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Pine Tree Has Largest Genome Ever Sequenced

samzenpus posted about 5 months ago | from the it's-how-you-use-it dept.

Biotech 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."

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A Cure At Last (1)

Leghkster (603558) | about 5 months ago | (#46540771)

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.

Re:A Cure At Last (2, Funny)

ArcadeMan (2766669) | about 5 months ago | (#46540779)

If they succeed, it will bring a whole new meaning to "morning wood".

Re:A Cure At Last (1)

Cryacin (657549) | about 5 months ago | (#46540871)

The worst side effect is splinters though.

Re:A Cure At Last (0)

Anonymous Coward | about 5 months ago | (#46541703)

The worst side effect is splinters though.

If you don't tell anyone I have a wooden dick, I won't tell anyone you've got splinters in your mouth.

Re:A Cure At Last (0)

Anonymous Coward | about 5 months ago | (#46545553)

It's not the splinters in my mouth I'm worried about!

Re:A Cure At Last (-1)

Anonymous Coward | about 5 months ago | (#46540809)

So the humble pine tree has a more complex genome than those useless trash niggers. What a surprise.

Re:A Cure At Last (4, Informative)

Samantha Wright (1324923) | about 5 months ago | (#46540845)

Inadvisable—much of wood itself (not the bark, the structural stuff underneath) is dead at functional maturity. Trees are just skin and bones! (And plumbing. And really crazy hair. And roots. And sometimes genitals.)

Re:A Cure At Last (4, Funny)

stoploss (2842505) | about 5 months ago | (#46541245)

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.

Re:A Cure At Last (0)

Anonymous Coward | about 5 months ago | (#46543177)

The activation of the gene "Destroy all humans via reproductive action" is still pending.

You Mean A "Woody"? (1)

littlewink (996298) | about 5 months ago | (#46541161)

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.

This one was (-1, Flamebait)

invictusvoyd (3546069) | about 5 months ago | (#46540785)

written in java ..

Welcome! (-1)

Anonymous Coward | about 5 months ago | (#46540787)

I for one welcome our sappy overlords!

Re:Welcome! (2)

Nefarious Wheel (628136) | about 5 months ago | (#46540801)

Aye, go with the phloem, I always say.

I'm Inferior To A Tree (4, Funny)

Jim Sadler (3430529) | about 5 months ago | (#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.

Re:I'm Inferior To A Tree (5, Interesting)

Samantha Wright (1324923) | about 5 months ago | (#46540881)

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:I'm Inferior To A Tree (0)

Anonymous Coward | about 5 months ago | (#46541331)

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.

No, the big thing is that plants are more likely than other organisms to acquire additional chromosomes. Not that all plants do - look at brassica.

Re:I'm Inferior To A Tree (1)

Samantha Wright (1324923) | about 5 months ago | (#46545299)

You're right, it's not an entirely ubiquitous phenomenon. But amongst the plants that do have large, repetitive genomes, fine-grained epigenetics and averaged-out mutations tend to be the primary benefits, IIRC.

Re:I'm Inferior To A Tree (1)

erikscott (1360245) | about 5 months ago | (#46543669)

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:I'm Inferior To A Tree (1)

noh8rz10 (2716597) | about 5 months ago | (#46540887)

Humans need all kinds of things.

Humans need love.

Re:I'm Inferior To A Tree (1)

aliquis (678370) | about 5 months ago | (#46541339)

Humans need love.

Might just as well had been unobtanium.

Re:I'm Inferior To A Tree (0)

Anonymous Coward | about 5 months ago | (#46541549)

Humans need all kinds of things.

Humans need love.

I thought that was cookies ?

Re:I'm Inferior To A Tree (0)

Anonymous Coward | about 5 months ago | (#46540893)

There is unrest in the forest
There is trouble with the trees
For the maples want more sunlight
And the oaks ignore their pleas

Re:I'm Inferior To A Tree (1)

pspahn (1175617) | about 5 months ago | (#46540895)

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 (3, Funny)

Samantha Wright (1324923) | about 5 months ago | (#46540903)

Yes. All old things are superior. Like typewriters, glaciers, and expired milk.

