A large group of genetic scientists has sequenced and analyzed the complete genome of the elephant shark (Callorhinchus milii).
The elephant shark, Callorhinchus milii. Image credit: Fir0002 / Flagstaffotos, via Max-Planck-Gesellschaft.
Their study, published in the journal Nature, is the first whole-genome analysis of a cartilaginous fish.
Cartilaginous fishes include sharks, rays and skates. Together with bony fish, birds, reptiles, amphibians and mammals, they make up the branch of jawed vertebrates on life’s family tree.
The elephant shark, also known as the Australian ghostshark or elephantfish, is a curious-looking fish with a snout that resembles the end of an elephant’s trunk.
Among the cartilaginous fishes, the elephant shark was selected for sequencing because of its compact genome, which is one-third the size of the human genome. The shark lives in the waters off the southern coast of Australia and New Zealand, at depths of 200 to 500 m, and uses its snout to dig for crustaceans at the bottom of the ocean floor.
By comparing the genome of this shark species with human and other vertebrate genomes, the team has revealed why the skeleton of sharks is cartilaginous.
The findings also have important implications for understanding bone diseases such as osteoporosis and for developing more effective therapies to treat these conditions. Findings related to the elephant shark’s immune system provide new opportunities for studying adaptive immunity in humans and for formulating new strategies to fine-tune the immune response.
“We now have the genetic blueprint of a species that is considered a critical outlier for understanding the evolution and diversity of bony vertebrates, including humans,” said senior author Wesley Warren, PhD, research associate professor of genetics at The Genome Institute at Washington University School of Medicine.
“Although cartilaginous vertebrates and bony vertebrates diverged about 450 million years ago, with the elephant shark genome in hand, we can begin to identify key genetic adaptations in the evolutionary tree.”
The elephant shark genome is relatively small, consisting of slightly fewer than a billion DNA base pairs compared with 3 billion base pairs in humans.
But this spare sequence has yielded some intriguing details. For instance, the elephant shark lacks the genes for secreted phosphoproteins, which may explain why their cartilage is not converted into bone as in the other jawed vertebrates.
They also lack the genes for several key immune system cells and protein receptors in the adaptive immune system. This finding may suggest that the adaptive immune system in jawed vertebrates gradually became more elaborate over time.
“One of the most notable features of the elephant shark’s genome is its incredibly slow rate of evolution. Even slower than in ‘living fossils’ such as the coelacanth, the elephant shark’s genome has not changed substantially in hundreds of millions of years,” said study co-author Dr Scott Roy of San Francisco State University.
This slow rate of evolution was uncovered in part by the analysis of the genome’s introns (the part of the genetic sequence that interrupts genes, and must be spliced out before the gene can be expressed). In vertebrates, these introns can be thousands of DNA letters long and must include their own splicing instructions.
There have been very few intron changes in the elephant shark genome, but this isn’t entirely surprising.
“It’s pretty well established in vertebrates that very little of this intron loss and creation occurs. It would be a rare and weird physical event for this many nucleotides to exactly appear or disappear in a genome. It’s unlikely to have that big of a change exactly and all at once,” Dr Roy said.
The elephant shark genome helps to confirm that the lack of intron loss and gain is a general characteristic of vertebrates. In close invertebrate relatives such as the tunicates (which include marine animals such as sea squirts), the rate of intron evolution is much faster.
“Because vertebrate introns are very long, this may make it harder to create and delete them. In some tunicates, introns are about 40 nucleotides long, and this simply may make it easier for them to come and go over time,” Dr Roy explained.
The time between generations also tends to be much swifter in invertebrates than vertebrates, which may increase the opportunity for mutations to accumulate in invertebrate genomes.
These slow-changing introns also helped the team clarify the relationship between cartilaginous fish and other jawed vertebrates. These relationships can be determined by comparing gene sequences between organisms, and introns can be especially helpful in this analysis.
“Because things are changing so slowly with introns, the chance that two species will share a change is likely to be very small unless they are closely related,” Dr Roy said.
The researchers found a very clear signal that bony fish and other bony vertebrates including mammals are all more closely related to each other than either group is to the cartilaginous fishes.
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Byrappa Venkatesh et al. 2014. Elephant shark genome provides unique insights into gnathostome evolution. Nature 505, 174–179; doi: 10.1038/nature12826
