Category Archives: Genome

Researchers have completed the first high-quality sequencing of a Neanderthal genome.

The genome produced from remains of a toe bone found in a Siberian cave is far more detailed than a previous "draft" Neanderthal genome sequenced three years ago by the same team at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

"The genome of a Neanderthal is now there in a form as accurate as that of any person walking the streets today," said Svante Paabo, a geneticist who led the research.

The Leipzig team has already been able to determine which genes the Neanderthal inherited from its mother and which from its father.

It now hopes to compare the new genome sequence to that of other Neanderthals, modern humans and Denisovans - another extinct human species whose genome was previously extracted from remains found in the same Siberian cave.

"We will gain insights into many aspects of the history of both Neanderthals and Denisovans, and refine our knowledge about the genetic changes that occurred in the genomes of modern humans after they parted ways with the ancestors of Neanderthals and Denisovans," Mr Paabo said.

His group plans to publish a scientific paper later this year, and in the meantime, the genome sequence is being made freely available so scientists elsewhere can conduct research on it. The announcement was welcomed by other researchers.

Wil Roebroeks, an archaeologist at Leiden University in the Netherlands who was not involved in the Leipzig study, said it was "exciting times" for comparative studies of humans and our closest extinct relatives.

By combining findings from genetics with studies of early diets, technology and physical anthropology of different human species, scientists would probably find new insights into our evolutionary past soon, he said.

Richard Klein, a paleoanthropologist at Stanford University in California who was not involved in the study, said it was "a monumental achievement that no one would have thought possible 10 or perhaps even five years ago". He said the comparisons might allow scientists to discover what makes our species unique and explain why we survive and others did not.

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Neanderthal's genome sequenced

The Neandertal research group at the Max Planck Institute.Frank Vinken / the Max Planck Institute

An international consortium of researchers has sequenced the 3 billion bases that make up the genome of our closest relative the Neandertal.Frank Vinken / the Max Planck Institute

Researcher Martin Kircher checking Illumina GAII flow cell.Frank Vinken / the Max Planck Institute

A flow cell used by the Illumina Genome Analyzer machine to study the Neanderthal genome.Frank Vinken / the Max Planck Institute

Reconstruction of a Neanderthal group.Johannes Krause / Atelier Daynes / Museum of the Krapina Neanderthals

Researchers in Germany said Tuesday they have completed the first high-quality sequencing of a Neanderthal genome and are making it freely available online for other scientists to study.

The genome produced from remains of a toe bone found in a Siberian cave is far more detailed than a previous "draft" Neanderthal genome sequenced three years ago by the same team at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

- Svante Paabo, a geneticist who led the research

"The genome of a Neanderthal is now there in a form as accurate as that of any person walking the streets today," Svante Paabo, a geneticist who led the research, told The Associated Press in an email.

Richard G. Klein, a paleoanthropologist at Stanford University in California who was not involved in the study, said it was "a monumental achievement that no one would have thought possible 10 or perhaps even five years ago."

Read more from the original source:
The Neanderthal Genome is Here

March 20, 2013

Image Caption: Reconstruction of a Neanderthal group. Credit: Johannes Krause, Neanderthal group by Atelier Daynes, Paris, France (Museum of the Krapina Neanderthals, Krapina, Croatia).

Lawrence LeBlond for redOrbit.com Your Universe Online

A team of German scientists have fully sequenced the genome of the Neanderthal and said they will be making the entire sequence freely available to the scientific community for research. The genome was produced from the remains of a toe bone found in a cave in Siberia, and is far more detailed than a previous mapping of the ancient genome published three years ago by the same team.

Svante Paabo and colleagues at the Max Planck Institute for Evolutionary Anthropology in Leipzig produced the first genome of the Neanderthal in 2009 using data collected from three bones found in a cave in Croatia. Now, using the toe bone fragment from the Denisova Cave, collected in 2010, the team has made the most accurate, high-quality sequence from a single Neanderthal.

The team utilized sensitive techniques they have developed over the past two years to sequence every position in the genome nearly 50 times over, and all from less than two-thousandths-of-an-ounce of sampling from a toe bone.

The analysis indicates that the individual is closely related to other Neanderthals in Europe and western Russia. Also, it shows evidence that Neanderthals and their Denisovan relatives were both present in the Siberian cave in the Altai Mountains, which borders Russia, China, Mongolia and Kazakhstan.

Institute researcher Kay Prufer told UPI that the updated sequence is of very high quality.

