Category Archives: Genome

April 12, 2017 by Pat Bailey Richard Michelmore, director of the UC Davis Genome Center, and colleagues have released the first comprehensive genome assembly for lettuce and the huge Compositae plant family, which includes diverse plants ranging from the sunflower to star thistle. Credit: Gregory Urquiaga/UC Davis

Today (April 12), UC Davis researchers announced in Nature Communications that they have unlocked a treasure-trove of genetic information about lettuce and related plants, releasing the first comprehensive genome assembly for lettuce and the huge Compositae plant family.

Garden lettuce, or Lactuca sativa, is the plant species that includes a salad bar's worth of lettuce types, ranging from iceberg to romaine. With an annual on-farm value of more than $2.4 billion, it is the most valuable fresh vegetable and one of the 10 most valuable crops, overall, in the United States.

Lettuce is a member of the huge Compositae family, which includes the good, the bad, and the ugly of the plant world, from the daisy and sunflower to ragweed and the dreaded star thistle.

The genome assemblya compilation of millions of DNA sequences into a useful genetic portraitprovides researchers with a valuable tool for exploring the Compositae family's many related plant species.

"This genome assembly provides the foundation for numerous further genetic, evolutionary and functional studies of this whole family of plants," said Sebastian Reyes-Chin-Wo, the lead author and a graduate student in the laboratory of plant geneticist Richard Michelmore.

"This is particularly significant because Compositae is the most successful family of flowering plants on earth in terms of the number of species and environments inhabited," said Richard Michelmore, who directs the UC Davis Genome Center.

Triplicate genes may explain success:

The researchers found that specific genes in the lettuce genome were consistent with certain physical traitslike the production of a rubber-containing milky sapthat have also been found in taxonomically distinct species, such as the rubber tree.

The study also provided evidence that somewhere during the evolution of lettuce about 45 million years ago, its genome was "triplicated." As a result, one-fourth of the genomeincluding about 30 percent of all of its identified genesnow appears in multiple related regions. Because such genomic duplications may give plant species an advantage in colonizing new environments, the ancient triplication event might, in part, explain the success of the Compositae plant family.

New technology yields more precise information:

Michelmore noted that this is the first reported genome assembly of a plant species resulting from use of a new technology that gives information about the physical proximity of the DNA sequences to which proteins are bound.

The new approach, developed by Dovetail Genomics, a company spun out from UC Santa Cruz, resulted in a more contiguous and accurate genome assembly, even though lettuce has one of the larger plant genomes sequenced to date, he said.

More information: Sebastian Reyes-Chin-Wo et al, Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce, Nature Communications (2017). DOI: 10.1038/ncomms14953

Provided by: UC Davis

Feb 20, 2014

Advances in DNA sequencing technologies have enormous potential for the plant sciences. With genome-scale data sets obtained from these new technologies, researchers are able to greatly improve our understanding of evolutionary ...

Apr 05, 2016

As vegetable growers face a lack of skilled farm labor and higher production costs, they are searching for effective, lower-cost mechanical means of getting their products to market. In a study in the February 2016 issue ...

Dec 03, 2015

Researchers from the University of Bristol have uncovered one of the reasons for the evolutionary success of flowering plants.

Mar 28, 2016

Like most annuals, lettuce plants live out their lives in quiet, three-act dramas that follow the seasons. Seed dormancy gives way to germination; the young plant emerges and grows; and finally in the climax of flowering, ...

Apr 06, 2015

Prickly lettuce, a common weed that has long vexed farmers, has potential as a new cash crop providing raw material for rubber production, according to Washington State University scientists.

May 15, 2015

U.S. Department of Agriculture (USDA) scientists in California have developed 16 new lettuce breeding lines. Lettuce production in the United States is concentrated mostly in California and Arizona, where it is grown year-round. ...

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Gene salad: Lettuce genome assembly published

SmartNews Keeping you current Sandy Maliki (Barry Eggleton/Pure Dingo)

smithsonian.com April 17, 2017

It sounds like an argument scientists might have during a night of drinking: Which creature has the world's most interesting genome? But the question is more than a passing musing.

San Francisco biotech company Pacific Biosciences held a public competition to determine which critter should receive the honor. The winner: Sandy Maliki, a pure-bred Australiandesert dingo. The company will now sequence the dingo's genometo help researchers study the process of domestication.

Sandy beat out four other interesting finalists in the competition, receiving 41 percent of the public votes, which were cast from around the world. This is the fourth year the company has sponsored the competition. The company invites researchers to send in grant proposals explaining why the interesting plants and animals they study should be sequenced. Then a committee of scientists whittles the entries down to five finalists for the final public vote.

