and genomes for a variety of significant crops using model plants. The regulatory genes that impact photosynthesis are critically important for enhancing growth
Retrieving small genomes from a mix of organismsscientists from the IZW led by Alex Greenwood publish in PLOS ONE a simple way to retrieve small genomes from a mix of various organisms.
how to retrieve the genome of a specific pathogen from a mixture of DNAS in a patient and its microbial cohabitants?
Analysis of the sequences and comparison with reference data demonstrated that the complete mitochondrial genome of the rodents had been retrieved from the DNA pool.
In fact entire mitochondrial genomes and almost the entire genome sequence of a bacterium were obtained when specifically tested for the efficiency of the by-catch principle.
Capflank opens doors to completely new possibilities e g. in the genetic analysis of pathogens. We can use short preserved gene sequences to yield the genome
(or at least large sections of it) from pathogenic variants of influenza viruses for example or from completely new pathogens explains Greenwood.
From the intestinal bacterium Escherichia coli contained in a human urine sample the scientists retrieved 90 per cent of the genome in one go.
and compare the sequences of multiple segments of many different types of EEHV genomes directly from pathological blood
The research is supported by the National Science Foundation's Plant Genome Research Program (PGRP) and Basic Research to Enable Agriculture Development (BREAD) the Howard Buffett Foundation the Burroughs Wellcome Fund and the Center for Data analytics at Georgia Tech.
so using natural plant breeding methods not transgenics said Rocheford the Patterson Endowed Chair of Translational Genomics for Crop Improvement.
They evaluated data sets from about 200 genetically diverse lines of corn at varying scopes of investigation--from the entire corn genome to stretches of DNA surrounding small sets of genes.
The study also showed that using a more targeted approach to predicting the usefulness of a small set of genes was as effective as evaluating the whole corn genome said Brenda Owens doctoral candidate and first author of the study.
and Genomics (CBGP UPM-INIA) has shown that by the contact of a plant with a strain of the Colletotrichum tofieldiae microorganism previously isolated this plant can increase the number size
Cattle genome cracked in detailby creating a global database an international consortium of scientists has increased the detailed knowledge of the variation in the cattle genome by several orders of magnitude.
It's momentous says one of the scientists behind the international effort associate professor Bernt Guldbrandtsen from the Center for Quantitative Genetics and Genomics Department of Molecular biology and Genetics Aarhus University.
The data consist of sequenced genomes for a number of bulls and are based on new sequencing techniques.
Currently the database contains genomes of more than 1200 animals of different cattle breeds but as more scientists from other countries gradually join the project there is a continual inflow of data.
Where previously only the location of the genes on the genome and some of the gene variants were known a large part of the total variation has now been identified
He is supplemented by professor Mogens Sandã¸Lund director of the Center for Quantitative Genetics and Genomics at the Department of Molecular biology and Genetics Aarhus University:
and for more information and studies on the history of cattle explains postdoc Rasmus Froberg Brã¸ndum also from the Center for Quantitative Genetics and Genomics.
The study Ecological genomics meets community-level modeling of biodiversity: mapping the genomic landscape of current and future environmental adaptation was published by Matthew Fitzpatrick of the University of Maryland Center for Environmental science and Steven Keller of the University of Vermont.
Genome sequencing revealed that the isolated B. pumilus contained three unique gene clusters for the production of antimicrobial peptide compounds known as bacteriocins.
When the genome of the black Perigord truffle was mapped in 2010 we thought that the fungus had sufficient genes to create its flavour on its own junior professor Richard Splivallo from the Institute for Molecular Life sciences at the Goethe University explained.
Now livestock such as sheep offer an intriguing animal to examine adaptation to climate change with a genetic legacy of centuries of selected breeding and a wealth of livestock genome-wide data available.
Their results could have significance for potential applications in functional genomics breeding and adaptation of livestock to climate change.
and Genomics (CBGP UPM-INIA) a joint centre of the Universidad Politã cnica de Madrid (UPM) and the The National Institute for Agricultural Research and Experimentation (INIA) have found a way of increasing
#Iberian pig genome remains unchanged after five centuriesa team of Spanish researchers have obtained the first partial genome sequence of an ancient pig.
Researchers from the Institute of Evolutionary Biology (CSIC-Pompeu Fabra University) and the National Centre for Genome Analysis (CNAG) also participated in the study.
and no great changes have been registered in this genome. Therefore more studies will be needed before we are able to distinguish the modern species from the older ones.
