Category Archives: Genome

Public release date: 19-Sep-2013 [ | E-mail | Share ]

Contact: Jia Liu liujia@genomics.cn BGI Shenzhen

September 20, 2013, Shenzhen, China An international team led by South Korea's Personal Genomics Institute and BGI unraveled the first whole genome of a 9-year-old male Amur tiger (Panthera tigris altaica), and compared it with the genomes of other big cats including the white Bengal tiger, lions, and snow leopards. The genomic data from this study provides an invaluable resource for the future studies of big cats and their whole family's conservation. The latest study was published online in Nature Communications.

Despite big cats' reputation for ferocity, these majestic species face more danger than they pose: All are endangered, mainly due to habitat loss, poaching, and dwindling food supplies. As the largest felid species on earth, tiger has become one of the world's most endangered species. Understanding of tiger's genetic diversity and demography has been very limited without the whole-genome sequence of tiger, or any of the Panthera species.

In this study, researchers sequenced the whole genome of an Amur tiger, also known as the Siberian tiger, and assembled it using BGI self-developed software SOAPdenovo. The Amur tiger genome was predicted to contain 20,226 protein-coding genes and 2,935 non-coding RNAs, and was enriched in olfactory receptor sensitivity, amino-acid transport, and metabolic-related genes, among others. Additionally, researchers found that the Amur tiger genome showed more than 95 percent similarity to the genome of domestic cat.

Researchers also sequenced the genomes of other Panthera-a white Bengal tiger, an African lion, a white African lion, and a snow leopard-using next-gen sequencing technology, and aligned them using the genome sequences of tiger and domestic cat. They discovered a number of Panthera lineage-specific and felid-specific amino acid changes that may affect the metabolism pathways. These signals of amino-acid metabolism have been associated with an obligatory carnivorous diet.

Furthermore, the team revealed the evidence that the genes related to muscle strength as well as energy metabolism and sensory nerves, including olfactory receptor activity and visual perception, appeared to be undergoing rapid evolution in the tiger.

Previous studies showed that the human loci EGLN1 (Egl nine homologue 1) and EPAS1 (endothelial PAS domain-containing protein 1) are two key factors for mediating high-altitude adaptation. In this study, the team found that the snow leopard had unique amino-acid changes in both genes that may have contributed to snow leopard's acquisition of an alpine, high altitude ecological niche.

In addition, researchers found that white lions contain a variant in the TYR gene. Variants in TYR were previously reported to be related with white coat color in domestic cats as well as with a form of albinism in people. The white lion variant appeared to lead to an amino acid change that seems to affect the charge of the resulting protein.

When observing the species' genetic diversity, researchers found the genetic diversity of tiger and lion were similar to that of human. Interestingly, the diversity of snow leopard genome was nearly half that of the other Panthera species and slightly lower than that of the Tasmanian devil.

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Tiger, lion and leopard genomes revealed assisting big cats' conservation

Sep. 20, 2013 An international research team headed by PD Dr Minou Nowrousian from the Ruhr-Universitt Bochum (RUB) has sequenced the genome of the ascomycete Pyronema confluens, thus closing a gap in the genetic map of fungi. For the first time, scientists have shown for fungi that, in the entire genome, those genes that are active during the sexual development evolve more rapidly than other genes. A similar effect was already described for animals and plants; for fungi, however, this question had hardly been addressed at all. The team from Germany, Spain and the USA has published their findings in PLoS Genetics.

Pyronema -- a typical representative of its systematic group

Today, the genomes of more than 250 fungi have been sequenced. Among the basal filamentous ascomycetes -- a group of ascomycetes that includes e.g. truffles and morels -- only one representative has been analysed so far: the truffle Tuber melanosporum. "With 125 million base pairs, the truffle genome is unusually big, yet it is coding for relatively few genes, namely some 7,500," says Minou Nowrousian from the Department of General and Molecular Botany. "Until now, it was not clear whether this is typical of basal filamentous ascomycetes or whether it is caused by the truffle's 'atypical' lifestyle." Unlike other filamentous ascomycetes, the truffle does not develop reproductive organs -- so-called fruiting bodies -- above ground but rather below ground. Moreover, it only grows in symbiosis with plant roots (mycorrhiza). Pyronema, on the other hand, is a typical representative of its group.

