A search of plant genome databases found them to contain no genes comparable to those of certain bacteria known to make the gas.
and precisely where they are located in the genome could speed things up significantly, breeders say.
Furthermore, the nuclear genome may have difficulty communicating with energy-producing structures called mitochondria which are inherited directly from the mother,
which bind to specific sites in a genome and then cut nearby strands of DNA.
Plant biologists have long been frustrated by the lack of a simple method for either deleting a specific gene from the genome or replacing it with another gene.
the fast-growing weed with a small genome favoured by many plant biologists as a model system,
complex genomes, chock full of large families of genes with very similar DNA sequences, says Vipula Shukla, a scientific group leader at Dow Agrosciences in Indianapolis, Indiana.
we insert the transgene somewhere in the genome, and we don't know exactly where it happens to insert,
Nature Newsa white-faced, red-coated Hereford cow named Dominette has become the first cow to have sequenced its genome.
Information from the 5-year, US$53-million cow-genome project is being used to trace the genetic legacy of bovine domestication after centuries of careful breeding.
But the bovine genome is large at 3 billion bases, it is roughly the same size as the human genome making it difficult to study.
In the absence of genomic information, breeding programmes have relied on tracking the physical characteristics of the animals,
says James Womack, a genome researcher at Texas A&m University in College Station, and another member of the consortium.
Dominette's genome sequence, published today in Science1, has revealed also a few genetic underpinnings of the bovine lifestyle.
Researchers have used also the genome sequence to assemble a collection of more than 37,000 locations in the genome that contain frequent single-base changes in DNA sequence2.
and much more diverse than dogs, says Kim Worley, a genome researcher at the Baylor College of Medicine in Houston, Texas,
But Harris Lewin, a genome biologist at the University of Illinois at Urbana-Champaign who also assisted with the analysis of the genome
estimates Van tassel. The new sequence also shows that the human genome is more similar to the genome of cattle than to mice suggesting that, for some diseases,
the need to engineer plants that generate their reproductive cells by mitosis rather than by meiosis, the form of cell division that shuffles the genome and passes different selections of genes into each reproductive cell.
these cells are diploid (containing two copies of the genome), like the body cells of the plant, rather than haploid (containing one copy of the genome) like normal reproductive cells.
The triple mutants are reminiscent of a mutant reported last year by Imran Siddiqi and his colleagues at the Centre for Cellular and Molecular biology in Hyderabad
Fungus genome boosts fight to save North american forests: Nature Newscanadian researchers have decoded the DNA of the tree-killing fungus found in the mouths of mountain pine beetles,
Further genome sequencing of the beetle and pine tree species should help forest managers design better pest-control tactics,
who is leading the Can$11. 9m (US$11. 1m) multi-species genome initiative. What really happens in nature is confined not to one species
Bohlmann and his colleagues assembled the fungus's 32.5-million-base-pair genome which is around a hundredth the size of the human genome,
using a combination of next-generation and traditional sequencing technologies the first time that a complex eukaryotic organism has been sequenced from scratch using such a hybrid approach
The genome was reported online this month in the journal Genome Biology1. They've done a very careful analysis of
says Steve Rounsley, a genome researcher at the University of Arizona in Tucson, who was involved not in the study.
For the other two species the beetle and the tree the researchers are concentrating mainly on expressed gene sequences, fragments of the complete DNA sequence, rather than the genomes in their entirety.
have taken the fungus genome, pinpointed the gene responsible for staining the pine wood blue and created a knockout strain that does not produce any pigment.
But the full utility of the fungus genome might only be realized after other related species are sequenced also,
You need more than one genome to do that. Using genomics to stop the bark beetles is a bit of a long shot
for sure, admits Chris Keeling, a research associate in Bohlmann's lab. But it might offer the best strategy for containing the forest pests,
Now Chad Nusbaum, co-director of the Broad Institute's genome sequencing and analysis programme in Cambridge, Massachusetts,
When comparing P. infestans with similar organisms in the same genus, stretches of the genome stood out as being highly variable,
and jump around in the genome. The researchers believe that the transposons, which make up about 74%of this unusually unwieldy genome,
code for the blight's'weapons'against potatoes. That is an insane number. For microbes 25%is a lot,
2008) mean corruption of traditional genomes is inevitable. Events Hwang convicted Disgraced South korean cloning scientist Woo Suk Hwang left Seoul Central District court on 26 october knowing that his sentence,
See also'Maize genome sequenced'.
Maize genome mapped: Nature Newsplant biologists have something special to be thankful for this US Thanksgiving day.
