Coffee genome sheds light on the evolution of caffeine

September 4, 2014, University at Buffalo
Coffee Plantation near Sakleshpur. Credit: Wikipedia

Enzymes that help produce caffeine evolved independently in coffee, tea and chocolate, say scientists who have newly sequenced the coffee plant genome.

The newly sequenced genome of the 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 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.

Next, the scientists looked at how coffee's genetic make-up is distinct from other species.

Compared to several other plant species including the grape and tomato, coffee harbors larger families of genes that relate to the production of alkaloid and flavonoid compounds, which contribute to qualities such as coffee aroma and the bitterness of beans.

Coffee also has an expanded collection of N-methyltransferases, enzymes that are involved in making caffeine.

Upon taking a closer look, the researchers found that coffee's caffeine enzymes are more closely related to other genes within the coffee plant than to caffeine enzymes in tea and chocolate.

This finding suggests that caffeine production developed independently in coffee. If this trait had been inherited from a , the enzymes would have been more similar between species.

"The coffee genome helps us understand what's exciting about coffee—other than that it wakes me up in the morning," Albert said. "By looking at which families of genes expanded in the plant, and the relationship between the of coffee and other species, we were able to learn about coffee's independent pathway in evolution, including—excitingly—the story of caffeine."

Why caffeine is so important in nature is another question. Scientists theorize that the chemical may help plants repel insects or stunt competitors' growth. One recent paper showed that pollinators—like humans—may develop caffeine habits. Insects that visited caffeine-producing plants often returned to get another taste.

The new Science study doesn't offer new ideas about the evolutionary role of , but it does reinforce the idea that the compound is a valuable asset. It also provides the opportunity to better understand the evolution of coffee's genome structure.

"It turns out that, over evolutionary time, the coffee genome wasn't triplicated as in its relatives: the tomato and chile pepper," Wincker said. "Instead it maintained a structure similar to the grape's. As such, evolutionary diversification of the coffee genome was likely more driven by duplications in particular gene families as opposed to en masse, when all in the genome duplicate."

This stands in contrast to what's been suggested for several other large plant families, where other investigators have noted correlations between high species diversity in a group and the presence of whole genome doublings or triplings.

"Coffee lies in the plant family Rubiaceae, which has about 13,000 species and is the world's fourth largest; thus, with no genome duplication at its root, it appears to break the mold of a duplication link to high biodiversity," Denoeud said.

Explore further: Ground pistachio coffee could be healthier alternative to decaf

More information: "The coffee genome provides insight into the convergent evolution of caffeine biosynthesis," by F. Denoeud et al. Science, 2014. www.sciencemag.org/lookup/doi/ … 1126/science.1255274

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21 comments

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supamark23
4.4 / 5 (14) Sep 04, 2014
...aaaand cue the crackpot anti-evolutionary idiots, now.
aroc91
4.8 / 5 (16) Sep 04, 2014
I hope you can understand, and think and reason as a normal person


What would a "normal person" infer from the phylogenetic data then? If we can't infer relatedness from the similarities and differences between genomes, what conclusions can we draw from it?

I am not "anti-evolution"


You call it a fallacy in the very next sentence, so yeah you are.

It is basically unscientific magic.


So what do you consider the more scientifically supported alternative?
supamark23
4.5 / 5 (15) Sep 04, 2014
Verkle, you're a crackpot and an idiot. Evolution perfectly explains how species develop, you just aren't able to comprehend it.

So, what better explaination do you have? Remember, it must better explain speciation than evolution using fossil record and molecular biology (which perfectly explains it, soooo good luck on that).
Vietvet
5 / 5 (9) Sep 04, 2014
@verkle

Why don't you just admit your anti-evolution views are shaped by your religious beliefs, not science. That would be the honest and honorable thing for you to do.
OZGuy
4.6 / 5 (10) Sep 04, 2014
@verkel
You are an idiot and a crackpot, that is self-evident from the drivel you regularly post.
Shootist
1.4 / 5 (9) Sep 04, 2014
caffeine can evolve?

no.

only living organisms can evolve.
DonGateley
1.8 / 5 (5) Sep 04, 2014
I want to know what is so specifically special about the caffeine molecule that three species independently selected genes to manufacture it.
yep
3.7 / 5 (3) Sep 05, 2014
Don, Michael Pollan's book Botany of Desire: A Plant's-eye View of the World, though not specifically about caffeine does have an interesting take on things. Its a good read if you get a chance. Liked most of his other books to.