This year, the finalists included the explosive bombardier beetle, which emits a boiling hot explosive gas when attacked; the pink pigeon, an endangered relative of the extinct dodo;a sea slugthatsteals chloroplasts from algaeand the temple pit viper, whose venom could have medicinal value.

While Rhett Jones at Gizmodo argues that the dingo won because it's cuteand the internet loves cutethe researchers from the University of New South Wales who put together the proposal think its genome has scientific merit, too.

Bill Ballard at UNSW tells Kim Arlington at The Sydney Morning Herald that Darwin believed domestication was a two-step process. The first step is a naturally occurring process called unconscious selection, which leads to traits in an animal that might make it suitable for domestication. The second step is artificial selection, in which humans selectively breed those animals to amplify or diminish specific traits.

Sandy is one of three wild desert dingo pups found abandoned in the desert in central Australia in 2014. Purebred dingoes are rare because of widespread interbreeding with domestic dogs. So Sandy can teach researchers about unconscious selection and what natural traits made wild dogs suitable for domestication.

There's a lot people don't know about dingos. It's not clear whether they are a type of domestic dog or a distinct species. It's also unknown how they arrived in the Land Down Under. But since native Australians did not domesticate dingos, purebred animals remain essentially unchanged since they arrived.

Sandy is truly a gift to science, Ballard says in a press release. [S]equencing Sandy's genome will help pinpoint some of the genes for temperament and behavior that underlie the transition from wild animals to perfect pets.

Ballard also says theres a conservation aspect to sequencing the genomesince it will allow researchers to improve tests to determine the genetic purity of dingoes.

The gene sequencing will take place at the University of Arizona using PacBios Single Molecule, Real-Time (SMRT) sequencing technique, which sequences much longer sections of DNA at one time compared to other techniques. The data will then be analyzed by the German company Computomics.

Last year, a type of plant that extracts heavy metals from the soil won the competition.

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Jason Daley is a Madison, Wisconsin-based writer specializing in natural history, science, travel, and the environment. His work has appeared in Discover, Popular Science, Outside, Mens Journal, and other magazines.

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Dingo Wins Competition for World's Most Interesting Genome ... - Smithsonian

Posted April 19, 2017 19:24:35

Australian researchers have played a pivotal role in a global project to map the barley genome.

Ten countries have spent a decade working on the genome project, which forms the basis for working out which genes control certain traits in the barley plant.

West Australian scientists from Murdoch University and the Department of Agriculture and Food of WA led the Australian research, with funding assistance from the Grains Research and Development Corporation (GRDC).

Lead researcher and Murdoch University Professor Chengdao Li said a better understanding of the barley genome would help the development of plants adapted for climate change.

But Professor Li said the genome map would also help improve the traits important in using malted barley for beer.

He said barley was a historically important crop because of its special "brewing genes".

"People believe human beings started to use the malt in the barley in the Stone Ages to make alcoholic beverages," he said.

"That's why [humans] started the plant cultivation process so long ago."

Scientists have previously mapped the rice genome, but Professor Li said it the barley genome was far more complicated.

He said Australian researchers had played such a significant role in mapping the barley genome because, along with wheat, it was such a significant crop for Australian farmers.

Barley exports are worth just under $1 billion to the West Australian economy with forty per cent of exports destined for malting, mainly for use in beer.

Department of Agriculture and Food principal scientist Dr Rob Loughman said mapping the barley genome would ultimately pave the way for better plant breeding.

Dr Loughman said improved breeding would provide marketing opportunities, but he said the main reason for breeding better plants would be to serve the growers.

"Farmers are certainly familiar with the importance of combining agronomic improvement with genetic improvement from new varieties," he said.

"The sorts of characteristics they look for are things that enhance productivity and yield, things that get their products into target markets and things that mitigate risks in cropping."

Dr Loughman said improved adaptability to climate change would be the most significant gain for farmers.

Topics: grain, genetics, research, research-organisations, perth-6000

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Barley genome will help crop adapt to climate change and improve malting for beer - ABC Local

19 Apr 2017 --- Scientists have created the most accurate navigation system for the bread wheat genome to date allowing academics and breeders to analyze its genes more easily than ever before.

Wheat is one of the world's most important staple cereals but is also the most complex. Three sub-genomes together contain around five times more DNA than the human genome. Nearly 80% of this genetic material is repetitive, making it even harder to sequence and analyze.