Re:I'm Inferior To A Tree (1)

VortexCortex (1117377) | about 5 months ago | (#46541719)

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 (4, Funny)

Cryacin (657549) | about 5 months ago | (#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.

Re:I'm Inferior To A Tree (1)

Samantha Wright (1324923) | about 5 months ago | (#46540921)

...perhaps your hatred towards trees has something to do with these auditory hallucinations?

Re:I'm Inferior To A Tree (0)

Anonymous Coward | about 5 months ago | (#46544505)

...perhaps your hatred towards trees has something to do with these auditory hallucinations?

Hey! What's a little mindless mayhem when it comes to showing the plant kingdom who's boss?

Re:I'm Inferior To A Tree (1)

fuzzyfuzzyfungus (1223518) | about 5 months ago | (#46540931)

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.

Re:I'm Inferior To A Tree (0)

Anonymous Coward | about 5 months ago | (#46540945)

And he looked up, and said, I see men as trees, walking.

- Mark 8:24

Re:I'm Inferior To A Tree (1)

jameshofo (1454841) | about 5 months ago | (#46540951)

Need is a rather subjective term.

Re:I'm Inferior To A Tree (1)

period3 (94751) | about 5 months ago | (#46540965)

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:I'm Inferior To A Tree (1)

TubeSteak (669689) | about 5 months ago | (#46541119)

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:I'm Inferior To A Tree (1)

ChromeAeonium (1026952) | about 5 months ago | (#46541145)

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:I'm Inferior To A Tree (1)

Dan Askme (2895283) | about 5 months ago | (#46542827)

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

Re:I'm Inferior To A Tree (1)

boristdog (133725) | about 5 months ago | (#46542865)

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 (1, Insightful)

cyberzephyr (705742) | about 5 months ago | (#46540833)

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

Re:As a Bonsai artist (0)

Anonymous Coward | about 5 months ago | (#46540875)

What is the relevance of being a bonsai artist?

Re:As a Bonsai artist (1)

cyberzephyr (705742) | about 5 months ago | (#46541109)

Have you grown one yet? I have done it for 20+ years.

Re:As a Bonsai artist (1)

Anonymous Coward | about 5 months ago | (#46542475)

Again, what relevance does this have? My barber has been cutting my hair for 20 years, but I don't think he has much insight into my genome. I could be wrong about him. Our discussions typically don't get around to molecular biology in the 15 minutes I'm on the chair, but maybe he's more like Johnny the Snitch from the Police Squad shows than I realize.

Re:As a Bonsai artist (1)

fuzzyfuzzyfungus (1223518) | about 5 months ago | (#46540923)

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:As a Bonsai artist (1)

period3 (94751) | about 5 months ago | (#46540985)

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

Re:As a Bonsai artist (4, Informative)

Calavar (1587721) | about 5 months ago | (#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.

Re:As a Bonsai artist (1)

Artifakt (700173) | about 5 months ago | (#46542601)

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 ancestry?

Re:As a Bonsai artist (0)

Anonymous Coward | about 5 months ago | (#46542639)

You said having a smaller genome allows for faster replication but another +5 post above states that corn (and other plants) and have a large genome which allows them to replicate and reproduce fast.

Re:As a Bonsai artist (1)

Calavar (1587721) | about 5 months ago | (#46567049)

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 involves the production and secretion of inter-cellular signals that tell cells how to differentiate, where to go, and when to pause or completely stop dividing. And there is also the fact that animals are not fertile right away. Human men have to develop for about 13 - 15 years before they are biologically able to have kids. I'd assume that similar things apply to plants.

Pine trees know how to make backups (4, Funny)

mysidia (191772) | about 5 months ago | (#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.

Re:Pine trees know how to make backups (0)

Anonymous Coward | about 5 months ago | (#46540849)

I wonder if the large backup is why they live so much longer than humans.

Re:Pine trees know how to make backups (1)

fuzzyfuzzyfungus (1223518) | about 5 months ago | (#46540877)

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.

