venom genes because of different evolutionary pressures, then we won't know that until we get some cobras from India. Taxonomic conclusions drawn from Boa constrictor gene sequences on GenBank are dubious because of the ambiguous origins of many of these specimens. The primary reasons to sequence a whole genome are subtly different from the reasons to sequence individual genes, and scientists doing these tasks have different questions. But, we should be cautious about inferring too much from the genome sequence of a single individual of any species.↩

4 Right now if you're a human you can actually get your whole genome sequenced for less than $5000, even though the first human genome cost over $3 billion, because we've optimized the process.↩

5 It's unclear how many venom proteins were originally made in the venom gland before they became toxic, and how many were recruited to this tissue following duplication. The original cobra genome paper by Vonk et al. implies that the latter is most common, whereas subsequent work by Hargreaves et al. uses gene expression data from Leopard Gecko salivary glands to suggest the former. Reyes-Velasco et al. used the python genome and transcriptome to suggest that venom genes are recruited preferentially from genes that are expressed at low levels in most tissues but at more variable levels than average across tissues.↩

6 Of the approximately 24 gene families that code for snake venom proteins, those that produce toxins that are known to be important in prey capture (e.g., the three-finger neurotoxins) have undergone repeated duplication and selection, whereas venom components that perform ancillary functions, such as helping the snake to relocate its bitten prey, do not show high rates of duplication or selection. These rates are probably further influenced by the need to target diverse receptors in different types of prey (in snakes with broad diets), and by predator-prey co-evolutionary arms races (in snakes with narrow diets).↩

7 A recent effort by a different research group generated a tree for Caenophidia using 333 loci totaling 225,140 base pairs for each of 31 snake species, almost 80,000 of which were informative. This is a drastic improvement on the 10 loci and maximum of 5,814 base pairs of the most comprehensive previous studies, but it is still a long way from the entire genome. Incredibly, they were still unable to resolve certain difficult parts of the snake family tree.↩

ACKNOWLEDGMENTS

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