Category Archives: Genome

BGI Tech and Hebei Agricultural University jointly announced the complete, high quality sequencing of the Jujube genome. Jujube is the most economically important member of the Rhamnaceae family, and the Jujube genome is particularly difficult to sequence due the high level of heterozygosity and other complicating factors. It is the first time that a genome in the Rhamnaceae (Buckthorn) family has been sequenced.

This study has been recently published in Nature Communications.

Jujube is a major commercial fruit with up to 30 million acres under cultivation -- close to that of apple and citrus -- and China accounts for 99% of the 6 million tons of dried fruit produced annually. Jujube has a much higher vitamin C content than other well-known vitamin C-rich fruits such as orange and kiwi fruit, and also high levels of nucleotides, polysaccharides and other important functional components. Furthermore, the jujube tree is highly resistant to salinity and drought, and grows well in sandy, alkaline and arid areas. Therefor, decoding the genome of the jujube tree will have great implications to exploit those important traits.

The Jujube genome has the highest degree of heterozygosity (1.9%) of plants sequenced to date using next generation sequencing (NGS). In addition, the very high density of simple sequence repeats and low GC content make the Jujube genome particularly challenging for whole genome sequencing and assembly. By using a combination of BAC-to-BAC sequencing and PCR-free whole genome sequencing, the researchers were able to successfully complete the high quality de novo sequencing of 98.6% of the estimated Jujube genome, identifying 32,808 genes.

"This study has accelerated the functional genomics research of the Jujube tree, and will facilitate the genetic improvement and selective breeding of Buckthorn fruit trees," said Professor Mengjun Liu, head of the research team, for Hebei Agricultural Unviersity. "This research not only shows the expertise of the team and the power of sequencing technology, but we also expect its future applications in bring more value and benefits in healthy food production."

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The above story is based on materials provided by BGI Shenzhen. Note: Materials may be edited for content and length.

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Genome sequencing of the jujube tree completed

Local researchers have new clues about a rare respiratory virus that caused a national outbreak and filled childrens hospital beds in August and September.

Researchers at the Genome Institute at Washington University mapped the genetic code of enterovirus D68 samples taken from nine children treated at St. Louis Childrens Hospital. Their work, along with about six other genome sequences of the virus from around the country, will be used to study the makeup of the virus with a goal of developing a better diagnostic test, treatments and potentially a vaccine.

Knowing the whole genome sequence is a very important starting point for research, said Dr. Gregory Storch, a professor of pediatrics who co-wrote a paper on their work in the journal Emerging Infectious Diseases. The next thing is that it could be helpful to us in designing better diagnostic tests, and further down the road, it can be very useful for people trying to develop new treatments.

The virus surprised disease investigators when it started showing up in children in Missouri and Illinois in August. Now 47 states have reported illnesses, according to the Centers for Disease Control and Prevention. The virus can cause severe symptoms, including coughing, wheezing and fever, especially in children with asthma. In rare cases, neurological symptoms have included paralysis linked to the virus, which is related to polio.

Respiratory viruses are seen every summer and fall, but the enterovirus D68 caused more serious, widespread illnesses and raised questions about its pathology.

Something has changed about the virus or the way it fits into the community, Storch said. It seems to be emerging as a cause of widespread respiratory disease. We dont know what the future holds, but we may see future outbreaks.

Since August, more than 1,100 confirmed enterovirus D68 cases have been confirmed in the country and eight deaths in children who tested positive for the virus.

But thousands more are probably sickened by the virus, including as many as 1,500 children treated at St. Louis Childrens Hospital for respiratory illness this year. Most of the cases did not receive comprehensive testing that would determine the strain. Storch said the genome sequencing could point to an easier way to diagnose the virus.

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Researchers dive deep into rare enterovirus

Researchers at Washington University School of Medicine in St. Louis have sequenced the genome of enterovirus D68 sampled from patients treated at St. Louis Children's Hospital. Nationwide, the virus has spread rapidly in recent months and caused severe respiratory illness in young children, with some patients requiring hospitalization.

