Corn Genome Sequenced

dooling writes "Later this week, the completion of the maize genome draft sequence will be announced. Maize has a large genome (slightly smaller than human) that is highly repetitive (about 80%). These facts made a whole-genome shotgun approach to sequencing infeasible. Therefore, a BAC-by-BAC approach was taken, similar to what was done for the Human Genome Project. Further work on the maize genome will focus on the parts of the genome that have genes, thereby avoiding the highly-repetitive regions of the genome (even though the maize genome is slightly smaller than human, it is thought to have about twice as many genes). You can read my take here."

Comments

Plants Humans

[imstanny]

Maize has a large genome (slightly smaller than human) that is highly repetitive (about 80%) Humans have about 22,000 genes. Plants tend to have in teh range of 40,000 genes - on average. THis is suprising initially, but human genes are more complex. Single genes can make at least 2 proteins, sometimes much more. Plants, on the other hand, have to produce a lot of chemicals for defence, since they can't run away from predators - which is the primary reason for increased gene count. Maze, it seems, is one the lower end for plant life in terms of gene count.

Re:So?

[moderatorrater]

Go sequence a mouse. What's the point of sequencing something that we kill? Corn's one of the more useful crops in the world, so sequencing it makes sense. If we understand the genome, we can make new varieties better.

Also, corn is where we first noticed jumping genes.

I just hope...

[Corpuscavernosa]

... that this will enable scientists to make a corn strain that will eliminate the "phantom" corn that mysteriously shows up in my poop when I have no recollection of eating any.

Re:So?

[dooling]

We've sequenced the genome of something we eat. This helps us why? Go sequence a mouse. We have already sequenced the mouse.

It had to be said...

[halivar]

You are in a maize of twisty genomes, all alike.

Fa fa fa fa!

Re:Plants Humans

[swid27]

(Food) plants also have a larger set of possible allele combinations per gene, as they usually have 3, 4, 6 or 8 copies of each chromosome. (You and I have to get by with "only" 2.)

My People...

[Bovarchist]

My people call it cr0n.

Re:Children of the Corn

[azuredrake]

Stop being so corny, guys.

Re:another possibility

[Quadraginta]

Sure, but retroviruses don't (on average) kill us before we can reproduce

Say what? That's a strange statement. First of all, it's true about all modern viruses and bacterial infections by definition, because we're a successful species, and any successful high-level species at this stage of the game has to be well-defended against bacteria and viral invaders. By analogy, you couldn't possibly introduce Windows 3.1 in today's environment without it being slaughtered immediately.

But what we're talking about is what things were like way back in the day, when complex animals first evolved, and the whole retroviral infection mechanism was just being tried out. At the beginning of the arms race, so to speak, before each side had armored up. In those days it's very likely retroviruses did kill many and many an individual before he could reproduce, until both sides evolved away from that mutually-assured-destruction scenario.

Re:another possibility

[HTH NE1]

A good defense against retroviruses would seem to be ruthlessly pruning out DNA that isn't functional, lest it be targeted by an invader. Have you considered that that DNA isn't functional because it is a decoy/shield against retroviruses finding the functional DNA and causing real havoc to befall cell function?

"No, no, no, don't tug on that. You never know what it might be attached to."
--Dr. Buckaroo Banzai

Re:I for one...

[Idiomatick]

George bush?

I once did a report on Libya for school

[Kagura]

The exports of Libya are numerous in amount. One thing they export is corn, or as the Indians call it, "maize". Another famous Indian was "Crazy Horse". In conclusion, Libya is a land of contrast. Thank you.

Finally

[MaizeMan]

Yes! After watching the sequences of things like grape and papaya being announced, it's good that the first draft of the corn genome is finally out there (or will be on Friday.) In terms of the potential benefits I'd put maize as around the third most important genome to go after (the first being humans, and the second being any other mammal to compare to the genome of humans) but as the article mentions, the percentage of repetitive elements, plus the fact that early plant genome funding in the US was aimed at model organisms like arabidopsis rather than agriculturally significantly species slowed it down significantly. That said I'm obviously very biased. Look at my name if nothing else. And thank god the information is in the public sector, rather than the proprietary knowledge of a private corporation.

Re:Finally

[jd]

There are a lot of downloadable sequences on the Internet for many agriculturally-significant plants. Personally, I consider those the least interesting, as they've been finely-tuned using those same agricultural mechanisms for millenia. Because of that, you've the least diversity and the greatest potential for noise (stuff that's coded for but basically bred out, so there's no real way to know what it does), so you get the least information for your money.

That's not to say that such plants should not be done. They should, and they really should have been sequenced fully BEFORE genetic engineering took hold. If you're going to modify code, at least read it before applying patches, and have a mechanistic (not a symptomatic) understanding of what the patches actually do. On the other hand, plants that are very information-rich - even if there is no known immediate or direct use - tell you the most about the system as a whole, refine the techniques for extracting that information, and build up more of an understanding of what it is that researchers are looking at.

Personally, I think that DNA labs are sufficiently easy to build at this point that it would be helpful for the Governments to splurge out a bit and accelerate the full sequencing process. There's a lot to be learned, including how to make wiser GM decisions at both the industrial and political levels. What is safe, and what the long-term impact would be could be more easily and more accurately determined with better quality data. Confidence is always going to be related to the ability to understand what it is you are confident about.

Re:another possibility

[Quadraginta]

Yeah. I don't find it creditable because decoys only work when bullets are more expensive than decoys. In this case viral particles are so "cheap" that I think they would overwhelm any such defensive mechanism.

I believe it is generally thought plausible, however, that the typical splicing that goes on to assemble a complete gene from all the exons, which requires at least some garbage DNA for the introns, is a viral defense. Basically it's sort of a genetic equivalent to using spread-spectrum in radio communications to cut through interference, in this case the genetic interference caused by the virii. Only if you know the secret decoder pattern does your message come through in the clear, otherwise it gets chopped to meaningless bits.

Who knows? If there's one general truth about biological systems, it's that they're an unbelievably hairy spaghetti-maze of jury-rigged weirdness, with at least five complicated mechanisms to get any one simple task done. How anyone thinks it generally represents proof of brilliant top-down divine engineering design is beyond me...