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

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

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...