The genome of maize (corn) a staple crop first introduced by Native americans to the European settlers centuries ago has finally been sequenced.
The genetic secrets of maize, one of the world's most widely grown grains, should accelerate efforts to develop improved crop varieties to meet the world's growing hunger for food, animal feed and fuel.
The genome is really a tremendous resource, says John Doebley, a maize geneticist at the University of Wisconsin-Madison who was involved not in the project.
US$31-million project to sequence maize (Zea mays) was led by a US-based consortium of researchers who decoded the genome of an inbred line of maize called B73, an important commercial crop variety.
which can move around the genome and cause mutations, are the most abundant parts of the sequence,
spanning almost 85%of the genome. What we have here is a crucial part of the instruction manual for how you breed a better corn plant
says Richard Wilson, director of the Genome Center at Washington University in St louis, Missouri, who led the maize-genome project.
You can now find where genes that underlie certain traits are located, and, thus, you have the tools for how you go off
Joachim Messing, director of the Plant Genome Initiative at Rutgers University in Piscataway, New jersey, who was involved not in the sequencing, says he was surprised by how well previous analyses based on small snippets of the genome predicted some of the overall trends.
Practically all the things that we had forecast before could be validated with the entire sequence he says.
The newly minted genome was published today in Science1, together with 13 companion analyses in Science and the Public library of Science Genetics.
After sequencing their first maize genome, researchers then tackled other corn varieties for comparison. Luis Herrera-Estrella and his colleagues at the Research and Advanced Studies Center of the National Polytechnic institute (CINVESTAV) in Irapuato, Mexico, sequenced a maize variety from the Mexican highlands called Palomero.
The team report that the Palomero genome is around 400 million nucleotides smaller and contains about 20%less repetitive DNA than B732.
You can contain three Arabidopsis genomes or one rice genome in the size difference between those two maize genomes, notes Virginia Walbot,
and complementary sets of genes, says maize geneticist Patrick Schnable, an author on the genome paper1.
In a separate study, Schnable and his colleagues at Iowa State university in Ames compared the genome structures of B73 with those of another inbred line called Mo17.
The resource can also be used to produce heartier corn varieties by systematically scanning the genome for genes that underlie key traits,
This genome will allow us to develop tools to make their jobs a little easier.
the director of the programme and clinical director at the National Human genome Research Institute in Bethesda says that of approximately 2, 500 inquiries,
The issue also included a four-page report by two evolutionary biologists, who disputed Williamson's hypothesis on the basis of published genome size data.
The giant panda genome, which was published online in Nature last month3, also revealed little sign of inbreeding, says Jun Wang of the Beijing Genomics Institute in Shenzhen, China.
But the genome is likely to prove invaluable for solving the mystery of the brown pandas of Qinling.
There are over 125 genes known to affect pigmentation in mice says Hopi Hoekstra, an evolutionary biologist at Harvard university in Cambridge, Massachusetts,
2001 papers announcing the draft sequence of the human genome. 1, 968 Number of authors on 2010 paper of initial results from the Compact Muon Solenoid detector at the Large Hadron Collider.
A team of European researchers has decoded the genome of the delectable PÃ rigord black truffle.
who was involved not in the genome study, which is published online in Nature1. People go out into the woods at night with dogs
The genome really changes everything, says Martin. We now have a few thousand markers that will clearly be useful for professionals.
The genome of the black truffle (Tuber melanosporum) includes genes encoding flavour-related sulphur metabolites
But we in fact demonstrated that the volatiles giving rise to the truffle's perfume are encoded in the truffle's genome.
The T. melanosporum genome also reveals that the fungus reproduces sexually more often than researchers thought.
in which two haploid cells from a single fungus each with one copy of the genome fuse to form the diploid fruiting body (the truffle),
In 2008, Martin and his colleagues reported the genome of Laccaria bicolor, another symbiotic fungus that is dependent on woody plants for nutrients2.
The 125-megabase black truffle genome is bigger than that of L. bicolor and four times larger than that of many fungi but it contains far fewer protein-coding genes.
Although the sequenced genome opens up the possibility of genetically engineering other fungi to pack the same aromatic punch as the PÃ rigord
Arabidopsis thaliana has been the darling of plant biologists for some 30 years because of its small genome and rapid growth,
and in 2000 it became the first plant to have sequenced its genome. To capitalize on this, the US National Science Foundation (NSF) soon afterwards dedicated US$200 million towards determining the function of every Arabidopsis gene by 2010.
and have large genomes. By studying thousands of plants in a single greenhouse, scientists can conduct experiments in a fraction of the time
. But sequencing technology is improving so quickly that genome size is no longer the barrier it once was.
