Category Archives: Genome

The newly sequenced genome of the coffee plant reveals secrets about the evolution of man's best chemical friend: caffeine.

The scientists who completed the project say the sequences and positions of genes in the coffee plant show that they evolved independently from genes with similar functions in tea and chocolate, which also make caffeine.

In other words, coffee did not inherit caffeine-linked genes from a common ancestor, but instead developed the genes on its own.

The findings will appear on Sept. 5 in the journal Science.

Why Coffee?

With more than 2.25 billion cups consumed daily worldwide, coffee is the principal agricultural product of many tropical countries. According to estimates by the International Coffee Organization, more than 8.7 million tons of coffee were produced in 2013, revenue from exports amounted to $15.4 billion in 2009-2010, and the sector employed nearly 26 million people in 52 countries during 2010.

"Coffee is as important to everyday early risers as it is to the global economy. Accordingly, a genome sequence could be a significant step toward improving coffee," said Philippe Lashermes, a researcher at the French Institute of Research for Development (IRD). "By looking at the coffee genome and genes specific to coffee, we were able to draw some conclusions about what makes coffee special."

Lashermes, along with Patrick Wincker and France Denoeud, genome scientists at the French National Sequencing Center (CEA-Genoscope), and Victor Albert, professor of biological sciences at the University at Buffalo, are the principal authors of the study.

Scientists from other organizations, particularly the Agricultural Research Center for International Development in France, also contributed, along with researchers from public and private organizations in the U.S., France, Italy, Canada, Germany, China, Spain, Indonesia, Brazil, Australia and India.

The team created a high-quality draft of the genome of Coffea canephora, which accounts for about 30 percent of the world's coffee production, according to the Manhattan-based National Coffee Association.

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Coffee genome sheds light on the evolution of caffeine

Now that the coffee plant genome has been sequenced, it's only a matter of time until we're all brewing up genetically engineered, super-caffeinated coffee beans, right? Maybe. Here's what we know now about coffee that we never knew before.

An international team of scientists has sequenced and published the coffee genome. More specifically, researchers have sequenced the genome of Coffea canephora. Better known as "robusta" coffee, C. canephora makes up roughly 30% of the world's commercial coffee production. The remaining 70% is accounted for primarily by C. arabica, a hybridized offspring of C. canephora.

Together, these species comprise one of the world's most treasured agricultural commodities, and are the starting materials for what is arguably the most highly prized beverage on Earth. Caffeine, after all, is far and away humanity's favorite psychoactive drug, and coffee is the vehicle by which most of us consume it to the tune of roughly 2.25-billion cups a day.

It's safe to wager, then, that coffee would not be so popular were it not for its caffeine content. And that's what makes the publication of the C. canephora genome so exciting. The researchers, it turns out, have done more than identified over 25,000 protein-making genes in the robusta coffee genome. By examining which families of genes expanded in the course of coffee's evolution, and comparing its genome to those of other plant species, researchers co-led by University of Buffalo genome scientist Victor Albert, were able to, in his words, "learn about coffee's independent pathway in evolution, including excitingly the story of caffeine."

The genes responsible for coffee's caffeine-production code for a group of enzymes called N-methyltransferases. The N-methyltransferase family is ancient, and has evolved and diversified over many millions of years to perform a variety of tasks in innumerable species of plants. Previous research has shown that the caffeine in plants like tea and cacao is also produced by N-methyltransferases. What the newly sequenced coffee genome reveals is that these C. canephora's caffeine-producing enzymes evolved independently from those in cacao and tea.

"If you were to look at the family tree of N-methyltransferases, you would find that the genes responsible for caffeine synthesis in coffee have evolved along an entirely separate branch from those in charge of caffeine synthesis in chocolate," says Albert. You might find enzymes in chocolate that are closely related to the caffeine-producing enzymes in coffee, he explains, but they would have nothing to do with chocolate's caffeine-producing enzymes. Both plants rely on N-methyltransferases to generate caffeine, but they took different evolutionary routes to do so. It's a classic example of what evolutionary biologists call "convergent evolution."

All this talk of N-methyltransferases and caffeine production likely has you wondering: Will having a sequenced coffee genome complete with brand new insights into the evolution of coffee's caffeine-production enable us to breed strains of highly caffeinated super-coffee?http://io9.com/5861402/10-rea...