Intermediary evolutionary stage

The genome of Pyronema confluens contains 50 million base pairs and some 13,000 genes; it is thus smaller than that of the truffle, and yet it contains more genes. These findings confirm the truffle's special position and provide new insights into the evolution of ascomycetes. "Pyronema confluens bears a stronger resemblance to higher ascomycetes than to the truffle," concludes Minou Nowrousian. However, the scientists have also discovered differences to higher ascomycetes, for example in the DNA sequence containing the genetic blueprint for mating type genes. Mating type genes are the main regulators of sexual development and, in Pyronema confluens, they do not show the standardised structure that is typical for higher ascomycetes. "Pyronema confluens may represent an intermediary evolutionary stage in the evolution of mating type genes," says the Bochum biologist.

Light-activated genes

One characteristic feature of the fungus under investigation is the fact that it produces fruiting bodies only in light. Fittingly, the researchers discovered genes in the Pyronema genome containing blueprints for photoreceptors for different wavelengths of visible light. The activity of some of those genes increased in light.

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Gap closed in the genetic map of fungi: Research team sequences genome of Pyronema confluens

Sep. 20, 2013 An international team led by South Korea's Personal Genomics Institute and BGI unraveled the first whole genome of a 9-year-old male Amur tiger (Panthera tigris altaica), and compared it with the genomes of other big cats including the white Bengal tiger, lions, and snow leopards. The genomic data from this study provides an invaluable resource for the future studies of big cats and their whole family's conservation.

The latest study was published online in Nature Communication.

Despite big cats' reputation for ferocity, these majestic species face more danger than they pose: All are endangered, mainly due to habitat loss, poaching, and dwindling food supplies. As the largest felid species on earth, tiger has become one of the world's most endangered species. Understanding of tiger's genetic diversity and demography has been very limited without the whole-genome sequence of tiger, or any of the Panthera species.

In this study, researchers sequenced the whole genome of an Amur tiger, also known as the Siberian tiger, and assembled it using BGI self-developed software SOAPdenovo. The Amur tiger genome was predicted to contain 20,226 protein-coding genes and 2,935 non-coding RNAs, and was enriched in olfactory receptor sensitivity, amino-acid transport, and metabolic-related genes, among others. Additionally, researchers found that the Amur tiger genome showed more than 95 percent similarity to the genome of domestic cat.

Researchers also sequenced the genomes of other Panthera-a white Bengal tiger, an African lion, a white African lion, and a snow leopard-using next-gen sequencing technology, and aligned them using the genome sequences of tiger and domestic cat. They discovered a number of Panthera lineage-specific and felid-specific amino acid changes that may affect the metabolism pathways. These signals of amino-acid metabolism have been associated with an obligatory carnivorous diet.

Furthermore, the team revealed the evidence that the genes related to muscle strength as well as energy metabolism and sensory nerves, including olfactory receptor activity and visual perception, appeared to be undergoing rapid evolution in the tiger.

Previous studies showed that the human loci EGLN1 (Egl nine homologue 1) and EPAS1 (endothelial PAS domain-containing protein 1) are two key factors for mediating high-altitude adaptation. In this study, the team found that the snow leopard had unique amino-acid changes in both genes that may have contributed to snow leopard's acquisition of an alpine, high altitude ecological niche.

In addition, researchers found that white lions contain a variant in the TYR gene. Variants in TYR were previously reported to be related with white coat color in domestic cats as well as with a form of albinism in people. The white lion variant appeared to lead to an amino acid change that seems to affect the charge of the resulting protein.

When observing the species' genetic diversity, researchers found the genetic diversity of tiger and lion were similar to that of human. Interestingly, the diversity of snow leopard genome was nearly half that of the other Panthera species and slightly lower than that of the Tasmanian devil.

The Amur tiger genome is the first reference genome sequenced from the Panthera lineage and the second from the Felidae species. The data from tigers, lions and snow leopards provides a rich and diverse genome resource that could be used in future studies of conservation and population genomics. Genetics underpins the local adaptation and potential inbreeding and/or outbreeding in wild and captive populations can be illuminated and thereby help ensure the future survival of these majestic species.

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Tiger genome sequenced: Tiger, lion and leopard genomes compared

Published: Sept. 18, 2013 at 2:44 PM

STATE COLLEGE, Pa., Sept. 18 (UPI) -- Two U.S. scientists said they discovered more on origin of genomic dark matter, non-coding RNA, which comprises more than 95 percent of the human genome.