The study also compared the ancient pig sample with the genome of modern pigs of different breeds including'Creole'pigs
Using DNA sequencing technology housed at the UO's Genomics Core Facility scientists sequenced the bacterial 16s RIBOSOMAL RNA gene isolated from the samples.
The researchers examined the entire corn gene blueprint--some 26.5 million points in the 2 to 3 billion base pair genome--to find the genes most closely associated with HR.
#Coffee genome sheds light on the evolution of caffeinethe newly sequenced genome of the coffee plant reveals secrets about the evolution of man's best chemical friend:
Accordingly a genome sequence could be a significant step toward improving coffee said Philippe Lashermes a researcher at The french Institute of Research for Development (IRD.
By looking at the coffee genome and genes specific to coffee we were able to draw some conclusions about
Lashermes along with Patrick Wincker and France Denoeud genome scientists at The french National Sequencing Center (CEA-Genoscope)
The team created a high-quality draft of the genome of Coffea canephora which accounts for about 30 percent of the world's coffee production according to the Manhattan-based National Coffee Association.
If this trait had been inherited from a common ancestor the enzymes would have been more similar between species. The coffee genome helps us understand what's exciting about coffee--other than that it wakes
and the relationship between the genome structure of coffee and other species we were able to learn about coffee's independent pathway in evolution including--excitingly--the story of caffeine.
It also provides the opportunity to better understand the evolution of coffee's genome structure.
It turns out that over evolutionary time the coffee genome wasn't triplicated as in its relatives:
Instead it maintained a structure similar to the grape's. As such evolutionary diversification of the coffee genome was driven likely more by duplications in particular gene families as opposed to en masse when all genes in the genome duplicate.
This stands in contrast to what's been suggested for several other large plant families where other investigators have noted correlations between high species diversity in a group and the presence of whole genome doublings or triplings.
thus with no genome duplication at its root it appears to break the mold of a genome duplication link to high biodiversity Denoeud said.
This suggests that the practices of the three communities leave their signature in the genomes of sorghum populations.
The researchers analysed the genomes of more than 300 people half of them village farmers and the other half Pygmies.
the genomes of the Pygmy communities today have up to 50%of the genetic material inherited from their farmer neighbours.
Genetic analysis sheds new light on the survival of whiteflies in Finland and helps to plan efficient pest management.
The scientists first sequenced the entire genome of one domestic rabbit to develop a reference genome assembly.
Then they resequenced entire genomes of domestic rabbits representing six different breeds and wild rabbits sampled at 14 different places across the Iberian peninsula and southern France.
Our data shows that domestication primarily involved small changes in many genes and not drastic changes in a few genes states Kerstin Lindblad-Toh co-senior author Director of Vertebrate Genome
and there were many more changes in the non-coding part of the genome than in the parts of the genome that codes for protein.
Kim Phillips a graduate student in Mcsteen's lab mapped the corn plant's genome and found that a genetic mutation stunted tassel growth
and expertise at MU including genomics translational experiments with frog eggs research in the field cellular testing
The team led by Gerald Tuskan of Oak ridge National Laboratory (ORNL) the Department of energy Joint Genome Institute (DOE JGI)--a DOE Office of Science user facility
--and Stephen Difazio of West virginia University used a combination of genome-wide selection scans and analyses to understand the processes involved in shaping the genetic variation of natural poplar (Populus trichocarpa) populations.
The shift from an approach focused on single candidate genes to the large-scale computational approach analyzing all of them is made possible by the availability of the poplar genome
Since the genome was made publicly available it has been used to understand woody perennial plant development and served as a model for genome-level insights in forest trees.
The publication itself has been cited more than 1000 times in a wide variety of journals. This is the first time that deep genomics resources have ever been applied to an ecological question in this case:'
'What does selection do at the genome level?''said Tuskan. In the past people looked at adaptation to factors such as temperature
and light levels and they examined variation in those genes as they vary across environmental gradients.
Here we took five major approaches applied them blindly to the whole genome and let the analysis show us where the fingerprints of selection are and
These data can be accessed at Phytozome DOE JGI's plant comparative genomics portal. That's a massive number of naturally occurring variants a lot in cell wall chemistry genes and other known productivity genes.
If you know every base in a genome you can skip whole generations and use genomic information to predict how well an individual will do said he.
The above story is provided based on materials by DOE/Joint Genome Institute. Note: Materials may be edited for content and length.
#Evolutionary history of honeybees revealed by genomicsin a study published in Nature Genetics researchers from Uppsala University present the first global analysis of genome variation in honeybees.