Re: Pine trees know how to make backups (0)

Anonymous Coward | about 5 months ago | (#46541217)

It just means they were coded by IBM back in the pay-per-line days.

Why loop when you can copy-pasta?

Re:Pine trees know how to make backups (1)

Warbothong (905464) | about 5 months ago | (#46541823)

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:Pine trees know how to make backups (1)

mysidia (191772) | about 5 months ago | (#46542637)

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:Pine trees know how to make backups (1)

Somebody Is Using My (985418) | about 5 months ago | (#46542619)

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

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

Even though (0)

Anonymous Coward | about 5 months ago | (#46540863)

there is that level of repetition it seems huge and makes me wonder just how much bacteria and mitochondrial DNA really plays in a human to make sense the discrepancy. Afaik in humans isn't human DNA.

Schweet. (1)

DrPBacon (3044515) | about 5 months ago | (#46540865)

Soon I shall imbue the soles of my feet and grow pine shoes.

I call BS (0)

omtinez (3343547) | about 5 months ago | (#46540905)

As someone who works on cancer research involving human genome, I can tell you that you should read any news/research related to genome sequencing with a pinch of salt. The methods used to sequence genome are notoriously unreliable, and the analysis performed on that genome is even worse. This is what happens when you get money if you publish results that sound "cool", but in reality our understanding and capacity to research stuff at the DNA level is much more limited than most people in the field are willing to admit.

Re:I call BS (3, Informative)

Samantha Wright (1324923) | about 5 months ago | (#46540937)

63x total coverage with from Illumina hardware using a mixture of paired-end libraries, ranging from 200 bp to a whopping 40 Kbp. I'm pretty sure that's sufficient information to estimate the number of large-scale repetitions. Sequencing projects of species for which there is no good relative to scaffold against are typically much more rigorous than what you'd see in cancer research.

Re:I call BS (1)

subanark (937286) | about 5 months ago | (#46542687)

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 Illumina is typically only short reads of around 100bp. Generally, throwing in some PacBio sequences helps with the scaffolding process with their long reads. You don't need much either, less than 1x is fine.

Also, it looks like they did do some transcription work, but I didn't see anything in the paper detailing what areas of the tissue they took samples from. Hopefully this is well documented so that appropriate expression analysis can be done, instead of simply relying on existing database gene information to determine traits.

Re:I call BS (2)

Samantha Wright (1324923) | about 5 months ago | (#46545195)

The hardware platform of choice is a matter of availability. Here [omicsmaps.com] is a map of where most/all of the NGS platforms are in the world; Illumina sequencers are the most common amongst the newer systems.

Re:I call BS (1)

subanark (937286) | about 5 months ago | (#46545917)

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:I call BS (1)

Samantha Wright (1324923) | about 5 months ago | (#46549431)

(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 (5, Informative)

Animats (122034) | about 5 months ago | (#46540959)

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:Not biggest known, and it doesn't mean much (1)

John.Banister (1291556) | about 5 months ago | (#46541285)

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.

Re:Not biggest known, and it doesn't mean much (1)

H0p313ss (811249) | about 5 months ago | (#46543269)

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:Not biggest known, and it doesn't mean much (1)

John.Banister (1291556) | about 5 months ago | (#46549399)

or accumulated baggage from a long trip, but I think the extra baggage might possibly become extra tools under certain circumstances

The Beauty of trees (2)

cyberzephyr (705742) | about 5 months ago | (#46541187)

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!

Re: The Beauty of trees (0)

Anonymous Coward | about 5 months ago | (#46543321)

Most oxygen on earth is produced by algae blooms

Pine ricer (1)

Trilkk (2007802) | about 5 months ago | (#46541663)

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

-funroll-loops

Code analogy (1)

kbahey (102895) | about 5 months ago | (#46554787)

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* (1)

TheHornedOne (50252) | about 4 months ago | (#46556685)

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 months of painstaking bioinformatics. In another month or so, this algorithm will be available via REST API [agaveapi.co] allowing, literally, "Annotation As A Service".

9th (1)

Vincie (918910) | about 5 months ago | (#46580227)

Your mom has the largest genome ever sequenced!
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