B. Franklin Pugh, the Willaman chair in Molecular Biology at Penn State University, and Bryan Venters, who is on faculty at Vanderbilt University, discovered essentially all coding and non-coding RNA originates at the same types of locations along the human genome, Penn State said Wednesday in a release.

The scientists said their findings could help pinpoint exactly where complex-disease traits reside, since genetic origins of many diseases are outside of the coding region of the genome.

Pugh and Venters set out to identify the precise location of the beginnings of transcription, the first step in the expression of genes into proteins but they determined where proteins that initiate transcription of non-coding RNA were located along human chromosomes.

"So rather than look for the RNA product of transcription we looked for the 'initiation machine' that makes the RNA," Pugh said. "This 'machine' assembles RNA polymerase, which goes on to make RNA, which goes on to make a protein."

Pugh and Venters determined non-coding initiation machines recognized the same DNA sequences as the ones at coding genes, indicating they have a specific origin and their production is regulated, Pugh said.

"These non-coding RNAs have been called the 'dark matter' of the genome because, just like the dark matter of the universe, they are massive in terms of coverage ... . However, they are difficult to detect and no one knows exactly what they all are doing or why they are there," Pugh said. "Now at least we know that they are real, and not just 'noise' or 'junk.'"

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Scientists uncover milestone in genome's 'dark matter'

Public release date: 18-Sep-2013 [ | E-mail | Share ]

Contact: Craig Boerner craig.boerner@vanderbilt.edu 615-322-4747 Vanderbilt University Medical Center

Using technology he helped develop, Vanderbilt University scientist Bryan Venters, Ph.D., has shed new light on the "dark matter" of the genome and has begun to explore a possible new approach to treating cancer.

"Clarity is everything," said Venters, assistant professor of Molecular Physiology and Biophysics who further developed the high-resolution technology as a postdoctoral fellow in the lab of Frank Pugh, Ph.D., at Pennsylvania State University before moving to Vanderbilt in January.

Venters and Pugh are co-authors of a paper published this week in the journal Nature that describes their finding.

Much of the DNA of the human genome has been called "dark matter" because only a tiny fraction, about 3 percent, makes up the approximately 20,000 protein-coding genes that are transcribed into RNA copies, and then translated into proteins.

Other parts of the genome are transcribed into non-coding RNA, presumably to perform other functions, but until recently the origin of this non-coding RNA was unknown.

Now, with a technique called ChIP-exo developed at Penn State that identifies protein-DNA interactions at near base-pair resolution, Venters and Pugh have shown that so-called transcription initiation complexes drive much of the non-coding transcription occurring throughout the genome.

In a model leukemia cell line, they discovered about 150,000 complexes along non-coding stretches of the DNA the most ever discovered. This suggests, they concluded, that "pervasive non-coding transcription is promoter-specific, regulated, and not that much different from coding transcription (of genes)."

Venters compared the technique to the highly sensitive satellite cameras that enable web-based map applications to zoom in from a continental view to street level, "and tell house from house."

Original post:
Study helps bring genome's 'dark matter' into light

Public release date: 18-Sep-2013 [ | E-mail | Share ]

Contact: Leah Ramsay lramsay@jhu.edu 202-642-9640 Johns Hopkins Medicine

The National Human Genome Research Institute has selected the Johns Hopkins Berman Institute of Bioethics to establish a "Center of Excellence" to study the ethical, legal and social implications (ELSI) of genomic research. The Berman Institute will receive three years of funding to build on its multidisciplinary expertise in the ethics of human genomics and public health, bringing the fields together in the largely unexplored but crucial study of genomics as applied to infectious disease. The center will be known as GUIDE: Genomic Uses in Infectious Disease & Epidemics.

Pandemic scares in recent years, from SARS to influenza to MERS, necessitate this research, says Gail Geller, a co-principal investigator for GUIDE and faculty member at the Berman Institute. "Infectious diseases account for a significant proportion of illness and death worldwide, across all aspects of society," Geller notes. Recent research has suggested that a person's genes can play a significant role in the severity of viral infection, and even a predisposition to death from flu.

"It is important to begin to map out and address the ELSI issues involved in the use of genomic information for major public health areas like infectious disease, as the science in this area is moving quickly," says Jeffrey Kahn, co-principal investigator with Geller and deputy director at the Berman Institute.

