Nav: Home

Scientists create new standard genome for heavily studied worm

May 23, 2019

ITHACA, N.Y. - A new Cornell University-led study finds that the genome for a widely researched worm, on which countless studies are based, was flawed. Now, a fresh genome sequence will set the record straight and improve the accuracy of future research.

When scientists study the genetics of an organism, they start with a standard genome sequenced from a single strain that serves as a baseline. It's like a chess board in a chess game: every board is fundamentally the same.

One model organism that scientists use in research is a worm called Caenorhabditis elegans. The worm - the first multicellular eukaryote (animal, plant or fungus) to have its genome sequenced - is easy to grow and has simple biology with no bones, heart or circulatory system. At the same time, it shares many genes and molecular pathways with humans, making it a go-to model for studying gene function, drug treatments, aging and human diseases such as cancer and diabetes.

Genetic studies of C. elegans were based on a single strain, called N2, which researchers have ordered for decades from the C. elegans stock center at the University of Minnesota. Though people tried to uphold a common standard, individual labs grew N2 strains on their own, which led to morphing.

"Over the last decade, with more advanced genetic experiments using high levels of DNA sequencing, scientists were alarmed to discover that there is no longer a single laboratory strain that everyone was using," said Erich Schwarz, assistant research professor in the Department of Molecular Biology and Genetics. "Over 40 years there have arisen many different N2 strains; we can't rely on any one of them to do experiments."

Schwarz is a senior author of a new study published in Genome Research that describes a single genetically clean strain, called VC2010, where each individual is truly identical. Schwarz and colleagues from the University of Tokyo, Stanford University, the University of British Columbia and the University of Minnesota used cutting-edge techniques to sequence VC2010's genome and create a new standard.

As part of the study, the researchers compared VC2010 to the original N2 genome. They expected a near-perfect match, but got a surprise. "Along with the 100 million nucleotides we expected to see, we discovered an extra 2 million nucleotides, an extra two percent of the genome," that was hidden in the original, likely due to limitations of old technology, Schwarz said.

Schwarz added that similar issues are likely occurring in the standard genomes of other organisms, including humans. "It shows us that having the true complete DNA of an animal is not as easy as we thought it was," he said.

Other labs have begun using modern sequencing tools to reassess other genomes, which has implications for synthetic biology, where scientists are creating life - such as bacteria - from scratch. "Having a really good DNA sequence is an important baseline," Schwarz said.
-end-
Lead authors include Jun Yoshimura and Kazuki Ichikawa in the lab of co-author Shinichi Morishita, professor of computational biology at the University of Tokyo, and Massa Shoura and Karen Artiles in the lab of co-author Andrew Fire, professor of pathology and genetics at Stanford University.

Cornell University has dedicated television and audio studios available for media interviews supporting full HD, ISDN and web-based platforms.

Cornell University

Related Genome Articles:

Breakthrough in genome visualization
Kadir Dede and Dr. Enno Ohlebusch at Ulm University in Germany have devised a method for constructing pan-genome subgraphs at different granularities without having to wait hours and days on end for the software to process the entire genome.
Sturgeon genome sequenced
Sturgeons lived on earth already 300 million years ago and yet their external appearance seems to have undergone very little change.
A sea monster's genome
The giant squid is an elusive giant, but its secrets are about to be revealed.
Deciphering the walnut genome
New research could provide a major boost to the state's growing $1.6 billion walnut industry by making it easier to breed walnut trees better equipped to combat the soil-borne pathogens that now plague many of California's 4,800 growers.
Illuminating the genome
Development of a new molecular visualisation method, RNA-guided endonuclease -- in situ labelling (RGEN-ISL) for the CRISPR/Cas9-mediated labelling of genomic sequences in nuclei and chromosomes.
A genome under influence
References form the basis of our comprehension of the world: they enable us to measure the height of our children or the efficiency of a drug.
How a virus destabilizes the genome
New insights into how Kaposi's sarcoma-associated herpesvirus (KSHV) induces genome instability and promotes cell proliferation could lead to the development of novel antiviral therapies for KSHV-associated cancers, according to a study published Sept.
Better genome editing
Reich Group researchers develop a more efficient and precise method of in-cell genome editing.
Unlocking the genome
A team led by Prof. Stein Aerts (VIB-KU Leuven) uncovers how access to relevant DNA regions is orchestrated in epithelial cells.
Why do we need one pair of genome?
Scientists have unraveled how the cell replication process destabilizes when it has more, or less, than a pair of chromosome sets, each of which is called a genome -- a major step toward understanding chromosome instability in cancer cells.
More Genome News and Genome Current Events

Trending Science News

Current Coronavirus (COVID-19) News

Top Science Podcasts

We have hand picked the top science podcasts of 2020.
Now Playing: TED Radio Hour

Listen Again: Reinvention
Change is hard, but it's also an opportunity to discover and reimagine what you thought you knew. From our economy, to music, to even ourselves–this hour TED speakers explore the power of reinvention. Guests include OK Go lead singer Damian Kulash Jr., former college gymnastics coach Valorie Kondos Field, Stockton Mayor Michael Tubbs, and entrepreneur Nick Hanauer.
Now Playing: Science for the People

#562 Superbug to Bedside
By now we're all good and scared about antibiotic resistance, one of the many things coming to get us all. But there's good news, sort of. News antibiotics are coming out! How do they get tested? What does that kind of a trial look like and how does it happen? Host Bethany Brookeshire talks with Matt McCarthy, author of "Superbugs: The Race to Stop an Epidemic", about the ins and outs of testing a new antibiotic in the hospital.
Now Playing: Radiolab

Dispatch 6: Strange Times
Covid has disrupted the most basic routines of our days and nights. But in the middle of a conversation about how to fight the virus, we find a place impervious to the stalled plans and frenetic demands of the outside world. It's a very different kind of front line, where urgent work means moving slow, and time is marked out in tiny pre-planned steps. Then, on a walk through the woods, we consider how the tempo of our lives affects our minds and discover how the beats of biology shape our bodies. This episode was produced with help from Molly Webster and Tracie Hunte. Support Radiolab today at Radiolab.org/donate.