Convergent evolution on the molecular level, and the visual evidence of physical traits shown in the fossil record, sure does seem to weigh heavy on the proving evolutionary theory side.
Mike_Massen
4.3 / 5 (12) Sep 05, 2014
verkle doesn't get it, he identified himself first - LOL with
Go ahead Supa, call me an idiot and a crackpot!
He didnt have to U accepted it. verkle went on with
Just first tell how how you can believe in the magic of evolution.
1.Its not about belief, its evidence
2. Understand math eg permutations in organic chemistry

Unfortunately for ALL religion, computers/genetic algorithms proved decades ago U don't need a singular act of creation of things. Great complexity arises from 3 key sources with environment & TIME
a. Discontinuous items Eg Atoms
b. Rules of interactions Eg Bonding
c. Energy differential

Now verkle U & others might argue a god (the 'god') put it all there, ok fine but, he/she/it is a worse communicator than most humans, Eg. bible, the god of that scifi story is:-

i. A bad communicator, dependent on lazy people
ii. Has problems with women, they r used
iii. ONLY report Status, Punishment & Authority
iv. Nasty

Very common; humans make their gods all the time.
Mike_Massen
4.1 / 5 (9) Sep 05, 2014
DonGateley asked a good question
I want to know what is so specifically special about the caffeine molecule that three species independently selected genes to manufacture it.
It has been a useful natural pesticide, plants generate it to generally ward off insect attack concentrate it in various parts as a probabilistic risk issue to dissuade those areas being consumed first - this is of course within the bell curve permutation base given plants are fairly simple organisms with negligible if any cognition of us (recent), ie farming & cultivation.

Its part of the normal brutality of nature ie. Eat & be eaten. The constant war of survival which, as we know full well from permutations & mutations is temporary, over enough time the so called balance see-saws wildly.

Adaptation is non-linear, sporadic & rooted in energy transfer, economies, risk & above all pressure from changing environments.- all within relatively simple chemical rules & all under the dispassionate gaze of physics !
antialias_physorg
4.6 / 5 (11) Sep 05, 2014
how you can believe in the magic of evolution

Erm...cause it ain't magic?

It is impossible that coffee could some magically develop the right enzymes for caffeine production

And it's impossible because... ? (Remember: mutation and selection. For something to be selected it need not me perfect. It just has to be ever so slightly better than its current competitors)

and think and reason as a normal person, without calling me an idiot.

Calling you an idiot is an insult to idiots (and I mean the technical medical/psychological term 'idiot', here)

Shootist, you are using some large words that you do not understand. "No" and "living" would be the two most important ones, i believe.

You owe me a new keyboard.
antialias_physorg
4.7 / 5 (12) Sep 05, 2014
call me a crackpot and idiot

Not 'call'. Show. You aren't a crackpot by say-so, but by hardcore proof. It is perfectly civil (and admissible) to call a duck a duck.

Notice how so many people have reacted to my post: in utter lunacy

The word you are looking for is incredulity. It is incredible how someone can be so benighted and still have learned how to breathe.

Showing that an organism has a certain characteristic or ability does not nothing to prove in any way the idea of evolution.

Evolution is already demonstrated. Your request that the existence of X show evolution is nonsensical at best and a red herring at worst.

Evolution is only proven scientifically if we can observe it and repeat it

Then you should google for any number of experiments that have been conducted (including all of animal breeding in the past)

There are virtually no evolutionary links in the vast fossil record

Source for that claim?
yep
5 / 5 (6) Sep 05, 2014
An amazing thing about this molecule, is not only can it act as Mike said a pesticide for some insects it acts as a attractant for others with a neuroenhancement benefit.
http://www.scienc...124/1202
OZGuy
4.6 / 5 (9) Sep 06, 2014
@verkle
With comments like -" Evolution is a made up story and people are now trying to "prove" it is right." you are continually publicly declaring your stupidity and opening yourself up for public derision.
You keep posting drivel, we'll keep deriding you, it's the natural order of events.
Captain Stumpy
4.6 / 5 (9) Sep 06, 2014
Just first tell how how you can believe in the magic of evolution
@verkle
evolution has empirical evidence: http://myxo.css.m...dex.html
your faith has none.
evolution has proof of existence: http://scholar.go...t=0%2C14
About 4,390,000 results (0.04 sec) on Google Scholar
faith, by definition is the belief in something without evidence... which is similar to magic, as your proof, per your own words refuting the reality of evolution should mean that we have talking snakes today, along with other suggested demons and angels, none of which have any empirical evidence

