Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Potato Blight Reveals Some Secrets as Genome Is Decoded

11.09.2009
Late blight caused the 19th century famine that sparked a wave of emigration from Ireland to the United States, but the disease has also infected tomatoes and potatoes this year. Potatoes, the world’s fourth-largest food crop, were raised on 65,500 acres in Wisconsin in 2007. If a potato field is not treated with pesticide, late blight can destroy the crop in a few days.

This week (Sept. 9), the online edition of the scientific journal Nature will report on the full genetic sequence, or genome, of Phytophthora infestans, the cause of late blight. The genome resulted from a large international effort, which benefited from significant contributions from scientists at the University of Wisconsin-Madison, to understand the genetics of a plant disease that has evaded many control efforts.

“This pathogen has an exquisite ability to adapt and change, and that’s what makes it so dangerous,” says senior author Chad Nusbaum, co-director of the Genome Sequencing and Analysis Program at the Broad Institute of MIT and Harvard, which directed the sequencing project.

About 75 percent of the genome contains repetitious DNA, which is now seen as key to understanding late blight’s destructive potential, Nusbaum adds. “We now have a comprehensive view of its genome, revealing the unusual properties that drive its remarkable adaptability. Hopefully, this knowledge can foster novel approaches to diagnose and respond to outbreaks.”

To cope with the confusing level of repetition, Broad Institute researchers contacted David Schwartz, a professor of chemistry and genetics at UW-Madison. Schwartz was the principal inventor of the “optical mapping” system, which uniquely complements the traditional, letter-by-letter approach to gene sequencing.

The DNA of late blight contains about 240 million sub-units, or “bases.” To efficiently identify these units, scientists first cut the DNA into shorter chunks, and later digitally reassemble the chunks into one long sequence. But traditional sequencing technology gets confused by genomes that contain so much repetition, Schwartz says.

The advantage of optical mapping can be seen by comparison to digital maps, Schwartz says. “In a digital map; you can see the streets; like optical mapping, this is a medium-resolution picture of the subject. Then you can switch to a high-resolution street view. You can count windows in the houses, but it’s hard to see how the houses fit together. It’s the same with traditional gene sequencing: You get a much higher resolution view, but it’s harder to know where the units are located.”

Optical mapping was particularly helpful with the nettlesome genome of late blight, Schwartz adds. “It’s full of repeated DNA sequences, so all the windows look the same and it’s hard to know where the house should go. Combining the letter-by-letter information from sequencing with the broader view from optical mapping allowed us to put the genome together.”

The DNA chunks that used optical mapping “are much longer than those used in traditional sequencing and mapping, which means we can span lots of gaps that others cannot,” adds Shiguo Zhou, Schwartz’s colleague in the Laboratory for Molecular and Computational Genomics and the principal scientist constructing the map. “We can characterize regions where you see the same code repeated over and over and put whole genome together.”

The study found that the late blight genome is two and a half to four times larger than those of its relatives, mainly due to a massive amount of repetitive DNA. Although these repetitive regions contain only a few genes, they are specialized for attacking plants, so understanding the repetitions may help explain why late blight is such an effective plant pathogen.

The research group hopes that further exploration of the genome will reveal weak links in the organism’s offensive strategy. According to co-lead author Brian Haas of the Broad Institute, “The repeat-rich regions change rapidly over time, acting as a kind of incubator to enable the rapid birth and death of genes that are key to plant infection. As a result, these critical genes may be gained and lost so rapidly that the hosts simply can’t keep up.”

Dave Tenenbaum | Newswise Science News
Further information:
http://www.wisc.edu

More articles from Life Sciences:

nachricht 'Y' a protein unicorn might matter in glaucoma
23.10.2017 | Georgia Institute of Technology

nachricht Microfluidics probe 'cholesterol' of the oil industry
23.10.2017 | Rice University

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Salmonella as a tumour medication

HZI researchers developed a bacterial strain that can be used in cancer therapy

Salmonellae are dangerous pathogens that enter the body via contaminated food and can cause severe infections. But these bacteria are also known to target...

Im Focus: Neutron star merger directly observed for the first time

University of Maryland researchers contribute to historic detection of gravitational waves and light created by event

On August 17, 2017, at 12:41:04 UTC, scientists made the first direct observation of a merger between two neutron stars--the dense, collapsed cores that remain...

Im Focus: Breaking: the first light from two neutron stars merging

Seven new papers describe the first-ever detection of light from a gravitational wave source. The event, caused by two neutron stars colliding and merging together, was dubbed GW170817 because it sent ripples through space-time that reached Earth on 2017 August 17. Around the world, hundreds of excited astronomers mobilized quickly and were able to observe the event using numerous telescopes, providing a wealth of new data.

Previous detections of gravitational waves have all involved the merger of two black holes, a feat that won the 2017 Nobel Prize in Physics earlier this month....

Im Focus: Smart sensors for efficient processes

Material defects in end products can quickly result in failures in many areas of industry, and have a massive impact on the safe use of their products. This is why, in the field of quality assurance, intelligent, nondestructive sensor systems play a key role. They allow testing components and parts in a rapid and cost-efficient manner without destroying the actual product or changing its surface. Experts from the Fraunhofer IZFP in Saarbrücken will be presenting two exhibits at the Blechexpo in Stuttgart from 7–10 November 2017 that allow fast, reliable, and automated characterization of materials and detection of defects (Hall 5, Booth 5306).

When quality testing uses time-consuming destructive test methods, it can result in enormous costs due to damaging or destroying the products. And given that...

Im Focus: Cold molecules on collision course

Using a new cooling technique MPQ scientists succeed at observing collisions in a dense beam of cold and slow dipolar molecules.

How do chemical reactions proceed at extremely low temperatures? The answer requires the investigation of molecular samples that are cold, dense, and slow at...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

3rd Symposium on Driving Simulation

23.10.2017 | Event News

ASEAN Member States discuss the future role of renewable energy

17.10.2017 | Event News

World Health Summit 2017: International experts set the course for the future of Global Health

10.10.2017 | Event News

 
Latest News

Flying: Efficiency thanks to Lightweight Air Nozzles

23.10.2017 | Materials Sciences

Salmonella as a tumour medication

23.10.2017 | Life Sciences

50th Anniversary at JULABO GmbH

23.10.2017 | Press release

VideoLinks
B2B-VideoLinks
More VideoLinks >>>