As an exploratory Center for Excellence in ELSI Research (CEER), the GUIDE Center will bring together a multidisciplinary team of Hopkins' global leaders in diverse fields including genomics, immunology and infectious disease, bioethics, epidemiology, public health preparedness, education, and health policy, in keeping with the intention that CEERs create opportunities for trans-disciplinary research. This team will initially explore public health genomics in two case studies of human-to-human infectious disease: pandemic influenza and Hepatitis C.

The research team will examine how the genome affects a person's response to a flu vaccine as well as to the virus. "Although vaccinations are generally safe and highly effective interventions for disease prevention, understanding more about the genetics of an individual's response may help us design vaccines that maximize protective efficacy while minimizing the potential for adverse events," says Ruth Karron, a co-investigator in the CEER and director of the Johns Hopkins Center for Immunization Research. She says that in the future, genomic information could result in the production and use of vaccines with more refined understanding of effects on particular subpopulations, which will necessitate decisions about prioritization, privacy, opt-out policies and genotyping for flu-resistant first responders.

The project will also assess the ELSI issues arising from recent Hepatitis C studies, including research conducted by GUIDE co-investigators Chloe Thio and Priya Duggal, showing that individuals with a specific variation of the gene IFNl3 had five times better response to treatment and three times better chance of clearing the virus spontaneously, without treatment. These discoveries raise important questions about disclosure of genetic status as well as the use of expensive therapies in those individuals carrying the mutation. Currently Hepatitis C is found in virtually every region of the world, with an estimated 123 million people chronically infected.

"Hepatitis C is a timely and crucial case study in the necessity of clear ethical guidance for rapidly advancing public health genomics," says Geller. "Should individuals with the IFNl3 variation receive different treatments and priority? Should reporting the IFNl3 variation be mandatory?" Kahn adds that "These are among the questions the Berman Institute's CEER will address in our Hepatitis C case study, with the goal of producing an ethical framework that can apply more widely to genomics in the context of infectious disease."

At the conclusion of the three-year grant period, GUIDE will apply to transition from an exploratory to a specialized CEER, a designation that would come with an additional five years of funding from the National Human Genome Research Institute.

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Personal genome, public health

US Human Genome News 2003
An international consortium of scientists announced Monday that it has completed the map of the human genetic code to an accuracy of 99.99 percent and said the accomplishment opens a new era...

By: tastatura wovessf

Excerpt from:
US Human Genome News 2003 - Video

The first sequenced tiger genome shows that big cats evolved to kill.

Genes for strong muscle fibers and for meat-eating appear narrowly shared, researchers reported, among species as distinct as the African lion and Asia's snow leopard.

Scientists mapped the genes of the endangered Siberian tiger (or Amur tiger), both to understand the genes that make big cat species distinct from one another and to aid efforts to preserve genetic diversity in wild tiger populations. (Also see "Isolated Tigers Travel Surprising Lands to Find Mates.")

The largest tiger subspecies, Siberian tigers weigh as much as 660 pounds (300 kilograms) and grow to some ten feet (three meters) in length. Only about 450 Siberian tigers exist in the wild, and around 4,000 tigers total are thought to remain in their natural habitats. (See a National Geographic magazine interactive of big cats in danger.)

"We looked at this very large tiger first to see what made it distinctive from other cats," said genome expert Jong Bhak of South Korea's Personal Genomics Institute in Suwon, a co-author of the Nature Communications study reporting the mapping of the Siberian tiger genome.

Bhak and colleagues sampled genes from a nine-year-old male tiger at the Everland Zoo in Korea, and compared them with gene map information from the Bengal tiger, lion, and snow leopard. (See tiger pictures.)

Natural Born Killers

"Genetically all the cats are very close, so we need close genetic mapping to find the small differences that make them distinct," Bhak said.

Some gene differences are apparent in the mapping, such as two genes likely involved in adaptation to high altitudes and thin air in snow leopards and white fur in white African lions.

But overall, the cat family seems to rely on a narrow set of 1,376 genes linked to strong muscle fibers and digestion of protein, the study shows, seen widely across the study species. The genes likely originated in large part with the earliest common ancestor of big felines some 11 million years ago, the study authors suggest.

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Tiger Genome Sequenced, Shows Big Cats Evolved to Kill

Published: Sept. 17, 2013 at 7:43 PM

SUWON, South Korea, Sept. 17 (UPI) -- International scientists say they've mapped the genomes of the tiger, lion and snow leopard, hoping to bolster efforts to protect the endangered species.