So can the righteous indignation and claims that there must be civility. You've been proven wrong so many times that you should know by now that science works, there is proof, you are wrong
no if's, and's or Butt's

you have offered ZERO evidence
you have received overwhelming evidence
you still ignore reality
Captain Stumpy
4.6 / 5 (10) Sep 06, 2014
attacking my character, call me names, etc. etc. And on a scientific discussion? These kind of people don't deserve respect or acknowledgment
@verkle
neither do people who refuse to see reality or empirical data and support conjecture without evidence
Evolution is only proven scientifically if we can observe it and repeat it, none of which has ever know to occur
this is called a blatant lie
I have given you LENSKI's page already once above, and many other times
this is the definition of stupidity, and therefore the claims of you being stupid are now substantiated by your own words
There are virtually no evolutionary links in the vast fossil record, of which we expect to find millions and billions
broken logic already proven wrong my links in the past
shall I again post them?
http://www.talkor...comdesc/
http://www.talkor...nal.html

Unsubstantiated conjecture like you've posted can be dismissed without cause for lack of evidence
Captain Stumpy
4.5 / 5 (8) Sep 06, 2014
An amazing thing about this molecule, is not only can it act as Mike said a pesticide for some insects it acts as a attractant for others with a neuroenhancement benefit.
http://www.scienc...124/1202
@Yep
good find... and fascinating
can you read the whole study?
Although plant-derived drugs like caffeine or nicotine are lethal in high doses (3–5), at low doses they have pharmacological effects on mammalian behavior. For example, low doses of caffeine are mildly rewarding and enhance cognitive performance and memory retention (6). Caffeine has been detected in low doses in the floral nectar and pollen of Citrus (7), but whether it has an ecological function is unknown.


Captain Stumpy
5 / 5 (8) Sep 06, 2014
I couldn't find anything related to true evolution
@verkle
then you didn't read the link
true evolution (macroevolution)
then you don't know the definition of Evolution nor the Theory of Evolution: https://en.wikipe...volution
from the link
Evolution is the change in the inherited characteristics of biological populations over successive generations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins
this has been repeatedly pointed out to you
therefore you are simply waffling and trying to avoid responsibility for posting blatant LIES
which, btw, are against almost EVERY religious dogma out there

your ignoring links only proves that you don't want to learn, see the evidence or accept reality, and therefore are nothing but a religious troll trying to spread his faith of LIES

Lenski PROVED evolution and gave you examples of it over time
antialias_physorg
5 / 5 (8) Sep 06, 2014
Macroeveolution is a series of microevolutions over a long time. You don't jump from bacterium to human over night (are you really expecting that when you hear the term evolution? Really?)

We have recorded instances of speciation and we have intermediary species (e.g. Volvox). Though it is only to be expected that specialists are more successfull, and that intermediary species don't last long (only during the time where the niche they are going for isn't settled yet).

In the end you just have to look at the handedness of amino acids. That doesn't make sense if not every living thing is evolved from a common ancestor (because the opposite handedness is exactyl as chemically active - but just doesn't occur in nature. If it all were a construct then there'd be no reason for a preference).
Captain Stumpy
5 / 5 (6) Sep 06, 2014
microevolution, which is not evolution at all, but only about recombining existing genetic material within the group.
I gave up reading your links, as it didn't support your claims
@verkle
this simple ending, more than ANYTHING ELSE you have posted, simply PROVES that:
you are NOT here to debate
you are not here for anything other than to undermine SCIENCE with your TROLL RELIGION

you are here only to post continual LIES based upon a delusional faith that has NO empirical evidence while ignoring REALITY

by all means, you are only proving the denigration by others... you are showing the world why they are correct in their derogatory remarks towards you

ThomasQuinn
4 / 5 (4) Sep 08, 2014
Evolution is a made up story and people are now trying to "prove" it is right.


I think you made a typing error - where you write "Evolution", you mean "Religion".

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