The new draft matches the quality of the Denisovan genome, presented last year, and is as good as or even better than the multiple present-day human genomes available to date, Prufer explained.

We will gain insights into many aspects of the history of both Neanderthals and Denisovans and refine our knowledge about the genetic changes that occurred in the genomes of modern humans after they parted ways with the ancestors of Neanderthals and Denisovans, Paabo said in a statement.

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Neanderthal Genome Fully Sequenced From Toe Bone

BERLIN (AP) Researchers in Germany said Tuesday they have completed the first high-quality sequencing of a Neanderthal genome and are making it freely available online for other scientists to study.

The genome produced from remains of a toe bone found in a Siberian cave is far more detailed than a previous draft Neanderthal genome sequenced three years ago by the same team at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

The genome of a Neanderthal is now there in a form as accurate as that of any person walking the streets today, Svante Paabo, a geneticist who led the research, told The Associated Press in an email.

Richard G. Klein, a paleoanthropologist at Stanford University in California who was not involved in the study, said it was a monumental achievement that no one would have thought possible 10 or perhaps even five years ago.

The Leipzig team has already been able to determine which genes the Neanderthal inherited from its mother and which from its father. It now hopes to compare the new genome sequence to that of other Neanderthals, modern humans and Denisovans another extinct human species whose genome was previously extracted from remains found in the same Siberian cave.

We will gain insights into many aspects of the history of both Neanderthals and Denisovans, and refine our knowledge about the genetic changes that occurred in the genomes of modern humans after they parted ways with the ancestors of Neanderthals and Denisovans, Paabo said.

Klein said the comparisons might allow scientists to determine what makes our species unique and explain why we survive and others didn't.

Paabos group plans to publish a scientific paper later this year.

In the meantime, the genome sequence is being made freely available so scientists elsewhere can conduct research on it, he said.

The announcement was welcomed by other researchers.

More here:
Researchers publish improved Neanderthal genome

Scientists at Germany's Max Planck Institute have released a final version of a high-quality sequencing of a Neanderthal genome, which could shed light on why humans survived and earlier hominid species did not.

"The genome of a Neanderthal is now there in a form as accurate as that of any person walking the streets today," Svante Paabo, a geneticist, told the Associated Press. Paabo led the research project as part of the Institutes Evolutionary Anthropology department.

Neanderthals are the closest relative to humans and existed as recently as 30,000 years ago. It is believed by many scientists that modern humans, Homo sapiens, drove them to extinction. Humans and Neanderthals became divergent branches on the evolutionary tree more than 300,000 years ago.

The DNA for the sequencing came from a toe bone found in a Siberian cave is far more detailed than a previous "draft" Neanderthal genome sequenced three years ago by the same team.

The DNA confirmed speculation that humans, interbred with Neanderthals as they spread from the African plains to the Middle East and northern Africa, but that it happened about 80,000 years ago, much earlier than previously thought.

The research team hopes to compare the new genome sequence to that of other Neanderthals, modern humans and Denisovans, another extinct hominid group, the genome of which was extracted from remains in the same cave.

Wil Roebroeks, an archaeologist at Leiden University in the Netherlands who wasn't involved in the Leipzig study, told the AP it was "exciting times" for comparative studies of humans and our closest extinct relatives.

More:
Neanderthal Genome Data Sheds Light on Human Ancestors

Public release date: 21-Mar-2013 [ | E-mail | Share ]

Contact: David Gilbert degilbert@lbl.gov 925-296-5643 DOE/Joint Genome Institute

The 8th Annual Genomics of Energy and Environment Meeting of the U.S. Department of Energy Joint Genome Institute (DOE JGI) will be held at the Marriott in Walnut Creek on March 26-28, 2013. The talks will focus on genomics research in the fields of clean energy generation and the environment. Keynote speeches will be delivered by Eric Karsenti of European Molecular Biology Laboratory on "TARA OCEANS: A global analysis of oceanic plankton ecosystems" and Chris Voigt of MIT on "Part mining for synthetic biology."

For further information about the agenda, visit http://bit.ly/JGI-UM8-agenda. For more details and for free media registration, contact David Gilbert, DOE Joint Genome Institute Public Affairs Manager at degilbert@lbl.gov.