"Having the DNA sequence of this virus enables additional research," said senior author Gregory A. Storch, MD, the Ruth L. Siteman Professor of Pediatrics. "It can be used to create better diagnostic tests. It also may help us understand why this epidemic seems to be producing severe and unusual disease, and why it's spreading more extensively than in the past."

The work appears Oct. 28 in Emerging Infectious Diseases. The investigators published the DNA sequences in GenBank, an open-access database maintained by the National Institutes of Health (NIH).

The new sequencing data, produced by The Genome Institute at Washington University, includes one complete genome sequence and eight partial sequences taken from patient samples. Further, scientists at the Centers for Disease Control and Prevention (CDC) contributed to GenBank seven complete or partial sequences of enterovirus D68 sampled in the Midwest.

Storch said routine laboratory tests can't identify specific enterovirus strains. Most hospitals and clinics only can perform tests to determine if a patient has a virus that fits broadly into the enterovirus/rhinovirus category. In the new study, Storch and his colleagues analyzed 14 patient samples testing positive for enterovirus/rhinovirus. Of those, nine were identified as enterovirus D68 using specialized laboratory techniques developed at Washington University and St. Louis Children's Hospital. The remaining five samples were other respiratory viruses.

While many children may contract enterovirus D68 and never know it because symptoms are mild, others may require hospitalization to support their breathing. Children with a history of breathing disorders such as asthma are at higher risk of severe disease.

In this study, seven of the nine patients with the D68 strain had severe disease that required admission to the pediatric intensive care unit. The remaining two had moderate symptoms resulting in general hospital admission. Of the five patients with other viruses, three were classified with severe disease. The only two patients discharged home with mild disease did not have the D68 strain.

"There is currently no specific treatment and no vaccine for this virus," said Storch, who treats patients at St. Louis Children's Hospital. "But having the DNA sequence available helps work toward both of those goals."

The data also allow comparisons between strains circulating in different parts of the country.

"The CDC has published some additional genomes from Missouri, Illinois and Kentucky," said first author Kristine M. Wylie, PhD, research instructor in pediatrics. "The Missouri genomes, including ours, are all very similar, but the Illinois and Kentucky genomes are different from the Missouri types, suggesting there are some distinct strains circulating in the U.S. right now."

Originally posted here:
Genome sequenced of enterovirus D68 circulating in St. Louis

PUBLIC RELEASE DATE:

29-Oct-2014

Contact: Press Office huwen@genomics.cn BGI Shenzhen

October 27, 2014 Cambridge, MA and Hebei, China BGI Tech and Hebei Agricultural University jointly announced the complete, high quality sequencing of the Jujube genome. Jujube is the most economically important member of the Rhamnaceae family, and the Jujube genome is particularly difficult to sequence due the high level of heterozygosity and other complicating factors. It is the first time that a genome in the Rhamnaceae (Buckthorn) family has been sequenced. This study has been recently published in Nature Communications.

Jujube is a major commercial fruit with up to 30 million acres under cultivation close to that of apple and citrus and China accounts for 99% of the 6 million tons of dried fruit produced annually. Jujube has a much higher vitamin C content than other well-known vitamin C-rich fruits such as orange and kiwi fruit, and also high levels of nucleotides, polysaccharides and other important functional components. Furthermore, the jujube tree is highly resistant to salinity and drought, and grows well in sandy, alkaline and arid areas. Therefor, decoding the genome of the jujube tree will have great implications to exploit those important traits.

The Jujube genome has the highest degree of heterozygosity (1.9%) of plants sequenced to date using next generation sequencing (NGS). In addition, the very high density of simple sequence repeats and low GC content make the Jujube genome particularly challenging for whole genome sequencing and assembly. By using a combination of BAC-to-BAC sequencing and PCR-free whole genome sequencing, the researchers were able to successfully complete the high quality de novo sequencing of 98.6% of the estimated Jujube genome, identifying 32,808 genes.

"This study has accelerated the functional genomics research of the Jujube tree, and will facilitate the genetic improvement and selective breeding of Buckthorn fruit trees", said Professor Mengjun Liu, head of the research team, for Hebei Agricultural Unviersity. "This research not only shows the expertise of the team and the power of sequencing technology, but we also expect its future applications in bring more value and benefits in healthy food production."

