Wednesday, 3 July 2013

Scientists Decode the Genomic Sequence of 700,000-year-old Horse

Scientists Decode the Genomic Sequence of 700,000-year-old Horse
Wednesday, 03 July 2013

The international team, which included researchers from University of Copenhagen, BGI and other institutes, has successfully sequenced and analysed the short pieces of DNA preserved in bone-remnants from a horse frozen for the last 700,000 years in the permafrost of Yukon, Canada. This is the oldest genome reported so far, which is ten times as old as the ancient Denisovan genome reported in last year. The work here laid a solid foundation for researchers to further decode other extinct species and clarify biology evolution.

The Thistle Creek horse fossil, found by Dr Duane Froese from the University of Alberta in 2003, was from an interglacial organic unit associated with the Gold Run volcanic ash, about 700,000 years old – representing some of the oldest known ice in the northern hemisphere. DNA molecules can be well reserved in species fossils, not as whole chromosomes but as short pieces, while theoretical and empirical evidence suggest the age of this horse fossil approaches the upper limit of DNA survival.

After analysis, the ancient horse bone revealed secondary ion signatures typical of collagen within the bone matrix, including blood-derived peptides. This is consistent with good biomolecular preservation thus possible DNA survival. The team then conducted larger-scale destructive sampling for Illumina and Helicos sequencing to identify molecular preservation niches in the bone and experimental conditions that enabled finishing the whole genome sequence.

Compared with the genomes of a pre-domestication horse, a modern donkey, five modern domestic samples and one modern Przewalski horse, researchers found all contemporary horses, zebras and donkeys originated 4.0~4.5 million years ago – twice the conventionally accepted time to the most recent common ancestor of genus Equus. The study also shows that there were many demographic fluctuations occurred in horse populations in the past two million years, especially during the period of major climatic changes.

The study suggests that the Przewalski and domestic horse populations may diverge 38,000-72,000 years ago, and there is no cross-breeding between the two types of horses. All these findings also provide the evidence that the Przewalski does represent the last survivor of wild horses. The team also found the evidence supporting the continuous selection of the immune system and olfaction throughout horse evolution, and dozens of genomic regions that are likely to be taken as genetic markers during the domestication.

About BGI
BGI was founded in Beijing, China, in 1999 with the mission to become a premier scientific partner for the global research community. The goal of BGI is to make leading-edge genomic science highly accessible, which it achieves through its investment in infrastructure, leveraging the best available technology, economies of scale, and expert bioinformatics resources. BGI, and its affiliates, BGI Americas, headquartered in Cambridge, MA, and BGI Europe, headquartered in Copenhagen, Denmark, have established partnerships and collaborations with leading academic and government research institutions as well as global biotechnology and pharmaceutical companies, supporting a variety of disease, agricultural, environmental, and related applications.

BGI has a proven track record of excellence, delivering results with high efficiency and accuracy for innovative, high-profile research: research that has generated over 200 publications in top-tier journals such as Nature and Science. BGI's many accomplishments include: sequencing one percent of the human genome for the International Human Genome Project, contributing 10 percent to the International Human HapMap Project, carrying out research to combat SARS and German deadly E. coli, playing a key role in the Sino-British Chicken Genome Project, and completing the sequence of the rice genome, the silkworm genome, the first Asian diploid genome, the potato genome, and, more recently, have sequenced the human Gut Metagenome, and a significant proportion of the genomes for the1000 Genomes Project.

Source: BGI Shenzhen 
Contact: Jia Liu

Reference:
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse
Ludovic Orlando, Aurélien Ginolhac, Guojie Zhang, Duane Froese, Anders Albrechtsen,Mathias Stiller, Mikkel Schubert, Enrico Cappellini, Bent Petersen, Ida Moltke, Philip L. F. Johnson, Matteo Fumagalli, Julia T. Vilstrup, Maanasa Raghavan, Thorfinn Korneliussen,Anna-Sapfo Malaspinas, Josef Vogt, Damian Szklarczyk, Christian D. Kelstrup, Jakob Vinther, Andrei Dolocan, Jesper Stenderup, Amhed M. V. Velazquez, James Cahill, Morten Rasmussen, Xiaoli Wang, Jiumeng Min, Grant D. Zazula, Andaine Seguin-Orlando, Cecilie Mortensen, Kim Magnussen, John F. Thompson, Jacobo Weinstock, Kristian Gregersen,Knut H. Røed, Véra Eisenmann, Carl J. Rubin, Donald C. Miller, Douglas F. Antczak, Mads F. Bertelsen, Søren Brunak, Khaled A. S. Al-Rasheid, Oliver Ryder, Leif Andersson, John Mundy, Anders Krogh, M. Thomas P. Gilbert, Kurt Kjær, Thomas Sicheritz-Ponten, Lars Juhl Jensen, Jesper V. Olsen, Michael Hofreiter, Rasmus Nielsen, Beth Shapiro, Jun Wang & Eske Willerslev
Nature 499, 74–78 (04 July 2013), doi:10.1038/nature12323

See also:
University of Alberta June 26, 2013
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