We have used state-of-the-art high-throughput genomics to address these questions and have identified high levels of genetic diversity in honeybees.
The evolutionary tree we constructed from genome sequences does not support an origin in Africa this gives us new insight into how honeybees spread
Hidden in the patterns of genome variation are signals that indicate large cyclical fluctuations in population size that mirror historical patterns of glaciation.
This sweet discovery all started with the chicken genome. Before scientists sequenced its genes people assumed that chickens
The gene for tasting sweetness is present in their genomes but it's nonfunctional. Scientists suspect that an interplay between taste receptors
The chicken genome is another story: It has no trace of a sweet-taste receptor gene.
More bird genomes were sequenced and still no sweet receptor. So began Baldwin's quest to understand how hummingbirds detected sugar
but is the result of a variety of genetic changes throughout the genome that influence height.
What we think we see is that regions of the genome that are involved in the Batwa's Pygmy phenotype do not look the same in West Africa said Perry.
This longest-surviving group was the only one that had the human thrombomodulin gene added to the pigs'genome.
Genomic prediction uses genome-wide markers to predict future individuals or species. These markers are genes
The method simply uses all markers of the entire genome to predict a trait. Classical marker-assisted selection only uses markers that have large effects on the trait Xu explained.
and genome prediction can be performed to predict disease risk for a person. Xu was joined in the research by Qifa Zhang and his student Dan Zhu at Huazhong Agricultural University China.
Recent advances that allow the precise editing of genomes now raise the possibility that fruit
Genome editing of fruit has become possible today due to the advent of new tools--CRISPR TALEN and the like--and also because of the extensive and growing knowledge of fruit genomes.
In a Phd project at the National Food Institute Technical University of Denmark the latest technologies within whole genome sequencing were exploited to develop new methods to identify genes which are important for the survival of MRSA in pigs.
In her Phd project at the National Food Institute Phd student Mette Theilgaard exploited the latest technologies within whole genome sequencing
They also combined 33 new transcriptomes a set of RNA molecules with 13 genomes both
#Generating a genome to feed the world: African rice sequencedan international team of researchers led by the University of Arizona has sequenced the complete genome of African rice.
The genetic information will enhance scientists 'and agriculturalists'understanding of the growing patterns of African rice as well as enable the development of new rice varieties that are better able to cope with increasing environmental stressors to help solve global hunger challenges.
The paper The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication was published online in Nature Genetics on Sunday.
The effort to sequence the African rice genome was led by Rod A. Wing director of the Arizona Genomics Institute at the UA and the Bud Antle Endowed Chair in the School of Plant sciences in the UA College of Agriculture
Now with the completely sequenced African rice genome scientists and agriculturalists can search for ways to cross Asian
and her book served as one of the inspirations behind sequencing the African rice genome.
The African rice genome is especially important because many of the genes code for traits that make African rice resistant to environmental stress such as long periods of drought high salinity in the soils and flooding.
Now that we have a precise knowledge of the genome we can identify these traits more easily
or through genetic modification techniques noted Wing who is also a member of the UA's BIO5 Institute and holds the Axa Endowed Chair of Genome Biology and Evolutionary Genomics at the International Rice Research
what geneticists call physical maps a tool that enables scientists to understand the structure of the genome.
and donated it to the Rice Genome Project making sequencing of that complete genome possible.
Much of the evolutionary analysis of the genome was performed by Muhua Wang a UA plant sciences doctoral candidate and by Carlos Machado of the University of Maryland.
Yeisoo Yu a research associate professor in Wing's research group at the Arizona Genomics Institute led the sequencing effort.
In analyzing the 33000 genes that make up the African rice genome the researchers discovered that during the process of domestication Africans
Additionally the sequenced genome helps resolve questions about whether African rice originally was domesticated in one region or in several locations across Africa.
By comparing the genome with what is known about the genetic structure of wild varieties Wing
From 1998 to 2005 Wing led the U s. effort to help sequence the genome of Asian rice which is the only other domesticated rice species. Those results were published in the journal Nature in 2005
and analyzing the genomes of the wild relatives of African and Asian rice. By understanding the entire genus at a genome level we have a whole new pool of genetic variation that can be used to combat pests
and plant pathogens Wing explained. One example he said would be adding disease resistance genes from all of the wild rice varieties to a species of cultivated rice creating a new super-crop that is resistant to diseases and pests.
In November Wing and his collaborators will celebrate the 10th anniversary of the completion of the Asian rice genome
and the new completion of the African rice genome at the 12th International Symposium on Rice Functional genomics a conference that will be held in Tucson Arizona.
