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For example, the current largest known genome belongs to a tree: http://motherboard.vice.com/read/the-largest-genome-ever-sequenced-belongs-to-a-tree

I have heard that this could potentially be because trees require many duplicates of certain genes because they live their entire life exposed to direct sunlight.

Does anyone know of some specific scientific hypotheses for why this might be the case?

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  • $\begingroup$ Old question, and obviously nobody else knows about the hypothesis quoted, but I changed longest to largest as its a question of polyploidy not length. $\endgroup$
    – David
    Commented Nov 17, 2018 at 17:09

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This study of the recently sequenced pine species states that 82% of genome is repetitive. This is characteristic of any complex genome, including humans. Such sequences have often been considered "junk DNA", though any scientist will tell you that just because we don't know its purpose doesn't mean it doesn't have one. That said, a good portion of repeats are due to transposable elements, effectively intracellular parasites, whose only purpose is presumably self-amplification and are more often than not deleterious. These interspersed repeats make up ~45% of the human genome. That paper mentions that, based on sequence homology, ~65% of the pine's genome is made of these repeats (that's 15 billion base pairs).

It's interesting that, even though the pine's genome is ~7 times larger than a human's, it has only twice as many predicted genes. The pine tree has ~50 000 hypothetical genes but only ~16 000 are what the authors call high confidence. When the human genome was first sequenced, there were ~35 000 hypothetical genes but now, some 10 odd years later, there are only ~21 000 predicted genes. It seems too early to compare the two. This also brings up the important point that the number of genes is not necessarily related to organismal complexity: the worm C. elegans has ~20 000 genes.

From the paper:

The large genome size has primarily been attributed to an extensive contribution of interspersed repetitive content (Morse et al. 2009; Kovach et al. 2010; Wegrzyn et al. 2013). Assembly of the Norway spruce genome has shown that LTR retrotransposons in particular are frequently nested within the long introns of some gene families (Nystedt et al. 2013). In addition, there is evidence for gene duplication, pseudogenes, and paralogs, although the extent of these is not clear (Kovach et al. 2010; Pavy et al. 2012).

I have never heard of the hypothesis you mention (not that that means anything), but it seems to me that it's far to early to tell.

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    $\begingroup$ There is another interesting thing to be noted — Plants (and yeasts too) tolerate polyploidy. I don't know the reason for it. There is one interesting fact that plants and yeasts don't have nuclear lamins; but I don't know how that connects to polyploidy. This article relates loss of lamins to polyploidy. I speculate (more of a wild guess) that these structural constraints could also limit the genome size. $\endgroup$
    – WYSIWYG
    Commented Nov 4, 2014 at 13:00
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    $\begingroup$ +1. Another interesting point is that there is some evidence that the retrotranspositions of repetitive sequences such as Alu (which represents 10% of the human genome) are activated under conditions of cellular stress and can help shuffle the genome, providing new variety. $\endgroup$
    – terdon
    Commented Nov 4, 2014 at 14:47
  • $\begingroup$ @WYSIWYG Yes that is interesting. Feel free to edit the answer if you see fit (I might add it too given the time). $\endgroup$
    – canadianer
    Commented Nov 4, 2014 at 17:12
  • $\begingroup$ @terdon That's also very interesting. There was a 2003 study of 3 Bordatella species that found that B. perrtussis (the cause of whooping cough) evolved from B. bronchispetica due to massive genome shuffling mediated by transposable elements. $\endgroup$
    – canadianer
    Commented Nov 4, 2014 at 17:17
  • $\begingroup$ @WYSIWYG Correct me if I'm wrong, but I think I read somewhere that plants can tolerate polyploidy due to the lack of sex chromosomes. Regarding genome size, biochemist Nick Lane considers that eukaryotes can "afford" very large and "truly wasteful" genomes because nucleotides are cheap to produce due to all the power provided by mitochondria. In essence, eukaryotes can tolerate large amounts of "truly junk" DNA. Junk DNA for bacteria would be highly detrimental on the other hand, as it is more expensive for them to synthesize nucleotides (many of them don't even have aerobic respiration). $\endgroup$
    – user38945
    Commented Nov 17, 2018 at 10:26

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