As more crop genomes are sequenced, including maize (corn) and rice, researchers can increasingly study crop species directly,
Annotation of the Arabidopsis genome the linking of biological data to sequence information is considered now among the highest quality of all sequenced genomes.
The NSF's Plant Genome Research Program and the Department of agriculture's competitive funding programme have favoured increasingly grants for work on agricultural species in recent years.
With the Dutch Institute for Public health and the Environment, Roest's team is carrying out genome sequencing and comparisons of different strains.
including genome sequences that are held currently in large repositories such as Genbank. The website (www. biotorrents. net) uses Bittorrent's peer-to-peer file sharing technology,
Pretorius and his team analysed the genomes of the new stem rust variants and compared them to the genome of a common
and less dangerous form of the fungus found in South africa in 2000. The team found that the variant detected in 2007 is likely to have arisen through a single mutation of the more common form,
Business Genome shopping: The US pharmacy chain Walgreens postponed plans to start selling a personal genome-testing kit in thousands of its shops last week,
after the Food and Drug Administration began an investigation into whether the kits require regulatory approval.
The $30 saliva-collection kit is manufactured by Pathway Genomics, a direct-to-consumer genetic testing company based in San diego, California.
Some argue that the many RNAS observed to be transcribed from the vast stretches of non-coding DNA between known genes are merely artefacts of the high-throughput technology used to detect RNAS on a genome-wide scale (see'Existence of RNA dark
In scans of the genome, a DNA sequence is considered generally not potentially protein-coding unless it can encode a string of more than 100 amino acids.
Short peptides could be lurking virtually anywhere in the genome, says Desplan. Sequence analysis suggests that DNA regions capable of encoding tiny peptides exist in front of many protein-coding genes,
It should be possible to scan the genome for sequences encoding peptides shorter than 100 amino acids
Business Genome market Complete Genomics, one of the handful of young US companies offering fast, cheap genome sequencing,
California, says it has sequenced more than 400 complete human genomes this year alone. On its first day of public trading
Smorgasbord of genomes for food lovers: Nature Newsgenome gastronomes rejoice! Today sees the publication of genome sequences behind two of the tastiest treats:
the cacao tree, whose beans yield chocolate, and the woodland strawberry. Earlier this year, a team backed by food giant Mars unveiled a preliminary sequence of the cacao tree Theobroma cacao.
Now a team partly supported by rival chocolate company Hershey has become the first to get a genome of the valuable plant into a peer-reviewed journal1.
the genome, published in Nature Genetics, looks at the Belizean Criollo variety of the crop.
This is an important factor in producing a high quality genome sequence. Although fine cocoa commands a high price,
Having two cacao genomes will be particularly valuable and should provide additional candidate genes for important traits,
research leader of the Stoneville, Mississippi-based Genomics and Bioinformatics Research Unit at the US Department of agriculture's Agricultural research service,
when the genome was assembled. There indeed might be chromosomal inversions distinguishing these varieties, because they are related distantly,
But determining that will probably require refinements to the assemblies of both genomes, and additional data.
The genome of the woodland strawberry, also known as the wild or alpine strawberry, is published also today in Nature Genetics2.
Fragaria vesca the fleshy shoot tips of which are technically neither fruit nor berry has a relatively small genome.
The authors of the new paper on its genome note that it takes up very little space
The researchers sequenced the nuclear genomes of both types of African elephant as well as that of the Asian elephant (Elephas maximus).
By comparing all these genomes, the team found that the forest and savanna elephants diverged into separate species between 2. 6 and 5. 6 million years ago.
Examining the nuclear genome which is around 200,000 times larger than that contained in mitochondria,
and helped to launch the field of proteomics. In 2005, Fenn lost a legal battle over the patent rights to Yale university in New haven, Connecticut,
they sequenced the genomes of four of the potato blight's sister species, including Phytophthera phaseoli,
and compared these genomes with the genome of the previously sequenced P. infestans. They discovered that the pathogens shared many'housekeeping'genes,
The genetically conserved part of the genome could be the potato blight pathogen's Achilles heel, adds Kamoun.
and pathogenicity are located also in areas of the genome that are enriched with non-coding DNA repeats.
it would need to simultaneously change its own genome and that of the enzyme in eight different spots a highly unlikely event.