WHO: Researchers working in the fields of genomics, bioenergy, carbon cycling and biogeochemistry WHAT: 8th Annual Genomics of Energy & Environment Meeting WHERE: Marriott in Walnut Creek (2355 North Main Street, Walnut Creek, California 94596) WHEN: 5 pm, Tuesday, March 26, 2013 to 5 pm, Thursday, March 28, 2013

The annual meeting draws several hundred attendees from around the world. This year's talks and poster presentations will cover a wide range of topics in the fields of metagenomics, plants, microbial genomics and synthetic biology. Among the projects to be discussed are:

###

Since 2005, the DOE Joint Genome Institute has focused on the application of genomics to bioenergy and environmental issues. Organisms are selected for sequencing based on their relevance to the DOE missions, judged by an independent peer review process. Many of the projects focus on one of three key aspects: the development of biofuel feedstocks; the identification of enzymes that can effectively break down plant fibers into sugar; and the development of processes to ferment plant-derived sugars into liquid biofuel.

AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert! system.

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DOE Joint Genome Institute 8th Annual Meeting on March 26-28, 2013

Researchers in Germany said Tuesday they have completed the first high-quality sequencing of a Neanderthal genome and are making it freely available online for other scientists to study.

The genome produced from remains of a toe bone found in a Siberian cave is far more detailed than a previous "draft" Neanderthal genome sequenced three years ago by the same team at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

"This allows even the small differences between the copies of genes that this Neanderthal individual inherited from its mother and father to be distinguished," the institute said in a statement.

The team led by geneticist Svante Paabo now hopes to compare the new genome sequence to that of other Neanderthals, as well as to that of a Denisovan - another extinct human species whose genome was previously extracted from remains found in the same Siberian cave.

"We will gain insights into many aspects of the history of both Neanderthals and Denisovans and refine our knowledge about the genetic changes that occurred in the genomes of modern humans after they parted ways with the ancestors of Neanderthals and Denisovans," Paabo said. The group plans to publish a scientific paper on the issue later this year.

In the meantime, the genome sequence is being made freely available so scientists elsewhere can conduct research on it, he said.

The announcement was welcomed by other researchers.

Wil Roebroeks, an archaeologist at Leiden University in the Netherlands who wasn't involved in the Leipzig study, said it was "exciting times" for comparative studies of humans and our closest extinct relatives.

By combining findings from genetics with studies of early diets, technology and physical anthropology of different human species, scientists would likely yield new insights into our evolutionary past soon, he said.

More:
German researchers publish full Neanderthal genome

Three years ago, an international team of scientists, led by researchers at the Max Planck Institute for Evolutionary Anthropology, in Leipzig, Germany published the first draft of the Neanderthal genome. Now the German group says they have computed a much higher quality genome.

The first draft was decoded using DNA fragments collected from three different bone pieces. The researchers have generated the new version from one toe bone, so it represents the genome of a single Neanderthal individual. They plan to publish a scientific paper later this year, but have already made the entire sequence freely available online for other scientists.

Computing the DNA blueprint of an extinct species is no easy task. Sophisticated DNA sequencing and computing techniques helped the team put together the first draft of the roughly 3.2-billion base-pair long genome (about the size of a modern human genome).

One challenge is that DNA fragments from fossil bones are typically only about 50 bases long; once these fragments are sequenced, assembly algorithms sort through the short sequences and string them together into longer and longer sections. During sequencing, though, some base positions get sequenced multiple times and others are missed completely. In the 2010 draft version, each position was determined once on average. New sequencing techniques the group has developed over the past two years have allowed them to sequence every position in the genome 50 times on average.

Seeing each position that often dramatically reduces the chance that we make an error in the sequence, says Janet Kelso, a bioinformatics researcher at the Max Planck Institute. This 50-fold coverage Neanderthal genome is as good as, or better than the genomes that have been sequenced for many present-day humans.

Heres the caveat: when genomes are sequenced with next-generation sequencing technologies, some regions, typically those composed of highly repetitive sequences, simply cannot be confidently reconstructed, says Kelso. So these regions are generally not included in the final sequence.

Thats why this ARS Technica article boldly, and rightly, says that the Neanderthal genome is not complete even though its about as good as we can probably get with prehistoric genomes.

But as Kelso points out, the problem exists for all genomes, be they old or new. In this sense, I would argue that there is no complete human genomemodern or ancient!

Read more:
Have Researchers Computed the Complete Neanderthal Genome ?

Search NCBI on Genome Compiler
Search NCBI on Genome Compiler. Uploaded by genomecompiler on Mar 11 2013. A guide to searching for genes and other parts on Genome Compiler using the inbuilt library and the NCBI database. Genome Compiler.

By: GenomeCompiler

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Human Genome Project Commercial
by Bear Comes and Erica Eisenhauer.

By: penguiuny

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Human Genome Project Commercial - Video