In a word: Yes. In any agricultural plant, genome sequences have become a prerequisite to doing any sort of advanced breeding or genetic modification.

The same could theoretically be said for traits like flavor and aroma. The researchers identify six genes responsible for the production of linoleic acid, a fatty acid that contributes to the the taste and smell of coffee. "We don't know the precise role of those genes in that flavor production," says Albert, but a sequenced genome will serve as a useful reference for anyone looking to develop new varieties of coffee."For [the contributions] we know about," says study co-author Patrick Wincker, a geneticist at France's Institut de Gnomique du CEA, "these findings open a new way to correlate aroma and gene families, and potentially to try new combinations of these genes."

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The Coffee Genome Has Been Sequenced. Here's What That Means For You.

Washington If you prefer your genetic research to be rich, bold, flavorful, steaming hot and with a bit of a kick, try a mug full of this: Scientists have deciphered thecoffeegenome and found genetic secrets that may make your cup of joe even better in the future.

An international team of researchers on Thursday unveiled the newly sequenced genome of thecoffeeplant. They pinpointed genetic attributes that could help in the development of newcoffeevarieties better able to endure drought, disease and pests, with the added benefit of enhancing flavor and caffeine levels.

The researchers studied the species Coffea canephora, better known as Robusta. It accounts for about 30 percent of the world'scoffeeproduction and is common in instantcoffee. It is second in importance to Arabica, generally known for a less strong, smoother taste. Separate work is under way on Arabica's genome.

Along with its the popular beverage's distinctive flavor and aroma, caffeine undoubtedly is a big part of its appeal. The researchers said their study, published in the journal Science, found, not surprisingly, that thecoffeeplant boasted a broad collection of enzymes involved in the production of caffeine.

They also concluded that thecoffeeplant's caffeine enzymes evolved independently from those in cacao (chocolate) and tea.

Compared with other plants the scientists examined,coffeepossessed larger families of genes related to making alkaloid and flavonoid compounds that contribute to the aroma and bitterness of beans.

"For any agricultural plant, having a genome is a prerequisite for any sort of high technology breeding or molecular modification," said plant genomistVictor Albertof the University atBuffalo, one of the researchers.

"Without a genome, we couldn't do any real advanced research oncoffeethat would allow us to improve it - not in this day and age," Albert added.

Coffeeis one of the world's most valuable agricultural commodities.

With an estimated 2.25 billion cups consumed every day worldwide, more than 8.7 million tons ofcoffeewere produced last year. Production and export are a multibillion-dollar enterprise, employing millions of people in more than 50 countries. A tropical and subtropical crop, it is vital to the economies of many developing countries.

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Coffee study reveals the genetics of java (+video)

Genome of the robusta variety reveals that caffeine-making evolved more than once, in part because pollinators developed a caffeine habit

Caffeine evolved long before sleep-deprived humans became addicted to it, probably to defend the coffee plant against predators and for other benefits. Credit: Thinkstock

Caffeine's buzz is so nice it evolved twice. The coffee genome has now been published, and it reveals that the coffee plant makes caffeine using a different set of genes from those found in tea, cacao and other perk-you-up plants.

Coffee plants are grown across some 11 million hectares of land, with more than two billion cups of the beverage drunk every day. It is brewed from the fermented, roasted and ground berries ofCoffea canephora andCoffea arabica, known as robusta and arabica, respectively. An international team of scientists has now identified more than 25,000 protein-making genes in the robusta coffee genome. The species accounts for about one-third of the coffee produced, much of it for instant-coffee brands such as Nescafe. Arabica contains less caffeine, but its lower acidity and bitterness make it more flavourful to many coffee drinkers. However, the robusta species was selected for sequencing because its genome is simpler than arabicas.

Caffeine evolved long before sleep-deprived humans became addicted to it, probably to defend the coffee plant against predators and for other benefits. For example, coffee leaves contain the highest levels of caffeine of any part of the plant, and when they fall on the soil they stop other plants from growing nearby.

Caffeine also habituates pollinators and makes them want to come back for more, which is what it does to us, too, says Victor Albert, a genome scientist at the University of Buffalo in New York, who co-led the sequencing effort. The results were published on September 4 inScience.