Whereas resistance to a particular herbicide might be pinned down to one gene, the response to drought plays out across the genome.
Coming up 22 23 february In La jolla, California, leading genetics researchers gather to discuss the promise of human genomics over the next decade. go. nature. com/w8zzsx 23 february NASA's Glory
or using biotechnology to alter its genome and increase its nutritional yield, explains Pena-Rosas.
Genome grants The US National institutes of health's ENCODE (Encyclopedia of DNA Elements) programme which aims to catalogue all the functional elements of the human genome,
has been granted a US$123-million expansion. On 16 may, an advisory council to the National Human genome Research Institute,
which runs the programme, approved the money to allow the agency to develop calls for research proposals.
Nature Newsfor Scott Cornman, the honeybee genome is prized a resource, yet he spends much of his time removing it.
His strategy is to subtract the honeybee genome from every other stray bit of genetic residue he can find in bee colonies, healthy and diseased.
or so researchers in attendance last week at the Honey Bee Genomics & Biology meeting, held at Cold Spring Harbor Laboratory in New york. It was dedicated the first conference on the topic
soon after the honeybee genome was sequenced (Honeybee Genome Sequencing Consortium Nature 443,931-949; 2006), and for many it was a chance to marvel at a field transformed.
Around the same time that the genome was published first, honey  bee colonies across much of the Northern hemisphere began to show alarming declines.
Genomics is yielding new clues to the still-mysterious phenomenon, as well as potential strategies for protecting the insects from a multitude of threats.
The genome offers a window into the bees'immune pathways, Evans adds. The goal is to identify the genes that are crucial in helping bees thwart attack,
The genome of strain O104: H4 has been sequenced, and it shares many genes with enteroaggerative E coli (EAEC) strains.
Scientists in Germany are feverishly analysing the genome sequence of the bacterium, and have found clues as to how this strain
Gad Frankel, a microbiologist at Imperial College London, suspects that the genome of this strain will reveal more information about the adherence mechanisms of E coli.
The bacterium Agrobacterium tumefaciens which can cause tumours on plants shuttled foreign genes into plant genomes.
By revealing similar elements in plants'DNA, genome sequencing has liberated developers from having to borrow the viral sequences.
Many companies are developing'mini-chromosomes'that can function in a plant cell without needing to be integrated into the plant's genome.
Other techniques under development insert foreign genes into designated sites in the genome, unlike the near-random scattering generated by Agrobacterium.
and Sangamo Biosciences in Richmond, California, announced that they had used enzymes called zinc-finger nucleases to insert a gene for herbicide resistance at a specific site in the maize genome (V. K. Shukla et al.
All eyes on the potato genome: Nature Newsa global effort has cracked finally the complex genome of the potato,
which is published today in Nature1. The not-so-humble potato (Solanum tuberosum) is the world's fourth most important food crop
Its genome comprises more than 39,000 protein-coding genes, and it is a highly heterozygous autotetraploid this means that it has four copies of every chromosome,
UK one of the 26 research institutes that came together from around the globe to form the Potato Genome Sequencing Consortium several factors made the sequencing possible.
But the key was finding a type of potato with a genome that could be simplified adequately.
has a diploid genome, meaning that it has a more manageable 2 copies of every gene.
although due to its heterozygosity were not able to assemble it into a complete genome. It's quite nice actually
But M. giganteus is a headache in the lab. Its genome has few markers to help would-be breeders keep track of desirable genes,
a quick-growing weed with a small genome that serves as a reference for plants that are harder to study.
) Many Arabidopsis researchers are now hoping to apply what they have learned from the weed to agriculturally important species with genomes once considered too big to tackle.
and what's coming out of the genome, says Andy Baxevanis, a genomicist at the National Human genome Research Institute in Bethesda, Maryland.
His team recently sequenced the genome of the comb jelly Mnemiopsis leidyi, and is now comparing it to sequences from sponges,
cnidarians, worms and other animals to sort out which lineages came first. So far, he says,
NHGRITREND watch The US National Human genome Research Institute (NHGRI) announced a four-year plan on 6 december that focuses heavily on the use of genome sequences in the clinic.
Business Cheap genomes The US$1, 000 genome has arrived according to US biotech firm Life Technologies of Carlsbad, California,
the latest version of the Ion Personal Genome Machine that it launched late in 2010 (see Nature 475,278;
2011), would be able to sequence a genome in a day for $1, 000. Hepatitis C hopefuls Pharmaceutical giant Bristol-myers squibb of New york city has become the latest company to spend billions on the promise of hepatitis C treatments.