The team led by Yun Sung Cho at the Genome Research Foundation in Suwon, South Korea, sequenced the genome of a female Siberian tiger at the Everland Zoo in South Korea.

Writing in the journal Nature Communications, the researchers said the sequencing revealed tigers share 96 percent of their genes with domestic cats.

The team then went on to sequence the DNA of four other big cat species -- the African lion, snow leopard, white Bengal tiger and white African lion.

The genomes show how big cats gained their superior muscle strength, the ability to digest large amounts of meat and a keen sense of smell, and also yielded genetic clues to how the white lion gained its pale coat and how the snow leopard adapted to the snowy mountain ranges, the researchers said.

The tiger genome map will be an important resource for looking at genetic diversity, they said, as the preservation of diminishing wild tiger populations is a major concern of animal conservationists.

"Our tiger reference genome can be used as the basis for comparing all the tigers in the world, so that we know the genetic diversity of tigers," researcher Jong Bhak told the BBC.

"And we can actually have a plan of how we can breed tigers effectively [in zoos] to save the genetic diversity."

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Scientists decode the genome of the world's big cats

Public release date: 17-Sep-2013 [ | E-mail | Share ]

Contact: David McKeon dmckeon@nyscf.org 212-365-7440 New York Stem Cell Foundation

New York, NY (September 17, 2013) The New York Genome Center (NYGC) announced today that The New York Stem Cell Foundation (NYSCF) has become an Associate Member, joining NYGC's growing consortium of 16 research and clinical institutions, all working together in new ways to utilize genomic data for better detection, treatment, and prevention of disease.

"Biologists at the NYSCF working with the genomic scientists at NYGC will help address some of the critical roadblocks in stem cell research," said Dr. Robert B. Darnell, President and Scientific Director of NYGC. "Modern genomics has the potential to provide vital missing information to help us learn how to harness stem cells for use in clinical medicine. We've developed techniques and ideas here at NYGC that will greatly synergize with the beautiful and pioneering work ongoing at the NYSCF."

Stem cell biology and genomic analysis are both critical to the advancement of precision medicine. The collaboration between the Genome Center and NYSCF will merge cutting-edge capabilities in human biology with genomic research, creating an optimal environment for translating research into a better standard of care for patients.

"We are excited to work with NYGC as we continue to accelerate cures for the major diseases of our time. This will enable collaboration within the growing biotechnology community in New York," said Susan L. Solomon, CEO of The New York Stem Cell Foundation. "NYSCF has a number of current projects in which additional genomic analysis may play a critical role in better understanding disease susceptibility and risk factors. We hope to work with NYGC to integrate their genomic analysis into our research."

The New York Genome Center provides an "Integrated Genomics Solution", which includes (1) scientific consultation, (2) next-generation sequencing services for exomes, whole genomes, and RNA, (3) bioinformatic analysis of sequencing results using a high performance computing environment, and (4) data storage so that researchers and clinicians can readily access these results.

As an Associate Member, NYSCF will have priority access to these services. NYSCF will also become a member of the NYGC's Scientific and Clinical Steering Committee (SCSC), which provides guidance on research direction and oversees research collaborations and related funding.

NYSCF employs 45 full-time scientists and engineers in its laboratory who are engaged in the most advanced stem cell research and technology development, including creating NYSCF's Global Stem Cell Array, an automated technology platform that for the first time makes it possible to create identical stem cell lines from a large number of patients in a massively parallel process. This is a revolutionary tool that takes the vast amount of information we have learned from sequencing the human genome and puts it into a biological context to accelerate the development of safe and effective medicine. This robotic system creates induced pluripotent stem (iPS) cell lines and cell derivatives in a standardized manner from genetically diverse patients and patients with disease. This program will create an array of stem cell lines representing the full range of human genetics and the diversity of the world's population.

"This collaboration will expand our resources to analyze our stem cell samples at the genetic level, as we continue to bring the latest discoveries in genome science to our work to understand, prevent, and eventually cure diseases like diabetes, Alzheimer's, and multiple sclerosis among many others," said Scott Noggle, Director of the NYSCF Laboratory and the Charles Evans Senior Research Fellow for Alzheimer's Disease.

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New York Genome Center announces the New York Stem Cell Foundation as an Associate Member