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Biotech Science

Pine Tree Has Largest Genome Ever Sequenced 71

Posted by samzenpus
from the it's-how-you-use-it dept.
sciencehabit (1205606) writes "Using a single pollinated pine seed, researchers have sequenced the entire genome of the loblolly pine tree--and it's a doozy. The tree's genome is largest yet sequenced: 22.18 billion base pairs, more than seven times longer than the human genome. The team found that 82% of the genome was made up of duplicated segments, compared with just 25% in humans. The researchers also identified genes responsible for important traits such as disease resistance, wood formation, and stress response."
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Pine Tree Has Largest Genome Ever Sequenced

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  • It just has to be said - they need to figure out how to integrate that wood formation sequence into human genes, before I get much older.

    Yes, I know. But it *did* have to be said.
  • by Jim Sadler (3430529) on Friday March 21, 2014 @12:52AM (#46540825)
    All those genes make humans look like flunkies. And knowing a tiny bit about Darwin maybe we could take into account that a pine tree can easily outlive any human ever born. And pine trees tend to have a very long history of reproduction compared to humans. So maybe all the thinking, feeling and running about that humans do is simply proof of our inferiority. think about it. The pine tree needs water, sunshine, a few minerals and an atmosphere and that is about it. Humans need all kinds of things. I've never seen a tree shoot anyone, go mental, or rape other trees. Trees might enjoy making humans feel like idiots.
    • by Samantha Wright (1324923) on Friday March 21, 2014 @01:14AM (#46540881) Homepage Journal

      While the set of large-genomed organisms does include some very sophisticated trees and flowers, it also includes several species of amoeba... so I wouldn't panic just yet.

      All a big genome really means for certain is that you're good enough at finding food that you can support it. The substance is a lot more important—some species of shrimp, for example, have 88 or 92 chromosomes, but they're mostly redundant duplicates. Wheat has five copies of every chromosome, too.

      Plants tend to have large genomes because they reproduce so rapidly—a field of corn has enough offspring every season to mutate every nucleotide in the whole kit and kaboodle at least once, and because they have very static, slow existences, they can afford to tune themselves very well to their environments. That's what the genes and duplicates are for—giving the plant very fine-grained control over things like how it prepares for the next season based on the weather from the last one.

      • Plants also have the advantage of being able to survive errors (or maybe "excursions"?) of miosis more often - polyploid mammals typically will spontaneously abort, but polyploid plants often become important to humans. Bread wheat and spelt are hexaploid because humans bred them that way millenia ago. The current record holder for largest genome, Paris Japonica, is huge only because it's octaploid. The loblolly gets props for having a big genome while being merely diploid.

    • by noh8rz10 (2716597)

      Humans need all kinds of things.

      Humans need love.

    • by pspahn (1175617)

      And pine trees tend to have a very long history of reproduction compared to humans.

      Do you suppose the reason they are that superior is precisely because they have been around as long as they have?

    • by Cryacin (657549) on Friday March 21, 2014 @01:21AM (#46540909)
      The last tree to call me a knuckle dragging, chainsaw wielding idiot didn't last too long after I got the mud out of my chainsaw.
    • If you want to assign bonus points for low-effort existence, how about viruses? It's a matter of some ambiguity whether they even bother to be alive; but that hardly stops them from being mind bogglingly numerous and found basically wherever there are hosts available.
    • Need is a rather subjective term.
    • by period3 (94751)

      All those genes make humans look like flunkies. And knowing a tiny bit about Darwin maybe we could take into account that a pine tree can easily outlive any human ever born. And pine trees tend to have a very long history of reproduction compared to humans. So maybe all the thinking, feeling and running about that humans do is simply proof of our inferiority. think about it. The pine tree needs water, sunshine, a few minerals and an atmosphere and that is about it. Humans need all kinds of things. I've never seen a tree shoot anyone, go mental, or rape other trees. Trees might enjoy making humans feel like idiots.

      Plants often have large genomes. One reason I've heard for this is that plants can't move, so they're much more exposed to the environment. As a result, they need a more diverse array of biochemical responses to stressors.

    • by TubeSteak (669689)

      I've never seen a tree shoot anyone, go mental, or rape other trees.

      Many plants are constantly battling each other: http://en.wikipedia.org/wiki/Allelopathy [wikipedia.org]

      It's a very slow combination of chemical warfare and forced starvation.

    • Hey now, just because what you've got is smaller doesn't make you any less of an organism. It's not the size that counts, its how you use it.

    • Yep, we are inferior to trees.
      22.18 billion base pairs makes for great wood burning!
      We humans, not so much :(

    • by boristdog (133725)

      I've never seen a tree shoot anyone, go mental, or rape other trees.

