Pine Tree Has Largest Genome Ever Sequenced 71
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."
A Cure At Last (Score:1)
Yes, I know. But it *did* have to be said.
Re: (Score:3, Funny)
If they succeed, it will bring a whole new meaning to "morning wood".
Re: (Score:2)
Re:A Cure At Last (Score:5, Informative)
Re:A Cure At Last (Score:5, Funny)
Trees are just skin and bones! (And plumbing. And really crazy hair. And roots. And sometimes genitals.)
You forgot the homunculi... tree reproduction is via proxy. Every spring I'm overwhelmed by billions of tree cumbots irritating my respiratory epithelium.
Let them take their filthy sperm tube forming function elsewhere.
You Mean A "Woody"? (Score:2)
Well, Boss, we have good news and bad news:
- the good news: we've got it up!
-the bad news: it's tossing off splinters!
Break to chorus of "Hurts So Good!" by John Mellencamp.
Re: (Score:2)
Aye, go with the phloem, I always say.
I'm Inferior To A Tree (Score:5, Funny)
Re:I'm Inferior To A Tree (Score:5, Interesting)
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.
Re: (Score:2)
Re: (Score:1)
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.
Re: (Score:2)
Humans need all kinds of things.
Humans need love.
Re: (Score:1)
Humans need love.
Might just as well had been unobtanium.
Re: (Score:2)
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?
Re:I'm Inferior To A Tree (Score:4, Funny)
Re: (Score:2)
If you don't like my trusty IBM Selectric, beautiful mountain passes, and delicious cheeses, then get off my damn lawn!
Re:I'm Inferior To A Tree (Score:5, Funny)
Re: (Score:2)
Re: (Score:2)
Re: (Score:1)
Re: (Score:2)
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.
Re: (Score:2)
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.
Re: (Score:2)
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.
Re: (Score:1)
Yep, we are inferior to trees. :(
22.18 billion base pairs makes for great wood burning!
We humans, not so much
Re: (Score:2)
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)
I'm not surprised. trees and plants were here before we were.
Re: (Score:2)
Have you grown one yet? I have done it for 20+ years.
Re: (Score:1)
Re: (Score:2)
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.
Re: (Score:2)
Bacteria were there even longer - but they often have very small genomes.
Re:As a Bonsai artist (Score:5, Informative)
Re: (Score:2)
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
Re: (Score:2)
Yeast and bacteria are single celled organisms. For them, reproducing means undergoing cell division (mitosis), and the single longest step of the preparation for mitosis is synthesizing a new copy of the DNA. I don't know the specifics of how bigger genomes make plants reproduce more quickly, but I can at least say that for large, multicellular organisms like plants and animals the rate limiting step in reproduction is not cell division. In animals, for example, a lot of the "waiting time" for gestation in
Pine trees know how to make backups (Score:5, Funny)
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.
Re: (Score:2)
Unfortunately for you, you are just a site, not the operation, so your continuity is a distinctly secondary objective.
Re: (Score:2)
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.
Re: (Score:2)
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.
Re: (Score:2)
Humans always forget the importance of backups, until it's too late.
Well, whaddaya expect? It's in our genes!
Schweet. (Score:1)
Re:I call BS (Score:4, Informative)
Re: (Score:2)
Well they do have a draft genome, not a "complete" one. A complete genome is really hard to generate, and doesn't really gain you a whole lot for all your effort for more complex organisms. Also, its not fair to compare cancer research, as they already have one of the best genomes sequenced to refer too, the human genome. Creating a new genome, de novo, is hard, and 63x is a good start, but not nearly enough.
Also, why did they just use Illumina? Yes it's nice they had multiple paired end ranges, but Illumin
Re: (Score:3)
Re: (Score:2)
One, that map is incomplete. Second, there are plenty of facilities, even if not as numerous, that can do other sequencing. As long as the assembly techniques support combining multiple sequencing technologies together, you should in order to call upon each's strength.
For example, look at the All Paths assembler that recommends adding in a touch of PacBio to connect scaffolds together.
Re: (Score:2)
(Sure, but PacBio in particular is quite new on the market still. Three years ago they were borderline vaporware!)
And, yeah, most serious sequencing projects I've seen do use a mixture of methods, particularly 454 stuff. But I'm sure they'll switch to IonTorrent and PacBio as opportunities allow.
Not biggest known, and it doesn't mean much (Score:5, Informative)
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.
Re: (Score:2)
Re: (Score:2)
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?
Re: (Score:2)
The Beauty of trees (Score:3)
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!
Pine ricer (Score:1)
The team found that 82% of the genome was made up of duplicated segments,
-funroll-loops
Code analogy (Score:2)
The codebase is huge, many many billion SLOCs.
But, most of the functions never get called, and the rest is code comments ...
Even cooler - the annotation was done on a *real* (Score:1)
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
9th (Score:1)