Dual origin When the team looked for gene families that distinguish coffee from other plants, those that make caffeine topped the list. The genes encode methyltransferase enzymes, which transform a xanthosine molecule into caffeine by adding methyl chemical groups in three steps. Tea and cacao, meanwhile, make caffeine using different methyltransferases from those the team identified in robusta. This suggests that the ability to make caffeine evolved at least twice, in the ancestor of coffee plants and in a common ancestor of tea and cacao, Albert says.

The genome could be used to identify genes that help the plant to combat diseases, such ascoffee rust, and to cope with climate change.

Caffeine-making genes might also be inactivated to create a tastier decaf. A coffee cultivar that is genetically engineered to be caffeine-free could be a welcome development for the many people who cannot tolerate the buzz. The process of removing caffeine currently involves chemical processing, and also affects the flavour (see 'Plant biotechnology: Make it a decaf'). I have to have a cup every morning, but I usually dont drink during the day because it makes me shaky, says Albert.

This article is reproduced with permission and was first published on September 4, 2014.

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Coffee's Caffeine Buzz Evolved Separately from Tea's

Washington If you prefer your genetic research to be rich, bold, flavorful, steaming hot and with a bit of a kick, try a mug full of this: Scientists have deciphered thecoffeegenome and found genetic secrets that may make your cup of joe even better in the future.

An international team of researchers on Thursday unveiled the newly sequenced genome of thecoffeeplant. They pinpointed genetic attributes that could help in the development of newcoffeevarieties better able to endure drought, disease and pests, with the added benefit of enhancing flavor and caffeine levels.

The researchers studied the species Coffea canephora, better known as Robusta. It accounts for about 30 percent of the world'scoffeeproduction and is common in instantcoffee. It is second in importance to Arabica, generally known for a less strong, smoother taste. Separate work is under way on Arabica's genome.

Along with its the popular beverage's distinctive flavor and aroma, caffeine undoubtedly is a big part of its appeal. The researchers said their study, published in the journal Science, found, not surprisingly, that thecoffeeplant boasted a broad collection of enzymes involved in the production of caffeine.

They also concluded that thecoffeeplant's caffeine enzymes evolved independently from those in cacao (chocolate) and tea.

Compared with other plants the scientists examined,coffeepossessed larger families of genes related to making alkaloid and flavonoid compounds that contribute to the aroma and bitterness of beans.

"For any agricultural plant, having a genome is a prerequisite for any sort of high technology breeding or molecular modification," said plant genomistVictor Albertof the University atBuffalo, one of the researchers.

"Without a genome, we couldn't do any real advanced research oncoffeethat would allow us to improve it - not in this day and age," Albert added.

Coffeeis one of the world's most valuable agricultural commodities.

With an estimated 2.25 billion cups consumed every day worldwide, more than 8.7 million tons ofcoffeewere produced last year. Production and export are a multibillion-dollar enterprise, employing millions of people in more than 50 countries. A tropical and subtropical crop, it is vital to the economies of many developing countries.

Read the original here:
Coffee study reveals the genetics of java

Dimas Ardian/Bloomberg/Getty Images

Robusta coffee berries left to dry in the Sun on Sumatra, in Indonesia.

Caffeine's buzz is so nice it evolved twice. The coffee genome has now been published, and it reveals that the coffee plant makes caffeine using a different set of genes from those found in tea, cacao and other perk-you-up plants.

Coffee plants are grown across some 11 million hectares of land, with more than two billion cups of the beverage drunk every day. It is brewed from the fermented, roasted and ground berries of Coffea canephora and Coffea arabica, known as robusta and arabica, respectively. An international team of scientists has now identified more than 25,000 protein-making genes in the robusta coffee genome. The species accounts for about one-third of the coffee produced, much of it for instant-coffee brands such as Nescafe. Arabica contains less caffeine, but its lower acidity and bitterness make it more flavourful to many coffee drinkers. However, the robusta species was selected for sequencing because its genome is simpler than arabicas.

Caffeine evolved long before sleep-deprived humans became addicted to it, probably to defend the coffee plant against predators and for other benefits. For example, coffee leaves contain the highest levels of caffeine of any part of the plant, and when they fall on the soil they stop other plants from growing nearby.

Caffeine also habituates pollinators and makes them want to come back for more, which is what it does to us, too, says Victor Albert, a genome scientist at the University of Buffalo in New York, who co-led the sequencing effort. The results were published on 4 September in Science1.

