Daily Archives: May 21, 2013

Future of Me: Your Accessible Genome
Advances in gene sequencing technologies plus increased computer capacity for information analysis means we are on the verge of being able to access and unde...

By: TheBridge8

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Future of Me: Your Accessible Genome - Video

The population of Ireland has yet to rebound from the deaths and migrations caused by the famine of mid-19th-century.

James Mahony/Wikimedia Commons

The great potato famine of the 1840s was a defining event in Irelands recent history. An Gorta Mr the Great Hunger in the Irish language caused millions to starve or emigrate and helped catalyse the countrys bloody war of independence from Great Britain.

Working from 150-year-old dried leaves, two competing teams have now sequenced the genome of the single-celled organism that wreaked havoc on the Irish potato crop. It is the first ancient plant pathogen to have its genome decoded. (In 2011, scientists reported the sequence of the plague-causing bacteria responsible for the Black Death of the 1340s.)

Phytophthora infestans, which causes potato late blight, is an oomycete a type of single-celled organism related to brown algae. Carried by infected potatoes, the disease probably arrived at the port of Antwerp in Belgium in the summer of 1845, before quickly spreading through the Low Countries and much of western Europe.

Irelands dependence on potatoes was the reason the epidemic exacted a far greater toll there than it did on the rest of the continent. Irish peasants working plots owned by absentee British landlords relied on potatoes for most of their calories, says Detlef Weigel, a plant geneticist at the Max Planck Institute for Developmental Biology in Tbingen, Germany, who co-led a study published today in the journal eLIFE1. The potato is really an amazing staple crop. If you have a diet of potato and milk, you dont need anything else.

The disappearance of that staple had devastating consequences, including 1 million deaths and still more emigrations. Irelands population of 4.5 million is still less than three-quarters of its pre-famine level. The perception that Britain did little to intervene in the catastrophe helped foment Irish nationalism, eventually resulting in the Irish War of Independence in 1919.

Long before it hit Europe, P. infestans probably circulated in the Toluca Valley in central Mexico, where it infected wild relatives of the potato. Until recently, only a single strain of P. infestans, dubbed US-1, plagued potatoes outside Mexico and South America. So it came as a surprise when, in 2001, scientists suggested that a different strain was responsible for the famine, after analysing a short stretch of P. infestans DNA from herbarium archives2.

Weigels team went to herbaria in Kew Gardens, outside of London, and at Germanys Botanische Staatssammlung in Munich and sequenced DNA preserved from the dried leaves of infected plants dating between 1845 and 1896.

Mitochondrial genomes from the famine strains showed they were more closely related to the US-1 strain than the earlier research suggested, and that the two strains diverged only in the early 1800s. Weigel says the split probably occurred in the United States, before the strain responsible for the famine was imported to Europe. That strain now appears to be extinct, or perhaps restricted to small pockets of the world.

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Pathogen genome tracks Irish potato famine back to its roots

Striking a blow at foodborne diseases, the 100K Pathogen Genome Project at UC Davis Tuesday announced that it has sequenced the genomes of its first 10 infectious microorganisms, including strains of Salmonella and Listeria.

"We are creating a free, online encyclopedia or reference database of genomes so that during a foodborne disease outbreak, scientists and public health professionals can quickly identify the responsible microorganism and track its source in the food supply using automated information-handling methods," said Professor Bart Weimer, director of the 100K Genome Project and co-director of BGI@UC Davis, the Sacramento facility where the sequencing is carried out.

Weimer estimates that the availability of this genomic information will cut in half the time necessary to diagnose and treat foodborne illnesses, and will enable scientists to make discoveries that can be used to develop new methods for controlling disease-causing microorganisms in the food chain.

The project is dedicated to sequencing the genomes of 100,000 bacteria and viruses that cause serious foodborne illnesses in people around the world.

In the United States alone, foodborne diseases annually sicken 48 million people and kill 3,000, according to the Centers for Disease Control and Prevention.

The initial 10 genome sequences mark the first in a series that the

"This initial release validates the entire process, from start to finish, of acquiring the bacterium, producing the genome sequence, and making automated public releases," Weimer said.

A genome is the complete collection of an organism's hereditary information.

Weimer said that the 100K Genome Project currently is sequencing a second set of 1,500 microbial genomes, with an anticipated release in the fall of 2013.

The 100K Genome Project was launched in March 2012 as a collaborative effort between UC Davis, Agilent Technologies, and the U.S. Food and Drug Administration. Since then, the U.S. Centers for Disease Control and Prevention, Department of Agriculture, and National Institutes of Health, as well as seven corporate partners, have joined the worldwide effort. For more information visit http://100kgenome.vetmed.ucdavis.edu.

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100K Pathogen Genome Project maps first genomes at UC Davis