Denisovan genome The complete genetic sequence of an extinct relative of humans the Denisovan was posted online (see go. nature. com/vvtcfi) on 6 february,
Researchers from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, mapped every position in the genome an average of 30 times, improving on the 1. 9-fold coverage in their 2010
draft genome (D. Reich et al. Nature 468 1053-1060; 2010). ) A 30,000-50,000-year-old finger bone found in the Denisova Cave, southern Siberia,
including the Influenza Genome Sequencing Project a major initiative run by the National Institute of Allergy and Infectious diseases (NIAID) to boost the sequencing of existing isolates.
The Influenza Genome Sequencing Project is also helping by generating vast quantities of sequences it now accounts for half of all avian
And the woman's genome provides clues as to how agriculture spread across Europe.""The farmer is most genetically similar to people living in Cyprus
Focusing on DNA from chloroplasts and mitochondria energy-producing structures in cells that have their own genomes the researchers produced 49,000 genetic sequences.
Tomato genome sequence bears fruitthe genome sequence of one of the world s highest-value salad plants the tomato has been decoded by an international team of scientists,
According to the leaders of the UK arm of the Tomato Genome Consortium, Graham Seymour at the University of Nottingham and Gerard Bishop, formerly of Imperial College London,
With more than 80%of the genome sequenced, and more than 90%of the genes within it identified,
It's one of the better genomes out there says Van Deynze. Giovanni Giuliano, from the Italian National Agency for New Technologies, Energy and Sustainable Economic Development in Rome,
and a lead researcher on the project, explains that the group started out using traditional tools to sequence the genomes of the domesticated tomato cultivar Heinz 1706 (the one used to make the famous ketchup) and its closest wild relative, Solanum pimpinellifolium.
and switched to the much faster method of whole-genome shotgun sequencing. In this technique, large chunks of DNA are sequenced separately
then assembled into the genome. Giuliano says that one of the most exciting discoveries was that the entire tomato genome was copied in triplicate on two separate occasions.
The earlier event occurred about 130 million years ago, and was identified first in grapes (Vitis vinifera) 2,
"Several of the genes born at that second triplication stayed in the genome for tens of millions of years,
UK,"is to link this genome sequence to traits that are useful and important, especially for food security and human health
Sequencing prize A US$10-million contest to sequence the genomes of 100 Â centenarians in 30 Â days has its first entrant:
Connecticut, said on 23 Â July that it would attempt to win the Archon Genomics X Prize,
The contest requires a cost-per-genome below $1, 000. See page 417 for more.
researchers could engineer these genes into the genome of a harmless virus to create a vaccine.
because the techniques available to introduce foreign genes into animal genomes were not precise, and misplaced genes failed to express themselves correctly.
They inserted DNA encoding a version of this microrna into the genome to create genetically modified cow embryos that they hoped would grow into cows without the allergen in their milk.
but each TALEN targets a specific DNA sequence in the genome and cuts it. As the body repairs the break
and leaves no mark in the genome, says Bruce Whitelaw, a molecular biologist at the Roslin Institute near Edinburgh in the United kingdom,
For the past couple of decades they have been slowly teasing information from the pig genome,
This week s draft sequence of T. J. s genome (see page 393 with its detailed annotation a reference genome will speed progress on both fronts,
and perhaps even allow pigs to be engineered to provide organs for transplant into human patients."
so that they could work on animals all with the same genome. One set of clones was created at the National Swine Resource and Research center (NSRRC) in Columbia, Missouri,
"Making such pigs has got increasingly easier as knowledge of the genome increases, says physiologist Randall Prather, a co-director of the NSRRC,
Geneticist Martien Groenen, part of the team that sequenced the pig genome, chews the fat with Thea Cunningham.
This work will be enriched by the discovery, reported in the genome paper, of 112 gene variants that might be involved in human diseases.
Knowledge of the genome is also allowing scientists to try to engineer pigs that could be the source of organs,
early knowledge about the pig genome led to the discovery in 1991 of a gene involved in porcine stress syndrome, in
Having the full genome should also help investigators to breed out susceptibility to porcine reproductive and respiratory syndrome (PRRS),
Archibald, who works on PRRS, says that the high-quality genome sequence should help investigators zero in on the genes responsible.
But the pig genome is not just about applications. Lead co-author Martien Groenen, a genome researcher from Wageningen University in The netherlands, has resequenced the genomes of scores of different strains of wild and domestic pigs,
and used the information to show that the pig was domesticated independently in Asia and Europe.
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