Gene salad: Lettuce genome assembly published – Phys.Org

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.

Explore further: Sequencing hundreds of nuclear genes in the sunflower family now possible

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

Journal reference: Nature Communications

Provided by: UC Davis

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 ...

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 ...

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

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, ...

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.

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. ...

Scientists at the University of California, Davis have discovered that DNA sequences thought to be essential for gene activity can be expendable. Sequences once called junk sometimes call the shots instead.

The hot springs of Yellowstone National Park may be extreme environments, but they are host to a diversity of microbes that could shed light on the evolution of life on Earth and, perhaps, what lurks on distant planets.

Breaks in DNA can wreak havoc in the body, giving rise to cancer and other health problems. Yet sometimes cells rupture their own DNA for a good reason.

How some industrial pollutants or abnormal levels of cellular metabolites contribute to diverse human diseases is now more clearly understood, based on a new study from the University of Wisconsin Carbone Cancer Center (UWCCC) ...

Cocaine, nicotine, capsaicin. These are just three familiar examples of the hundreds of thousands of small molecules (also called specialized or secondary metabolites) that plants use as chemical ammunition to protect themselves ...

A Florida Museum of Natural History study provides new insights into the complex, shared history between blood-sucking lice and the vitamin-producing bacterial sidekicks that enable them to parasitize mammals, including primates ...

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

See the original post here:
Gene salad: Lettuce genome assembly published - Phys.Org