Now, harnessing advanced sequencing technology and computational approaches, scientists from the Earlham Institute, with colleagues at the John Innes Centre, have published the world's most complete picture of the wheat genome. It includes the location and detailed annotation of over 100,000 wheat genes. More than a fifth (22%) of these were completely absent from earlier assemblies, or found only as fragments.

"We applied the latest sequencing and bioinformatic techniques we have developed at our institute to the huge and complex wheat genome. We were able to achieve the best results anyone had seen, including uncovering previously hidden genes," says senior author Matthew Clark, Head of Technology Development at the Earlham Institute (EI).

"Moreover, all our methods are open, and available for anyone to use. This is critical as wheat DNA varies across the world, which is key to its success in different environments. We have already started to sequence many varieties of UK wheat using these methods, and we hope others will sequence the genomes of wheat important in their country," he says.

The results, published in Genome Research, focus on the variety called Chinese Spring -- the standard cultivar for genomic research. The genome and annotation have been accessed more than any other resource on the genomic portal Plant Ensembl , where they have been available for a over year for thousands of researchers and breeders to use. The project was funded by Biotechnology and Biological Sciences Research council grants to EI, John Innes Centre (JIC), European Bioinformatics Institute and Rothamsted Research, with contributions from international partners at the PSGB (Munich, Germany) and University Of Western Australia.

The improved genome assembly combined with high quality sequencing data and novel methods allowed EI scientists to more accurately identify genes and areas of the genome with interesting functions. In previous assemblies, many genes were missing or found only as fragments. By identifying the entire DNA sequences of genes, EI scientists have made it possible to identify more complete sets of similar genes -- called gene families -- that are important for yield, disease resistance or other qualities important for agriculture.

EI scientists have already used the advances to explore UK varieties and they have released six wheat genomes on the EI's open data website Grassroots Genomics. They and scientists from the John Innes Centre and The Sainsbury Laboratory have also started to use the results to provide a more accurate picture of where to find disease resistance genes and genes important for the visco-elastic properties of bread - which make it soft and spongy.

More than two billion people worldwide rely on wheat as a staple food, making it a vital crop for global food security. However, yield increases have stagnated since the mid-1990s. A better map of the wheat genome is essential for breaking the deadlock. It will help reveal the location of important traits that can be bred into elite varieties.

Lead author Bernardo Clavijo from the Earlham Institute says: "Scientists all over the world are already using these new results. But even more importantly, our open methods allow a new level of accuracy for any wheat line, and many other complex genomes. Assembly for this complexity of genome has always been a bit of a one-off work of art. Now we have a way to do it reliably and to a standard that enables thorough analysis."

"We are moving towards a scenario where more and more wheat lines will be sequenced and compared using these and similar techniques. This kind of detail on every wheat line will enable new discoveries and accelerate breeding. We are already working with the breeding industry as well as other researchers to enable more detailed analysis of elite varieties, which will impact the wheat breeding programs directly."

Ksenia Krasileva, a co-author on the new study, likens the creation of an assembly to navigating using GPS: "Breeders might know there is something really useful in wheat, for example for protecting crops against disease or for improving gluten for bread-making, but without a good quality genome assembly it's like driving through thick fog. Full genome assembly and annotating genes provides a sat nav view of wheat genes to signpost the way to useful genes in all varieties of the species."

EI group leader David Swarbreck says: "This is the most comprehensive wheat gene annotation to date, it represents a significant advance that will assist wheat breeders and researchers in accelerating further improvements, particularly as the results are freely available for anyone to use."

Co-author Michael Bevan from the John Innes Centre says: "The new resources we have helped develop have already broken down barriers and are providing new ways of studying wheat. They will allow breeders to more accurately predict which lines to breed from, and to directly identify the most promising progeny. This could save years when making new varieties."

Business News

19 Apr 2017 --- As British MPs prepare to vote on Prime Minister Theresa Mays call for a June 8 general election later today, the food and farming industries are urging the UK government to support the sectors which are vital to the UK economy.Mays snap call for a general election is due to be backed by MPs this afternoon, so the UK government can make a success of Brexit and focus on negotiating the best deals as the country exits the European Union.

Business News

19 Apr 2017 --- Mondelez International is shaking up its leadership with the announcement that executive vice president of North America Roberto Marques is leaving his role and Tim Cofer will step in as interim president adding to his current role spearheading the companys global growth strategy.