      You didn't listen to enough Rush as a youth.

  • As a Bonsai artist (Score:2, Insightful)

    by cyberzephyr (705742)

    I'm not surprised. trees and plants were here before we were.

    • I'm not surprised. trees and plants were here before we were.

      Genome sizes can drift in either direction over time(or just sort of wander), though, so finding a radically pruned minimum-functional-genome would also be a possible consequence of a long evolutionary history. Redundancy is nice; but DNA synthesis isn't metabolically free.

    • by period3 (94751)

      Bacteria were there even longer - but they often have very small genomes.

    • by Calavar (1587721) on Friday March 21, 2014 @02:28AM (#46541107)
      Why is this modded up? First it is wrong even on the surface. Chordates (the phylum containing humans) first appeared around 550 million years ago. Conifers (the division -- plant equivalent of phylum -- containing pines) first appeared around 300 million years ago. Second, even trees and humans are descended from a single common ancestor, so how can trees be "evolutionarily" older than humans? Third, more time does not equal bigger genome. Genomes can shrink over time. This has happened in many species of yeast and bacteria, as smaller genomes allow them to replicate faster. Even macroscopic organisms such as birds have had their genomes shrink over time.
      • by Artifakt (700173)

        If anything, it makes sense to count how long a species has been evolving in terms of generations, not years. Most conifers have a longer time between generations than humans, so they have fewer evolutionary intervals than humans. I don't even know how you could get an average of how long a generation is for the human evolutionary history, back to tree shrews or even to the first chordates - how could we calculate the total number of evolutionary steps our ancestors made and compare this to a pine tree's an

  • by mysidia (191772) on Friday March 21, 2014 @01:00AM (#46540843)

    The team found that 82% of the genome was made up of duplicated segments, compared with just 25% in humans.

    See! The pine trees are smart and make multiple copies of their genome segments, for backup purposes. Humans always forget the importance of backups, until it's too late.

    • Most human genes are backed up in numerous copies; but they are spread between sites for continuity of operations purposes.

      Unfortunately for you, you are just a site, not the operation, so your continuity is a distinctly secondary objective.
    • More like the pine trees don't understand their genome properly, so they do a copy/paste before applying a mutation. They'd be less reluctant to refactor it in-place if only compilation didn't take so long.

      • by mysidia (191772)

        They'd be less reluctant to refactor it in-place if only compilation didn't take so long.

        They have version control comparable to a 'git reset --hard ...' using nonsense codons.. via NMD / Nonsense-Mediated RNA decay.

    • Humans always forget the importance of backups, until it's too late.

      Well, whaddaya expect? It's in our genes!

  • Soon I shall imbue the soles of my feet and grow pine shoes.
  • by Animats (122034) on Friday March 21, 2014 @01:40AM (#46540959) Homepage

    That's the largest genome that's been fully sequenced, not the largest genome known. See Comparison of different genome sizes. [wikipedia.org] Genome sizes for plants vary over a huge range, and aren't closely related to organism complexity. The largest genome known is for an amoeboid.

    • When I look at that list, I start to think that "living fossils" have large repetitive genomes. I looked up an article on the mitochondrial genome of the chambered nautilus, and I got the impression that more than anticipated repetition was found.
      • by H0p313ss (811249)

        When I look at that list, I start to think that "living fossils" have large repetitive genomes. I looked up an article on the mitochondrial genome of the chambered nautilus, and I got the impression that more than anticipated repetition was found.

        Survival trait?

        • or accumulated baggage from a long trip, but I think the extra baggage might possibly become extra tools under certain circumstances
  • by cyberzephyr (705742) on Friday March 21, 2014 @03:00AM (#46541187) Journal

    You have to pay attention to the fact that they were here before we were.

    We would not be able to breathe if they were not here!

    Wake up!

  • The team found that 82% of the genome was made up of duplicated segments,

    -funroll-loops

  • The codebase is huge, many many billion SLOCs.

    But, most of the functions never get called, and the rest is code comments ...

  • Genome annotation (finding all the interest features in the sequence) is really computationally intensive, due in large part to the number of separate (often sub-optimally written) algorithms that have to be chained together and interpreted. My team at the iPlant Collaborative [iplantcollaborative.org] worked with the authors of a popular open-source annotation tool called "MAKER" to get it running at scale on the 302 TFLOP Lonestar 4 [utexas.edu] supercomputer, which in turn was used by the pine team to do in a few hours what used to be 6 month

  • by Vincie (918910)
    Your mom has the largest genome ever sequenced!

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