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Biotech Science

Corn Genome Sequenced 64

Posted by kdawson from the what-fuels-these-morsels-be dept.
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."
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Corn Genome Sequenced More

Corn Genome Sequenced

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  • er... (Score:1, Offtopic)

    by n0dna ( 939092 )
    ALL YOUR CORN...

    I got nothin.

  • Plants Humans (Score:5, Informative)

    by imstanny ( 722685 ) on Tuesday February 26, 2008 @03:20PM (#22563296)

    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.
    • I think a better argument would be that humans and other much more complex animals are far more potentially vulnerable to viruses than corn plants, in the same way that Windows Vista has far more potential vulnerabilities than DOS 3.3.

      A good defense against retroviruses would seem to be ruthlessly pruning out DNA that isn't functional, lest it be targeted by an invader. It's the molecular analog of the old security advice to turn off any RPC service you're not actually using.
      • Sure, but retroviruses don't (on average) kill us before we can reproduce, so there's no reason for us to have selected for a defense that works like that.

        There's no point in writing security updates for new software once the next version is already released.

        • Re: (Score:3, Insightful)

          by Quadraginta ( 902985 )
          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

      • Re: (Score:3, Interesting)

        by HTH NE1 ( 675604 )

        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: (Score:3, Interesting)

          by Quadraginta ( 902985 )
          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 co

          • Re: (Score:2)

            by hawkfish ( 8978 )

            How anyone thinks it generally represents proof of brilliant top-down divine engineering design is beyond me...
            Just because you don't understand it doesn't mean it's not brilliant ;-)
            • Well, yes, that would be true. But there are plenty of cases where I do understand the mechanism and it sure looks like it was "designed" (if it was) by an idiot, or someone with a weird sense of humor.

              The prototypical example is the vertebrate eye. In our eyes, the entire optical sensor system faces backward, towards the inside of our head. Blood and nerves connect to the retina from the front, passing right across the face of this light-gathering instrument. It's kind of like having a CCD device in a
      • http://notexactlyrocketscience.wordpress.com/2006/09/16/hidden-junk-gene-separates-human-brains-from-chimpanzees/ [wordpress.com]

        Eliminating junk genes could have some nasty unintended effects.

    • Re: (Score:3, Informative)

      by swid27 ( 869237 )
      (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.)

    • Re: (Score:2)

      by jd ( 1658 )
      So corn's genetic code is the least a-maizing and less of a maize than the DNA of other plants?

    • Re: (Score:2)

      by dintech ( 998802 )
      This has to be one of the most interesting factoids I've read on slashdot. The difference in numbers is counterintuitive until you factor in the reasons you describe. Thanks!

  • Hopefully this will lead to more corn in our diets!

    /sarcasm

    • Hopefully this will lead to more corn in our diets!
      Yeah, and then they'll make another wonderful scientific break through with corn and send the price sky rocketing... /scarcasm
  • welcome our vegetative overlords.

  • I just hope... (Score:3, Funny)

    by Corpuscavernosa ( 996139 ) on Tuesday February 26, 2008 @03:33PM (#22563500)
    ... 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.

  • It had to be said... (Score:4, Funny)

    by halivar ( 535827 ) <bfelger@gmai l . com> on Tuesday February 26, 2008 @03:35PM (#22563524)
    You are in a maize of twisty genomes, all alike.

    Fa fa fa fa!
  • Go to the source [wikipedia.org]!
  • Children of the Corn, or we'll hear "May the farts be with you"

  • My people call it cr0n.
    • If I had mod points and had not already posted to this article, I would have definitely given you a funny mod. For some reason your comment seriously cracked me up.

    • Re: (Score:2)

      by dintech ( 998802 )
      I use cr0n to schedule my jobs every morning. cr0n contains lots of fibre [wikipedia.org] and helps to reduce (ahem) "server load".
  • Hopefully, this will lead to new methods to cure stalks of corn that have developed terminal cancer.

    • Re: (Score:2)

      by dintech ( 998802 )
      Surely it'll just be used to take over the world with giant triffid like corn beasts. Just saying...
  • It's only a matter of time before we have this:

    http://goats.com/archive/060403.html [goats.com]

  • Finally (Score:2, Interesting)

    by MaizeMan ( 1076255 )
    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 aim

    • Re: (Score:3, Interesting)

      by jd ( 1658 )
      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

      • The government's biggest contribution to sequencing is probably the Joint Genome Institute (http://www.jgi.doe.gov). Until recently they'd focused more on animals and bacteria, but they are now also turning out a number of plant genomes. I don't know what genomes of agriculturally important plants you are saying can be found online. The only one in the same range of corn that I know of is rice (which was a huge deal with it came out too.) I'd also disagree with your position that agricultural plants are le

        • Re: (Score:2)

          by jd ( 1658 )
          I'm basing this on the contents of the BLAST ftp archive [nih.gov], where the plants directory covers almond, barley, various beans, beet, cocoa, corn, eggplant, oat, wheat, onion and tomato, amongst others. These files are down to the nucleotide level and can be processed with any of the open-source BLAST applications (which is good), but I will admit I can't be sure which of these are complete genome sequences and which are partial.
          • Ok, now I understand what you're talking about. You're right, there's genetic data for a wide range of species, but that's because it's a lot easier to clone and sequence individual genes, (or randomly sample the parts of the genome that are being expressed as RNA using rtPCR techniques) than it is to sequence the whole genome and put all the pieces of each chromosome together in the correct order. That's why there's such a long gap between the isolation of the first gene in 1969 and the sequencing of the f
  • I wonder who has the patent. Hmmm,Monsanto... Can you say monopoly ???
    • See subject line. If anything this underscores the need for continued government investment in R&D. This was a government funded program, and the information is going to be in the public domain. Which makes this one more small check on the power of individual large corporations, and one more victory for public sector improvement of crop germplasm.
      • So was the human genome project. I may be wrong, but to me it looked like everything went into the front door of Celera and then left through the back door in the form of patents.
    • We joke, but someone at monsanto undoubtedly at least thought about ways to steal a patent on this. See the link to the blog. The submitter talks about how monsanto is claiming they contributed. Maybe they were thinking "Step one, sneak a comment in there about how we contributed. Step two, use that lie as a basis for claiming we should get patent. Step three, anyone who has eaten corn owes us annual royalties, since you are what you eat."
      • In the financial news,The title was, Monsanto Decodes Corn Genome. Its going to be an interesting chase no matter what.

  • Now.. (Score:1)

    by Indes ( 323481 )
    I want hard ball sized popcorn.
  • Although the maize geneome is of comparable size to the human genome, it could theoreticaly be simplified a dozen fold and retain the same amount of information... it's an allopolyploid. It has heaps and heaps of copies of the same genetic material. In fact, this has been selected for so that they grow bigger which seems to work for plants. For humans though, having just three copies of a particular chromosome can give you a disease, like Downs Syndrome!
  • Corn is no place for a mighty warrior!

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