Business News

19 Apr 2017 --- What happens when meat scientists get their hands on nearly 8,000 commercially raised pigs? They spend a year running dozens of tests and crunching numbers to arrive at research-backed management recommendations for pork producers.

Business News

18 Apr 2017 --- The UKs iconic cereal brand Weetabix is reportedly being swallowed up by US Post Holdings in a 1.4 billion (US$1.7 million) deal. Chinese owners, The Bright Group, took a 60% share in Weetabix in May 2012 with Baring Private Equity Asia acquiring the remaining 40% from Lion Capital in 2015.

Food Ingredients News

18 Apr 2017 --- Texture makes foods and beverages vividly memorable and enjoyable. It's in line with taste in defining the eating and drinking experience. Ingredion has more than 60 years experience in texturizing food and beverages. The companys' extensive product portfolio offers a wide choice of texturizing ingredients, including base viscosifiers and co-texturizers, as well as gelling, crisping and pulping agents all are used to create different textures and claims.

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Bread Wheat Genome: Researchers Develop More Accurate Navigation System - FoodIngredientsFirst

Posted April 18, 2017 07:41:19

She is not the prettiest cow you have ever seen, but she is becoming one of the most important Brahmans in the business.

Elrose Naomi 3492 was 14 years old and had had eight calves when she made the ultimate sacrifice for science.

Now her lung tissue sits in a freezer as the final touches are put on a million-dollar project to sequence her genome.

She is not the first cow to have her DNA pulled apart and its order identified, but she will be the first Brahman, a tropically adapted breed found in Australia's north.

Eight years ago, the DNA of a Hereford cow called Dominette was unpacked and scrutinised by a team of international researchers at a cost of $US52 million.

Now, amid huge technological advances and for a fraction of that cost, Queensland researchers are keen to know more about what makes the northern cattle tick and, more importantly, how to improve it.

It is all part of a project to understand how genes from temperate cattle have influenced important production traits in the modern Brahman breed.

Professor Steve Moore, from the Centre for Animal Sciences, is director of the Queensland Alliance for Agriculture and Food Innovation (QAAFI).

He said northern cattle were not as productive as their southern Bos taurus counterparts.

"Their meat quality is not as good and their meat quality is penalised under MSA [Meat Standards Australia] if they have a hump," he said.

"We have to turn that around. We want to raise the value of the northern herd."

The Sequencing the Legends project, jointly funded by the Department of Agriculture and the University of Queensland, has resulted in the DNA of 50 top Brahman bulls picked apart and sequenced, with genes associated with specific traits being studied.

"We are unpacking the entire DNA sequences of 50 influential animals, then honing in on the genes associated with specific traits in order to capture the best genetics in the Brahman breed," Professor Moore said.

Brahmans are adapted to tropical climates, and there have been more than 300,000 years of separation between Bos indicus cattle such as Brahman and the Bos taurus cattle breeds that are important to temperate production systems.

Up until now, much of the world's genetics research has surrounded the Bos taurus, hence the sequencing of Hereford cow Dominette.

But Professor Moore said understanding the genetics underlying production traits in Australian tropically adapted cattle was essential for further breed development and crossbreeding strategies.

"We hope to improve the predictions and that will be delivered via something like Breedplan," he said.

"We will identify some of the mutations underlying some of the traits, but we're confounded by the fact we're working with the Bos taurus reference genome assembly and we get ambiguous results."

And that is where Elrose Namoi comes in.

Once her complete DNA sequence has been determined, she will become a reference animal for the Brahman breed, allowing the DNA of sequenced Brahman bulls to be "put back together" more accurately.

"We sequence a cow because a cow doesn't have a Y chromosome," Professor Moore said.

"The Y chromosome is a pain, so we try to avoid it. She's got two X chromosomes, which makes the X chromosome easier to assemble.

"Once we have Elrose Naomi sequenced, we'll be able to map those bulls onto the Brahman reference, so we'll hopefully have a complete picture of the majority of the Brahman population in Australia."

Professor Moore said for Australia to remain competitive, the industry had to do better with the animals it had in terms of markets, and that meant quality and productivity.

He said producers would start reaping the benefits of the genomics project through Breedplan within a "couple of years".

