Monday, February 09, 2009

Evolution of Pine Genomes

 
There are about 120 species of pine trees (genus Pinus). Their genome sizes range from 18,000 Mbp to 40,000 Mbp, which is about 6x - 13x the size of mammalian genomes.

In some species the increase in genome size among closely related species is due to polyploidization but that's not the case with pine species. All of them have 24 chromosomes and the differences in DNA content are due to increases in the lenghts of the chromosomes.

It's possible that different species of pine could have larger or smaller gene families. This would mean that the species with larger genomes have many more copies of some genes than species with smaller genomes. However, this is unlikely to account for much of the difference since simultaneous duplication events in all parts of the genome.

The most logical explanation is an increase in the amount of junk DNA, specifically the number of retrotransposons. Flowering plants have retrotrapsposons with long terminal repeats (LTRs) just like those found in animal genomes [Junk in your Genome: LINEs].

Morse et al. (2009) have studied the retrotransposons in Pinus taeda and related species. The discovered a new retrotransposon family called Gymny that appears to be confined to Pinus taeda and very closely related members of the same subgenus. Each Gymny element is 6.2 kb in length and the genome contains about 22,000 copies. The total amount of Gymny DNA is equivalent to the size of the Arabidopsis genome (157 Mbp).

In addition to the full length copies there are many fragments of Gymny retrotransposons and probably many degenerated copies that can no longer be readily detected. The copies are spread out over all chromosomes as shown in the photograph. (Gymny sequences are stained red.)

In addition to Gymny, the authors also found other abundant retrotransposons in the Pinus taeda genome (e.g. Gyspy and Copia) but the Gymny elements appear to be confined to a subset of species in the Pinus genus. They are not found in other flowering plants.

The evolutionary history of these Pinus species suggests that there was a huge expansion of Gymny elements about 50 Myr ago and the expansion of retrotransposons accounts for much of the increase in genome size among these species.

There are now several examples of genome size increase due to expansion in the number of retrotransposons. The authors discuss several of these previously known cases.

It is difficult to imagine how a huge increase in the amount of retrotransposon DNA could be a selective advantage in some species. The most reasonable explanation is that these sequences play no significant role in the life of the organism. It's just junk DNA that's not harmful.


[Photo Credit: Pinus taeda, loblolly pine]

Morse, A.M., Peterson, D.G., Islam-Faridi ,M.N., Smith, K.E., Magbanua, Z., et al. (2009) Evolution of Genome Size and Complexity in Pinus. PLoS ONE 4(2): e4332. [doi:10.1371/journal.pone.0004332]

6 comments :

  1. "It's just junk DNA that's not harmful."

    Or insufficiently harmful to overcome intragenomic selection or mutation pressures.

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  2. "Or insufficiently harmful to overcome intragenomic selection or mutation pressures."

    Or very harmful on the level of random insertion disrupting coding sequences, but this is compensated for by (unspecified) selectable usefulness.

    I think it's going to be difficult to convincingly argue that random insertion of 22000 6.2 kb pieces of non-functional DNA is going to be non-disruptive, particularly if the accretion was rapid, as appears to be the case here.

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  3. So now we know that it takes 6-13X as much DNA to make a pine tree than it does to make a genome researcher. Well, duh.

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  4. "Or insufficiently harmful to overcome intragenomic selection or mutation pressures."

    Or very harmful on the level of random insertion disrupting coding sequences, but this is compensated for by (unspecified) selectable usefulness.

    I think it's going to be difficult to convincingly argue that random insertion of 22000 6.2 kb pieces of non-functional DNA is going to be non-disruptive, particularly if the accretion was rapid, as appears to be the case here.


    Actually, it is easy to argue this, because any insertion that was really disruptive, e.g. in the middle of an important exon, would have been selected out very early, at the stage of a pollen grain, seed, or seedling, and it's removal from the population would have been a trivial and unnoticed affair with no impact on the population of millions of trees (except that the insertions that survived were not highly detrimental).

    So the observed non-functional DNA distribution is not really the same thing that you would get if you randomly tossed 22,000 insertions into a single modern living individual, and we can't make inferences as if it were.

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  5. It will be very interesting to see some of these genomes sequenced. But at 40Gb, it's no wonder it's not likely to happen soon

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  6. Actually, it is easy to argue this, because any insertion that was really disruptive, e.g. in the middle of an important exon, would have been selected out very early, at the stage of a pollen grain, seed, or seedling, and it's removal from the population would have been a trivial and unnoticed affair with no impact on the population of millions of trees (except that the insertions that survived were not highly detrimental).

    Who says there were million of trees?
    I think it is plausible that the population fitness was severely reduced during the expansion of the retrotransposons, and that the species barely survived. Would it be possible to find out, I wonder?

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