When the team looked for gene families that distinguish coffee from other plants, those that make caffeine topped the list. The genes encode methyltransferase enzymes, which transform a xanthosine molecule into caffeine by adding methyl chemical groups in three steps. Tea and cacao, meanwhile, make caffeine using different methyltransferases from those the team identified in robusta. This suggests that the ability to make caffeine evolved at least twice, in the ancestor of coffee plants and in a common ancestor of tea and cacao, Albert says.

The genome could be used to identify genes that help the plant to combat diseases, such as coffee rust, and to cope with climate change.

Caffeine-making genes might also be inactivated to create a tastier decaf. A coffee cultivar that is genetically engineered to be caffeine-free could be a welcome development for the many people who cannot tolerate the buzz. The process of removing caffeine currently involves chemical processing, and also affects the flavour (see 'Plant biotechnology: Make it a decaf'). I have to have a cup every morning, but I usually dont drink during the day because it makes me shaky, says Albert.

Read more here:
Coffee got its buzz by a different route than tea

Wake up and smell the genome.

Researchers have pieced together the genetic atlas of the parent of the most commonly cultivated species of coffee plant and uncovered a rather independent streak in its evolution.

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FOR THE RECORD

An earlier version of this post said 39 countries had exported 5.3 metric tons of coffee last year. Those countries exported 5.3 million metric tons.

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Coffee developed its caffeine-generating capacity independently from its cousin, cacao, according to the first whole genome study of the plant behind the brew quaffed every morning by about 100 million Americans, published online Thursday in the journal Science.

Theres been a lot of genetic sleuthing on coffee, most of it far from the tree. We have a good idea about how caffeine affects animal (particularly human) genes and alters brain chemistry. We know which of our own genes seem to draw us toward consuming coffee, tea or chocolate as well. And theres also been a heady, if somewhat contradictory, brew of studies purporting to demonstrate caffeines beneficial and deleterious effects on humans.

But how caffeine production got started has been as hard to see as a spoon in a demitasse of espresso.

Coffee has been kind of an orphan crop," said UC Davis geneticist Juan F.Medrano, who was not involved in the study. "It has been kind of forgotten in terms of DNA research. Perhaps this opens the door to expand that area.

Read more:
Meet the genes in the beans of your coffee

Genome Corporate film short
A corporate film made for GENOME, one of the largest Infertility clinic in India.

By: Saugata Mukherjee

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Genome Corporate film short - Video

The newly sequenced genome of the coffee plant reveals secrets about the evolution of mans best chemical friend: caffeine.

The scientists who completed the project say the sequences and positions of genes in the coffee plant show that they evolved independently from genes with similar functions in tea and chocolate, which also make caffeine.

In other words, coffee did not inherit caffeine-linked genes from a common ancestor, but instead developed the genes on its own.

The findings will appear on Sept. 5 in the journal Science.

Why coffee?

With more than 2.25 billion cups consumed daily worldwide, coffee is the principal agricultural product of many tropical countries. According to estimates by the International Coffee Organization, more than 8.7 million tons of coffee were produced in 2013, revenue from exports amounted to $15.4 billion in 2009-2010, and the sector employed nearly 26 million people in 52 countries during 2010.

Coffee is as important to everyday early risers as it is to the global economy. Accordingly, a genome sequence could be a significant step toward improving coffee, says Philippe Lashermes, a researcher at the French Institute of Research for Development (IRD). By looking at the coffee genome and genes specific to coffee, we were able to draw some conclusions about what makes coffee special.

Lashermes, along with Patrick Wincker and France Denoeud, genome scientists at the French National Sequencing Center (CEA-Genoscope), and Victor Albert, UB professor of biological sciences, are the principal authors of the study.

Scientists from other organizations, particularly the Agricultural Research Center for International Development in France, also contributed, along with researchers from public and private organizations in the U.S., France, Italy, Canada, Germany, China, Spain, Indonesia, Brazil, Australia and India.

The team created a high-quality draft of the genome of Coffea canephora, which accounts for about 30 percent of the worlds coffee production, according to the Manhattan-based National Coffee Association.

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Coffee genome sheds light on evolution of caffeine

Full of Excuses ~ Strong ~ The Human Genome
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Full of Excuses ~ Strong ~ The Human Genome - Video