Topics: rural, cloning-and-dna, dna, beef-cattle, university-of-queensland-4072

Continue reading here:
Cow genome map set to improve Brahman breed - ABC Online

Perhaps it will be well if I first state a few personal disclaimers. I have: 1) no problem with the idea that different areas of knowledge require different methodologies to arrive at theories that explain the facts; 2) also no problem with the usual observation that the Bible is not a scientific textbook, it does not teach cosmology, biology, anthropology, geology etc. 3) no problem with the observation that a proper critique of modern science cannot rest solely on pointing out gaps in the fossil record, or the lack of positive evidence for missing link creatures to connect critter A to critter B through evolutionary processes; 4) also no problem with the notion that a species can adapt and change as its environment changes over time, indeed being effected by the environment. In other words, I have no issues with micro-evolution within a species; and finally 5) I have no problem with the notion of a very old earth and a long pre-history before human kind created in Gods image shows up on planet earth. Genesis 1 is a piece of Hebrew poetry that demonstrates the divine origins and design of it all. It does not tell us how long it took to accomplish the process, nor does it fill in all the blanks along the way. In a broad sense, in any case, it comports with evolutionary ideas about human beings being the apex and most complex of all living things.

On the other hand, what is a problem with science is an assumption that one can globalize a scientific theory to be all encompassing, even impinging on areas outside the discipline of genetics, areas such as history and theology. What I mean by that is that the presuppositions of modern science are purely naturalistic or better said materialistic. All things can be explained if we just figure out the natural processes which produced these facts, and then connect the dots.

The problem with this is of course it assumes that God, at least in these spheres, only works by natural processes. It rules out miracles a priori. For example, it takes for granted that when you find common physical features in a whale and in a tetrapod that is a purely land-based creature, there must be a link and a transition between A and B. This leads to the quite proper question If God is the CEO and director of all creation (not merely the one who fired the starter gun, having provided the raw materials for the human race and other creatures) why in the world could God not simply use some of the same features in two different species of creatures? No reason is given. Why for example is it not possible that God decided fish would have vertebrae and at least front limbs, and so would humans without any necessary connection between these species? These differing types of creatures could have each developed along their own natural lines, but shared some features in common with other species. Genetic similarities do not necessarily lead to the conclusion of genetic connections.

The real problem here is when science impinges on human history, not animal history. The Bible may not teach science, but it certainly teaches some specific things about human history, as we shall see in this review.

Continued here:
Adam and the Genome Part Two - Patheos (blog)

Francis S. Collins, M.D., Ph.D., director of the National Institutes of Health since 2009 and spearhead of the Human Genome Project (HGP), is scheduled to speak at SMUs 102nd Commencement on Saturday May 20 in Moody Coliseum.

Collins career has been all but lackluster. His own personal research has led to the isolation of genes causing cystic fibrosis, neurofibromatosis, Huntingtons disease, and Hutchinson-Gilford progeria syndrome. During his tenure as director of NIHs National Human Genome Research Institute, Collins oversaw the 13-year international collaborative effort to map and sequence James Watson and Francis Cricks double helix structure of DNA, with the conclusion of the project in 2003 coinciding with the 50th anniversary of Watson and Cricks seminal publication.

Overseeing what remains the worlds largest collaborative biological projectspossibly the most significant scientific undertaking in modern historyis only one aspect of Collins impressive resume. Appointed by President Obama and asked by Trump to remain in his position, Collins has launched groundbreaking research into increasing our understanding of neural brain networks to improve treatments for brain diseases, and has attempted to advance the use of precision medicine in hopes for more individually tailored healthcare.

The Virginia native earned his Bachelor of Science from the University of Virginia, Ph.D. from Yale University and an M.D. from the University of North Carolina at Chapel Hill.

Collins has received various awards, including the Presidential Medal of Freedom and the National Medal of Science. He will soon receive a Doctor of Science degree from SMU during the Commencement ceremony.

An elected member of the Institute of Medicine and the National Academy of Sciences, Collins has valuable insight to share with SMUs soon-to-be graduates.

Read more from the original source:
Human Genome Project leader and NIH director set to speak at 102nd SMU Commencement - The Daily Campus

UC Davis researchers announced inNature Communicationsthat they have unlocked a treasure-trove of genetic information about lettuce and related plants, releasing the first comprehensive genome assembly for lettuce and the hugeCompositaeplant family.

With an annual on-farm value of more than $2.4 billion, it is the most valuable fresh vegetable and one of the 10 most valuable crops, overall, in the United States.

The genome assembly a compilation of millions of DNA sequences into a useful genetic portrait provides researchers with a valuable tool for exploringCompositaefamilys many related plant species.

This genome assembly provides the foundation for numerous further genetic, evolutionary and functional studies of this whole family of plants, said Reyes-Chin-Wo, the lead author and graduate student in thelaboratoryof plant geneticist Richard Michelmore.

