Horse Genome

In the movie Jurassic Park dinosaurs were cloned from old DNA genome that had miraculously survived from millions of years ago, In practice this is not very likely. The oldest genome so far from a prehistoric creature has been sequenced by an international team, led by scientists from the Natural History Museum of Denmark (University of Copenhagen). The team, which included Dr Jakob Vinther of the University of Bristol, sequenced and analyzed short pieces of DNA molecules preserved in bone-remnants from a horse frozen for the last 700,000 years in the permafrost of Yukon, Canada.

By tracking the genomic changes that transformed prehistoric wild horses into the present domestic breeds, the researchers have revealed the genetic make-up of modern horses with unprecedented detail. Their findings are published today in Nature.

The horse genome was first sequenced in 2007. The Horse Genome Project mapped 2.7 billion DNA base pairs. The horse genome is larger than the dog genome, but smaller than the human genome or the bovine genome. It encompasses 31 autosomes and two sex chromosomes.

DNA molecules can survive in fossils well after an organism dies, but not as whole chromosomes but as short pieces that could be assembled back together, like a puzzle. Sometimes enough molecules survive so that the full genome sequence of an extinct species could be resurrected and over the past few years, the full genome sequence of a few ancient humans and archaic hominid has been characterized but so far, none have been dated back more than 70,000 years. Now Dr Ludovic Orlando and Professor Eske Willerslev from Copenhagen's Center for GeoGenetics and colleagues have beaten this DNA-record by about 10 times to 700.000 years.

Sequencing the first genome from the Middle Pleistocene was by no means straightforward and involved collaboration between researchers from Denmark, China, Canada, the USA, Switzerland, the UK, Norway, France, Sweden and Saudi Arabia.

Dr Vinther's contribution to the study involved looking at the amino acid composition of the bone with a Time of Flight Secondary Ion Mass Spectroscope (TOF-SIMS). This analysis revealed the presence of abundant secondary ions characteristic of amino-acid peptides, particularly glycine, proline and alanine. These amino acids are characteristic of collagen which suggested that proteins had survived in situ.

Dr Orlando said: "We first got excited when we detected the signature of amino-acids that suggested proteins had survived. We got more excited when we proved able to directly sequence collagen peptides. When we detected blood proteins, it really started looking promising because those are barely preserved. At that stage, it could well be that ancient DNA could also be preserved."

Using Helicos true Single DNA Molecule Sequencing, the researchers managed to identify molecular preservation niches in the bone and experimental conditions that enabled finishing the full genome sequence.

Sequencing the genome allowed the scientists to track major genomic changes over the last 700,000 years of evolution of the horse lineage. By comparing the genome in the 700,000-year-old horse with the genome of a 43,000-year-old horse, six present day horses and the donkey, they found that the last common ancestor of all modern equids was living about 4.0-4.5 million years ago. Therefore, the evolutionary radiation underlying the origin of horses, donkeys and zebras reaches back in time twice as long as previously thought.

The evolution of the horse pertains to the descent of the modern horse from the small, dog-sized, forest-dwelling Eohippus over a period of some 50 million years. Paleozoologists have been able to piece together a more complete picture of the modern horse's evolutionary lineage than that of any other animal.

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Horse Genome