Sequencing of the African rice genome was made possible by National Science Foundation grants#0321678#0638541#0822284 and#1026200 to the Oryza Map Alignment and Oryza Genome Evolution Projects.
#Stress-tolerant tomato relative sequencedthe genome of Solanum pennellii a wild relative of the domestic tomato has been published by an international group of researchers including the labs headed by Professors Neelima Sinha and Julin
The new genome information may help breeders produce tastier more stress-tolerant tomatoes. The work published July 27 in the journal Nature Genetics was lead by Bjã rn Usadel and colleagues at Aachen University in Germany.
Using the new genome data the researchers found genes related to dehydration resistance fruit development and fruit ripening.
As we isolate viruses we can completely sequence their genomes Hause said. We can get a good understanding of
#Genome analysis helps in breeding more robust cowsgenome analysis of 234 bulls has put researchers including several from Wageningen Livestock Research on the trail of DNA variants
These are the first results of the large 1000 Bull Genomes project on which some 30 international researchers are collaborating.
and Genomics Centre of Wageningen UR investigated whether the genomes of all the common bulls in The netherlands can be filled with the help of these 234 bulls.
Currently these bulls have been genotyped with markers of 50000 or 700000 DNA variants. The positive results indicate the direction for further research into the practical use of genome information in breeding.
Dairy and beef cattle The project demonstrates how useful large-scale DNA analyses can be says Professor Roel Veerkamp Professor of Numerical Genetics at Wageningen University and board member of the 1000 Bull Genomes project.
He emphasises that the requirements for dairy and beef cattle are becoming ever more exacting: Until the mid nineties a cow primarily had to produce a lot of milk.
and by means of genome analysis we want to improve this further says Veerkamp. Bull genome The genome of a bull consists of 3 billion'letters'.
'In the 234 bulls studied the researchers found a total of over 28 million positions on the DNA
whether the new genome information can help to predict even better which characteristics the offspring will have.
The bull analysis presented at this time is the first phase of the 1000 Bull Genomes project a database which is planned to incorporate the genomes of a thousand bulls from all over the world.
Chinese pigsthe Wageningen research has demonstrated that different parts of the genome of commercial pigs are much closer to Chinese pigs than to European wild boar.'
#Chromosome-based draft of the wheat genome completedseveral Kansas State university researchers were essential in helping scientists assemble a draft of a genetic blueprint of bread wheat also known as common wheat.
The International Wheat Genome Sequencing Consortium which also includes faculty at Kansas State university recently published a chromosome-based draft sequence of wheat's genetic code
which is called a genome. A chromosome-based draft sequence of the hexaploid bread wheat genome is one of four papers about the wheat genome that appear in the journal Science.
The genetic blueprint is an invaluable resource to plant science researchers and breeders said Eduard Akhunov associate professor of plant pathology
and a collaborator with the International Wheat Genome Sequencing Consortium. For the first time they have at their disposal a set of tools enabling them to rapidly locate specific genes on individual wheat chromosomes throughout the genome Akhunov said.
This resource is invaluable for identifying those genes that control complex traits such as yield grain quality disease pest resistance and abiotic stress tolerance.
The wheat genome sequence provides a foundation for studying genetic variation and understanding how changes in the genetic code can impact important agronomic traits.
Akhunov Shichen Wang a programmer and bioinformatics scientist in plant pathology and Jesse Poland assistant professor of plant pathology collaborated with the International Wheat Genome Sequencing Consortium to order genes along the wheat chromosomes.
and director of the Wheat Genetics Resource Center and Bernd Friebe research professor who developed genetic material that was essential for obtaining the chromosome-based sequence of the wheat genome.
The wheat genome only has 21 chromosomes but each chromosome is very big and therefore quite complicated Akhunov said.
This is nearly three times more information than is in the entire rice genome. So trying to sequence this chromosome
--and this genome--end-to-end is complicated an extremely task. In order to analyze the vast amount of genetic information researchers used a technique called shotgun sequencing.
This divided the wheat genome into chromosomes and then split each chromosome into smaller segments.
The chromosome-based daft sequence the critical step before the full wheat genome is sequenced Akhunov said.