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About Agricultural University of Hebei

Founded in 1902, Agricultural University of Hebei (AUH) is one of the main universities of Hebei province. Its five campuses are located in the cities of Baoding, Qinhuangdao, Huanghua and Dingzhou, covering the areas of more than 1.9 million square meters. Since 1989, the university has won 6 national awards and 163 provincial awards for its excellence in teaching and research, making it the top ranked university among all Chinese provincial universities, for ten years in a row. AUH has also ranked among the top 10 agricultural universities in China for decades.

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BGI Tech and Hebei Agricultural University complete the genome sequencing of the jujube tree

PUBLIC RELEASE DATE:

29-Oct-2014

Contact: Carola Grimminger carolagrimminger@eurofins.com 49-809-282-89921 Eurofins Genomics

Eurofins Genomics, pioneer and key provider of next generation sequencing services (NGS), and Igenbio, leading provider of microbial bioinformatics and gene manipulation tools and services, have announced a co-operation agreement to combine their expertise in sequencing and analysis services for microbial, fungal and algal organisms.

With the cooperation, customers benefit from "one-stop-shopping" for complete genomics projects that deliver analysis results from the raw extracted DNA. Both companies together serve a worldwide market for their products and services.

"We take specific care to build up a technical and operational pipeline which is suitable to meet our quality standards and the high service level we want to provide to our customers", says Bruno Poddevin, Senior Vice President Eurofins Genomics. "The specific know-how and bioinformatics capabilities of Igenbio are an excellent fit to our portfolio for prokaryotic, yeast and fungal genome sequencing services."

"As global leader in next generation sequencing technologies, Eurofins has long been our preferred sequencing partner. With the increased integration we are now able to provide complete genome analysis, transcriptomics data integration along with gene manipulation tool set and for synthetic biology platform for our customers", says Vinayak Kapatral, President, and CEO of Igenbio, Inc.

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Comprehensive solutions for genome analysis and synthetic biology projects

UC Santa Cruz Banana Slug Genome Project
Learn more at crowdfund.ucsc.edu/sluggenome!

By: UCSantaCruz

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UC Santa Cruz Banana Slug Genome Project - Video

PUBLIC RELEASE DATE:

27-Oct-2014

Contact: Craig Brierley craig.brierley@admin.cam.ac.uk 44-012-237-66205 University of Cambridge @Cambridge_Uni

The team of researchers, led by Dr Rafael Carazo Salas from the Department of Genetics, combined high-resolution 3D confocal microscopy and computer-automated analysis of the images to survey the fission yeast genome with respect to three key cellular processes simultaneously: cell shape, microtubule organisation and cell cycle progression. Microtubules are small, tube-like structures which help cells divide and give them their structure.

Of the 262 genes whose functions the team report in a study published today in the journal Developmental Cell, two-thirds are linked to these processes for the first time and a third are implicated in multiple processes.

"More than ten years since the publication of the human genome, the so-called 'Book of Life', we still have no direct evidence of the function played by half the genes across all species whose genomes have been sequenced," explains Dr Carazo Salas. "We have no 'catalogue' of genes involved in cellular processes and their functions, yet these processes are fundamental to life. Understanding them better could eventually open up new avenues of research for medicines which target these processes, such as chemotherapy drugs."

Using a multi-disciplinary strategy that took the team over four years to develop, the researchers were able to manipulate a single gene at a time in the fission yeast genome and see simultaneously how this affected the three cellular processes. Fission yeast is used as a model organism as it is a unicellular organism in other words, it consists of just one cell whereas most organisms are multicellular, yet many of its most fundamental genes carry out the same function in humans, for example in cell development.

The technique enabled the researchers not only to identify the functions of hundreds of genes across the genome, but also, for the first time, to systematically ask how the processes might be linked. For example, they found in the yeast and, importantly, validated in human cells a previously unknown link between control of microtubule stability and the machinery that repairs damage to DNA. Many conventional cancer therapies target microtubular stability or DNA damage, and whilst there is evidence in the scientific literature that drugs targeting both processes might interact, the reason why has been unclear.

