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Corn Genome Sequenced

Posted by kdawson on 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."

64 comments

  1. er... by n0dna · · Score: 1, Offtopic

    ALL YOUR CORN...

    I got nothin.

  2. Plants Humans by imstanny · · Score: 4, Informative

    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.
  3. Yay! by evil+agent · · Score: 1

    Hopefully this will lead to more corn in our diets!

    /sarcasm

    --
    End transmission.
    1. Re:Yay! by techpawn · · Score: 1

      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
      --
      Ask not what you can do for your country. Ask what your country did to you
  4. Coming soon... by Anonymous Coward · · Score: 0

    "This corn doesn't look different..."
    "That's not corn--that's baby corn!"

  5. I, for one, by Anonymous Coward · · Score: 0

    do not revere our corn-based wannabe-overloads now that we've sequenced their genome.

  6. Re:So? by moderatorrater · · Score: 3, Informative

    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.
  7. another possibility by Quadraginta · · Score: 1

    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.

    1. Re:another possibility by loimprevisto · · Score: 1

      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.

      --
      Much Madness is divinest Sense --
      To a discerning Eye --
      Much Sense -- the starkest Madness
    2. Re:another possibility by Quadraginta · · Score: 2, Insightful

      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.

    3. Re:another possibility by HTH+NE1 · · Score: 2, Interesting

      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
      --
      Oh, say does that Star-Spangled Banner entwine / The myrtle of Venus with Bacchus's vine?
    4. Re:another possibility by Quadraginta · · Score: 2, Interesting

      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...

    5. Re:another possibility by hawkfish · · Score: 1

      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 ;-)
      --
      You will not drink with us, but you would taste our steel? - Walter Matthau, The Pirates
    6. Re:another possibility by Quadraginta · · Score: 1

      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 telescope and running the cables that connect to the sensor in front of the CCD device. Seems kind of silly, no?

      There are counter-arguments about why this is really actually brilliant, but they seem to me rather ad hockish and full of special pleading. Not very convincing.

      I'm agnostic on the existence of a Designer, precisely because the evidence we have is all of this ambiguous, unconvincing type. Sure, it could be so brilliant I don't recognize its brilliance. But to believe that takes an act of faith, not reason.

    7. Re:another possibility by Devin+Jeanpierre · · Score: 1

      http://notexactlyrocketscience.wordpress.com/2006/09/16/hidden-junk-gene-separates-human-brains-from-chimpanzees/

      Eliminating junk genes could have some nasty unintended effects.

      --
      -Devin Jeanpierre
  8. I for one... by Kinthelt · · Score: 0

    welcome our vegetative overlords.

    --

    "Evil will always triumph over good, because good is dumb." - Dark Helmet (Spaceballs)

    1. Re:I for one... by Idiomatick · · Score: 3, Funny

      George bush?

  9. I just hope... by Corpuscavernosa · · Score: 3, Funny

    ... 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.

    --
    We figured out a long time ago that it's easier to elect seven judges than to elect 132 legislators.
  10. Re:So? by dooling · · Score: 4, Informative

    We've sequenced the genome of something we eat. This helps us why? Go sequence a mouse. We have already sequenced the mouse.
    --
    dd
    "if you hang the blame on the wall
    there'd be a frame around us all" - Jay Farrar
  11. It had to be said... by halivar · · Score: 3, Funny

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

    Fa fa fa fa!

    1. Re:It had to be said... by phouqhue · · Score: 1

      Yay!! Hooray for corn!!!

  12. Korn genome sequenced? by davidwr · · Score: 1

    Go to the source!

    --
    Knowledge is how to play a game, intelligence is how to win, wisdom is knowing what game to play.
    1. Re:Korn genome sequenced? by Wandering+Wombat · · Score: 1

      Dead... kernels... everywhere....

      --
      I like to place meaningful quotes in my sig, so people will know that I know what meaningful quotes are.
  13. Re:Plants Humans by swid27 · · Score: 2, Informative

    (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.)

  14. Children of the Corn by davidwr · · Score: 1

    All your scary movies are ...

    Nope, that doesn't work either.

    --
    Knowledge is how to play a game, intelligence is how to win, wisdom is knowing what game to play.
    1. Re:Children of the Corn by Anonymous Coward · · Score: 0

      I, for one...

      Nope. Nada.

    2. Re:Children of the Corn by azuredrake · · Score: 3, Funny

      Stop being so corny, guys.

      --
      Quis custodiet ipsos custodes?
    3. Re:Children of the Corn by Brian+Gordon · · Score: 1

      In soviet... corn... never mind.

    4. Re:Children of the Corn by Anonymous Coward · · Score: 0

      Corn, corn, the magical fruit
      the more you eat, the...

      No, that's not right either.

      DAMN YOU CORN!

  15. As long as we don't EAT the... by davidsyes · · Score: 1

    Children of the Corn, or we'll hear "May the farts be with you"

    --
    Previously: "Linux... Toward the Sunrise..." Now: "Linux... Toward the-- No, now, part of Every Sunrise"
  16. Re:So? by Anonymous Coward · · Score: 0

    We did.

    http://genome.wustl.edu/genome.cgi?GENOME=Mus%20musculus

  17. My People... by Bovarchist · · Score: 2, Funny

    My people call it cr0n.