The consortium estimates the full genome sequence will be available in three years. The research is funded by the U s. Department of agriculture's National Institute of Food and Agriculture.
and Genomics (CBGP) of Universidad Politã cnica de Madrid (UPM) conducted infection assays of commercial kiwis with Alternaria alternata spores which is a pathogenic fungus involved in chronic asthma
#A-maize-ing double life of a genomeearly maize farmers selected for genes that improved the harvesting of sunlight a new detailed study of how plants use'doubles'of their genomes reveals.
when the plant made a double of its genome--a'whole genome duplication'event. They then traced how maize evolved to use these'copied'genes to cope with the pressures of domestication
A report of the research is published this week in the journal Genome Research.''Although whole genome duplication events are widespread in plants finding evidence of exactly how plants use this new'toolbox'of copied genes is said very difficult Dr Steve Kelly of Oxford university's Department of Plant sciences
lead author of the report.''With crops like wheat it's not yet possible for us to unravel the'before
'It is particularly useful for such genetic detective work that close relatives of maize did not duplicate their genomes 10 million years ago:
'Whole genome duplication events are key in allowing plants to evolve new abilities'said Dr Kelly.'
and assembled a draft genome of wild soybean W05 and developed a recombinant inbred population for genotyping-by-sequencing
Through this study researchers developed an efficient strategy using the combination of whole-genome de novo sequencing high-density-marker QTL mapping by re-sequencing and functional analyses
Whole-genome sequence analysis of the yogurt isolate confirmed it as being closely related to Mcc and also revealed the possibility that this fungus could produce harmful metabolites that were previously unknown in this species. The researchers then tested the strain on mice where the fungus showed an ability to cause lethal infections
In some cases the virus incorporated part of a cow gene or another virus in the part of the genome in which most mutations take place Chase explains.
The researchers from the Australian Centre for Plant Functional genomics at the University of Adelaide's Waite campus within the University's School of Agriculture Food and Wine say that in soils where boron toxicity is reducing yields genetic improvement
Dr Sutton says wheat has been difficult to work with in genomics. The wheat genome is very large with about six times the number of genes as humans.
This complexity has meant that genes controlling yield and adaptation to environmental stresses have remained extremely challenging to identify.
Advances in molecular biology and genetics technologies of the past few years coupled with the extensive collections of wheat genetic material available around the world have paved the way for a new era in the analysis of complex genomes such as
#Pig whipworm genome may aid to treat autoimmune diseasesan international team composed of 11 institutions from six countries including BGI presented the whole-genome sequence of Trichuris suis a parasitic worm in pig.
In this study researchers sequenced the genomes of single adult female and male pig whipworm at about 140-fold coverage producing draft assemblies of 76 Mb and 81 Mb respectively.
Li Hu Project Manager from BGI said The constructed pig whipworm genome sequence provides us a genetic resource for deeply investigating the mechanisms underlying human autoimmune diseases.
so a team of researchers led by the US Department of energy Joint Genome Institute (DOE JGI) deployed high throughput DNA sequencing
The study was published online June 6 2014 in Genome Research We wanted to understand why some sheep produce a lot
The above story is provided based on materials by DOE/Joint Genome Institute. Note: Materials may be edited for content and length.
Scientists sequence genome of eucalyptus--a global tree for fuel and fiberfrom antiseptic oils to the construction of didgeridoos the traditional Australian Aboriginal wind instrument the eucalyptus tree serves myriad purposes accounting for its status as one of the world's most widely planted hardwood trees.
and analyze the 640 million base pair genome of Eucalyptus grandis engaged more than 80 researchers from 30 institutions representing 18 countries The project was led by Zander Myburg of the University of Pretoria (South africa);
Gerald Tuskan of the Oak ridge National Laboratory and the Bioenergy Science Center and U s. Department of energy Joint Genome Institute (DOE JGI;
Combing through the 36000-plus genes found in Eucalyptus (nearly twice as many as in the human genome) the researchers homed in on those that may influence the production of secondary cell wall material that can be processed for pulp paper biomaterials and bioenergy applications.
Our comparative analysis of the complex traits associated with the Eucalyptus genome and other large perennials offers new opportunities for accelerating breeding cycles for sustainable biomass productivity and optimal wood quality noted Grattapaglia.
Genome sequencing is an essential diagnostic tool for understanding the basis of its superior growth properties attributes that can be propagated to other candidate biofuel feedstock species. Because of its wide adaptability extremely fast growth rate
The team's detailed analysis of the Eucalyptus genome revealed an ancient whole-genome duplication event estimated to have occurred about 110 million years ago as well as an unusually high proportion of genes in tandem duplicate arrays.
Our results in Eucalyptus suggest that cumulative effects of many small genetic variants throughout the genome are responsible for these fundamental genetic phenomena.
The above story is provided based on materials by DOE/Joint Genome Institute. Note: Materials may be edited for content and length.
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