Gene salad: Lettuce genome assembly published

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 , 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 , 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 —a compilation of millions of DNA sequences into a useful genetic portrait—provides researchers with a valuable tool for exploring the Compositae family's many related plant species.

"This assembly provides the foundation for numerous further genetic, evolutionary and functional studies of this whole family of ," 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 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—including about 30 percent of all of its identified genes—now 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 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

Related Stories

Automated thinner benefits romaine lettuce size, uniformity

April 5, 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 ...

16 new lettuce breeding lines from ARS

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. ...

Recommended for you

Stressed-out meerkats less likely to help group

September 22, 2017

Dominant female meerkats use aggression to keep subordinates from breeding, but a new study finds this negative behavior also can result in the latter becoming less willing to help within the group.

Why poison frogs don't poison themselves

September 21, 2017

Don't let their appearance fool you: Thimble-sized, dappled in cheerful colors and squishy, poison frogs in fact harbor some of the most potent neurotoxins we know. With a new paper published in the journal Science, scientists ...

0 comments

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

Click here to reset your password.
Sign in to get notified via email when new comments are made.