"Both the technique and the data it produces are likely to be a very valuable resource to the scientific community in the future," adds Dr Carazo Salas. "It allows us to shine a light into the black box of the genome and learn exciting new information about the basic building blocks of life and the complex ways in which they interact."

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Imaging the genome: Cataloguing the fundamental processes of life

PUBLIC RELEASE DATE:

27-Oct-2014

Contact: Susan Brown sdbrown@ucsd.edu 858-246-0161 University of California - San Diego @UCSanDiego

A hinge in the RNA genome of the virus that causes hepatitis C works like a switch that can be flipped to prevent it from replicating in infected cells. Scientists have discovered that this shape is shared by several other virusesamong them one that kills cancer cells.

That's Seneca Valley virus, which seems harmless to healthy human cells but lethal to cancer stem cells.

"Clearly we'd like to understand it better," said Thomas Hermann, professor of chemistry and biochemistry at the University of California, San Diego.

Hermann's research group has determined the molecular structure of this critical switch in the Seneca Valley virus and found that it matches the L-shaped switch in hepatitis C virus, which his group had previously described.

The similarity was a surprise.

"It wasn't immediately apparent to us from the genome sequence alone," said Mark Boerneke, a graduate student in chemistry and lead author of the report in the Proceedings of the National Academy of Sciences online the week of October 27. "This is a different virus that regulates protein production in a similar fashion."

This kind of viral on-off switch is part of an IRES, for internal ribosome entry site. Ribosomes are the structures inside cells that make proteins. Lacking their own protein-making machinery, viruses use the IRES to hijack the ribosomes of cells they've infected to produce proteins they need to replicate.

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Viral switches share a shape

The Genome Analysis Centre (TGAC) in Norwich will lead research into the development of bioinformatics to support the identification and characterisation of viruses through metagenomics.

The BBSRC-funded research, led by TGACs Dr Richard Leggett, aims to develop computational algorithms that can accurately assemble viral genomes contained within metagenomic samples. These microbial samples pose a challenge to researchers as, not only do they contain numerous different viral species, it is also difficult to locate precisely which species are present.

As a currently under-explored area, the research is vital to improve our ability to identify viruses. Beneficial to researchers involved in the study of animal-to-human transmitted viruses, disease diagnostics and epidemiology, the three-year project will demonstrate the practical value of the developed bioinformatics tool by testing it against real datasets taken from species expected to host a variety of viruses, including a set of African rodent samples.

Samples are being provided by collaborators led by Pablo Murcia at the MRC-University of Glasgow Centre for Virus Research.

Metagenomics is broadly defined as environmental genomics, allowing the study of microbial communities of our living world. While the sequencing of metagenomic samples follows the same process as that for sequencing a single genome, it becomes more complex at the assembly stage where the short sequenced fragments of DNA must be correctly arranged into the genomes of multiple species.

This intricacy is compounded by the currently limited bioinformatics tools available to conduct the assembly for metagenomic samples, particularly for those containing viruses. Having demonstrated the possibility and feasibility of such a tool by the Institutes previous MetaCortex project, the new research will create the algorithms required to address this gap in metagenomic capabilities.

Dr Richard Leggett, project leader at TGAC, said: This is an exciting project and we hope the work will equip researchers who are looking at a wide range of viral infections, including those affecting humans and agriculturally important livestock.

The project, titled: Development of computational strategies for identification and characterisation of viruses in metagenomic samples is funded by the BBSRC Responsive Mode Award.

The Genome Analysis Centre (TGAC) is a world-class research institute focusing on the development of genomics and computational biology.

TGAC is based within the Norwich Research Park and receives strategic funding from the Biotechnology and Biological Science Research Council (BBSRC) 7.4 million in 2013/14 as well as support from other research funders.

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TGAC leads research to identify animal-human transmitted diseases

Unraveling the Mysteries of the Human Genome
Mission in a Minute: Kathryn Phillips, PhD http://profiles.ucsf.edu/kathryn.phillips http://healthpolicy.ucsf.edu/content/center-translational-and-policy-per...

By: UC San Francisco (UCSF)

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Unraveling the Mysteries of the Human Genome - Video