    --
    Hell is other people's code.
    1. Re:My People... by Corpuscavernosa · · Score: 1

      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.

      --
      We figured out a long time ago that it's easier to elect seven judges than to elect 132 legislators.
    2. Re:My People... by dintech · · Score: 1

      I use cr0n to schedule my jobs every morning. cr0n contains lots of fibre and helps to reduce (ahem) "server load".

  18. highly repetitive? by Anonymous Coward · · Score: 0

    highly repetitive (about 80%). unless its code consists of something other a, c, t and g, I would hope that its genetic code would be highly repetitive

  19. Re:So? by Tinyn · · Score: 1

    Fuck that, we sequence everything http://www.ncbi.nlm.nih.gov/projects/mapview/mvhome/mvhome.cgi

  20. Excellent News! by NMR+Dude · · Score: 1

    Hopefully, this will lead to new methods to cure stalks of corn that have developed terminal cancer.

    1. Re:Excellent News! by dintech · · Score: 1

      Surely it'll just be used to take over the world with giant triffid like corn beasts. Just saying...

  21. I once did a report on Libya for school by Kagura · · Score: 2, Funny

    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.

  22. Just a Matter of Time Now... by W.+Justice+Black · · Score: 1

    It's only a matter of time before we have this:

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

    --
    "Time flies like an arrow; fruit flies like a banana." --Groucho Marx
    1. Re:Just a Matter of Time Now... by W.+Justice+Black · · Score: 1

      Nah. It's reasonably safe for (e.g.) work. Sorry for the scare.

      --
      "Time flies like an arrow; fruit flies like a banana." --Groucho Marx
  23. why not? by davidwr · · Score: 1

    Chris Weber told us to Beware Of the Sentient Chili overlords, and chili goes good with cornbread.

    --
    Knowledge is how to play a game, intelligence is how to win, wisdom is knowing what game to play.
  24. Finally by MaizeMan · · Score: 2, Interesting

    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.

    1. Re:Finally by jd · · Score: 2, Interesting
      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.

      --
      It's a small world and it smells funny; I'd buy another if it wasn't for the money; Take back what I paid (SoM)
    2. Re:Finally by MaizeMan · · Score: 1

      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 less interesting because of domestication. If anything I think we can learn even more from them because we can look at the changes to their genomes as the result of 1000's of a years of human selection for the things that make plants more beneficial to us. A good example of this is the work done by a guy named John Doebley (http://teosinte.wisc.edu/) on identifying the mutant alleles of genes that were under strong selective pressure during the domestication of maize from its wild ancestor. But obviously the genomes of non-domestic plants also hold important secrets. Like the resurrection plants of the american southwest that can survive complete dehydration. Thanks for commenting, it was an enjoyable read.

    3. Re:Finally by jd · · Score: 1

      I'm basing this on the contents of the BLAST ftp archive, 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.

      --
      It's a small world and it smells funny; I'd buy another if it wasn't for the money; Take back what I paid (SoM)
    4. Re:Finally by MaizeMan · · Score: 1

      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 first genome in the mid-1990s. Until recently the only two published plant genomes where arabidopsis and rice. There are now arguably (depending on when you want to call a genome complete) close to 10 sequenced genomes, the new ones I can name off the top of my head are: maize, pea, grape, papaya, and poplar. Sorghum has been sequenced, but I don't think they're done assembling it yet.

  25. Re:Plants Humans by jd · · Score: 1

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

    --
    It's a small world and it smells funny; I'd buy another if it wasn't for the money; Take back what I paid (SoM)
  26. Oblig ATHF by bckrispi · · Score: 1

    Gentlemen, behold!!

    CORN!!!

    --
    Xenon, where's my money? -Borno
  27. protect the patent by lazy+genes · · Score: 1

    I wonder who has the patent. Hmmm,Monsanto... Can you say monopoly ???

    1. Re: protect the patent by philspear · · Score: 1

      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."

    2. Re: protect the patent by lazy+genes · · Score: 1

      In the financial news,The title was, Monsanto Decodes Corn Genome. Its going to be an interesting chase no matter what.

  28. Re:So? by philspear · · Score: 1

    Quit blogging and hurry up with the chicken and platypus sequencing!

    I use chickens for my research. Platypi are wierd. I do think they would make an interesting model organism, if only to study platypi. Either way, I want them both by the end of the week.

    Phil

  29. It's in the public domain! by MaizeMan · · Score: 1

    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.

    1. Re:It's in the public domain! by lazy+genes · · Score: 1

      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.

  30. Now.. by Indes · · Score: 1

    I want hard ball sized popcorn.

  31. Plant Vs Human by MassiveForces · · Score: 1

    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!

  32. Oblig. by Rob+T+Firefly · · Score: 1

    Corn is no place for a mighty warrior!

    --
    Slashdot Burying Stories About Slashdot Media Owned
  33. Re:Plants Humans by dintech · · Score: 1

    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!

  34. Re:So? by Anonymous Coward · · Score: 0

    *I* eat mice, you insensitive clod!

  35. Gentlemen! Behold! by Anonymous Coward · · Score: 0

    CORN! (NSFW!)

    /Let the mating begin! MUHAHAHAHAHA!