Daily Archives: September 20, 2013

Chinese scientists complete wheat genome A -amp D drawings 2013 News
Chinese scientists complete wheat genome A -amp D drawings.

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Chinese scientists complete wheat genome A -amp D drawings 2013 News - Video

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

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

NEW YORK, Sept. 19, 2013 /PRNewswire/ --The New York Genome Center (NYGC) officially launched its scientific and clinical consortium of academic and industry leaders focused on harnessing genomics to advance the understanding and treatment of disease. The announcement was made at the start of NYGC's inaugural scientific symposium with New York City Mayor Michael Bloomberg speaking at a ribbon cutting ceremony.

The two-day scientific symposium kicks off the opening of NYGC's new 170,000 square foot research facility in Manhattan and brings together leaders of 16 member institutions to discuss the importance of genomics research for the detection, diagnosis, and treatment of human disease.

The symposium features a number of prominent speakers, including Dr. Harold Varmus, Director of the National Cancer Institute, Marc Tessier-Lavigne, President of The Rockefeller University, Nobel Laureate Dr. James Watson, Cold Spring Harbor Laboratory, and Dr. Tom Maniatis, Chairman of the Department of Biochemistry and Molecular Biophysics at Columbia University and Chair of NYGC's Scientific and Clinical Steering Committee, as well as panelists discussing Pharmacogenomics, Genomics, Quantified Health, and the Future of Big Data on Patient Care.

"The opening of the New York Genome Center is a major achievement in the City's ongoing efforts to advance the bioscience sector in New York City part of our commitment to diversify the city's economy and create jobs," said Mayor Bloomberg. "The Genome Center's new facility and its groundbreaking approach to collaboration will help solve some of medicine's most challenging problems by bringing together the city's best academic and clinical institutions."

"We applaud Mayor Bloomberg's longstanding support and unwavering commitment to the technology and science community here in New York City," said Dr. Robert Darnell, President and Scientific Director of NYGC. "Modern genomics has the power to transform medicine. NYGC will provide the leadership to change the standard of care of patients from day one. This new facility represents the intersection of the clinic and the lab--translational science. As a physician-scientist, I recognize the importance of uniting these two worlds. The collaboration we've formed with our member institutions will not simply just do great science but will work to save lives."

"Collaboration is essential for solving the most complex and difficult problems in biomedical science," said Dr. Tom Maniatis, Chair of NYGC's Scientific and Clinical Steering Committee. "I have been involved from the beginning in a city-wide effort to create a consortium that effectively marshals the resources, identifies the critical questions, and creates the environment to tackle problems that are too big for individual researchers or institutions to solve alone. By bringing together some of the best minds in science and the intellectual diversity represented in New York into the NYGC consortium, we believe that we can push forward the boundaries of biomedical science in an unprecedented manner."

"No other city in the world has the breadth of scientific talent, healthcare delivery systems, and demographically diverse population that can be found in New York," said Russ Carson, Co-Chair of NYGC's Board of Directors. "The New York Genome Center will be a catalyst to promote greater interaction and collaboration among the City's premier institutions and scientists by integrating basic research, diagnosis, and clinical care. Collectively this consortium has the potential to effectively change the paradigm in medicine by incorporating genomics across the spectrum of their activities."

About the New York Genome Center

The New York Genome Center (NYGC) is an independent non-profit organization that leverages the collaborative resources of leading academic medical centers, research universities, as well as pharmaceutical, biotech, and technology companies. The vision of NYGC is to transform medical research and clinical care in New York and beyond through the creation of one of the largest genomics research facilities in North America, integrating sequencing, bioinformatics, data management, and genomics research.

NYGC represents an unprecedented sharing of data and resources among premier institutions, which will dramatically increase the quality and speed of research outcomes to advance clinical care. The collaborative power of NYGC's members will help nurture scientific advances leading to accelerate the development of new diagnostics and treatments for human diseases, and provide an engine for life science commercialization in the region.

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New York Genome Center Launches Groundbreaking Consortium to Accelerate Scientific and Clinical Discoveries

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