This is particularly significant becauseCompositaeis the most successful family of flowering plants on earth in terms of the number of species and environments inhabited, said Richard Michelmore, who directs the UC Davis Genome Center.

[Read the full study here]

The GLP aggregated and excerpted this blog/article to reflect the diversity of news, opinion, and analysis. Read full, original post:Gene Salad: Lettuce Genome Assembly Published

For more background on the Genetic Literacy Project, read GLP on Wikipedia

Read more here:
Gene salad: First comprehensive genome assembly of lettuce reveals 'treasure-trove of genetic information' - Genetic Literacy Project

Genomic changes in individual cells can eventually lead to cancer or other diseases. So scientists would like to be able to sequence the genome in a single cell. But the methods to do so can be plagued by the preferential amplification of some regions of the genome over others, leading to incomplete sequence coverage.

A team led by X. Sunney Xie of Harvard University and Peking University has developed a whole-genome amplification method that reduces such bias and errors (Science 2017, DOI: 10.1126/science.aak9787).

In the method, called LIANTI, researchers fragment genomic DNA from a single cell by inserting pieces of DNA called transposons. The transposons tag the DNA fragments so that they get amplified linearly instead of exponentially. The amplified DNA is then used to generate a library for subsequent DNA sequencing.

Compared with other whole-genome amplification methods, LIANTI has more uniform amplification and higher sequence coverage. The method enabled the detection of a type of mutation called copy-number variation, which involves the gain or loss of regions of the genome, which is hard to detect with high resolution using other amplification methods. The researchers were even able to characterize so-called micro-copy-number variations, which are smaller than 100,000 bases, with a resolution of about 10,000 bases.

Xie and coworkers used this ability to detect gains and losses of sequences to show that initiation of DNA replication is random and differs from cell to cell. They also showed that many single-nucleotide variations detected in previous single-cell sequencing are artifacts caused by instability of the DNA bases.

Originally posted here:
Method improves single-cell genome analysis - Chemical & Engineering News (subscription)

The researchers made the announcement in Nature Communications.

UC Davis researchers have announced in Nature Communications that they have unlocked a treasure-trove of genetic information about lettuce and related plants, releasing the first comprehensive genome assembly for lettuce and the huge Compositae plant family, according to a press release.

Garden lettuce, or Lactuca sativa, is the plant species that includes a salad bars worth of lettuce types, ranging from iceberg to romaine. With an annual on-farm value of more than $2.4 billion, it is the most valuable fresh vegetable and one of the 10 most valuable crops, overall, in the United States.

Lettuce is a member of the huge Compositae family, which includes the good, the bad, and the ugly of the plant world, from the daisy and sunflower to ragweed and the dreaded star thistle.

The genome assembly a compilation of millions of DNA sequences into a useful genetic portrait provides researchers with a valuable tool for exploring Compositae familys many related plant species.

This genome assembly provides the foundation for numerous further genetic, evolutionary and functional studies of this whole family of plants, said Reyes-Chin-Wo, the lead author and graduate student in the laboratory of plant geneticist Richard Michelmore.

This is particularly significant because Compositae is the most successful family of flowering plants on earth in terms of the number of species and environments inhabited, said Richard Michelmore, who directs the UC Davis Genome Center.

Triplicate genes may explain success

The researchers found that specific genes in the lettuce genome were consistent with certain physical traits like the production of a rubber-containing milky sap that have also been found in taxonomically distinct species, such as the rubber tree.

The study also provided evidence that somewhere during the evolution of lettuce about 45 million years ago, its genome was triplicated. As a result, one-fourth of the genome appears in multiple related regions. Because such genomic duplications may give plant species an advantage in colonizing new environments, the ancient triplication event might, in part, explain the success of the Compositae plant family.

New technology yields more precise information

Michelmore noted that this is the first reported genome assembly of a plant species resulting from use of a new technology which gives information information about the physical proximity of the DNA sequences to which proteins are bound.

The new approach, developed by Dovetail Genomics, a company spun out from UC Santa Cruz, resulted in a more contiguous and accurate genome assembly, even though lettuce has one of the larger plant genomes sequenced to date, he said.

The sequencing was done in collaboration with the genomics firm BGI. Funding was provided by 10 plant breeding companies through the Lettuce Genomics Sequencing Consortium, UC Davis Genome Center, National Science Foundation and U.S. Department of Agriculture.

Go here to see the original:
University of California, Davis researchers publish lettuce genome assembly - Produce Grower (press release)