The bigger the genome, the less efficient?

Researchers at Kew Gardens’ Jodrell Laboratory*  have identified the largest genome so far discovered. It belongs to the Paris japonica, a slow-growing herb native to the mountains of  the Japanese island of Honshu and  to the chagrin of many a frustrated gardener trying to cultivate in gardens , a very difficult plant to grow.  The difficulty in reproduction is probably related to the size of the genome,  for the larger the genome , the greater the difficulty in reproducing because every time a cell divides it has to reproduce the DNA. The more DNA, the longer that process takes and the more resources it requires. 

Homo sapiens has a measly three billion base pairs in its genome. (Two nucleotides on opposite complementary DNA or RNA strands that are connected via hydrogen bonds are called a base pair.  Adenine (A) forms a base pair with thymine (T) and guanine (G) with cytosine (C). In RNA, thymine is replaced by uracil (U)). Paris japonica has  150 billion base pairs.  Paris japonica replaces the previous record holder for the largest genome ,  the marbled catfish (Protopterus aethiopicus), which had 130 billion base pairs. At the other end of the genome size scale there is a bacterium called Carsonella ruddii, which has fewer than 160,000 base pairs.

This  immense disparity in genome size raises an interesting question. Why should genomes in general vary so widely and why does homo sapiens, indubitably the organism which has the most varied behaviour by far of any animal (arguably the best benchmark to judge the sophistication and capacities of an organism)(  should have a genome so much smaller than a plant or a fish? Efficiency is a plausible reason.

Efficiency improves with fewer components. Take the analogy of  written languages. Ideographic languages such as Chinese have  thousands of characters to do the same job that the alphabet does with 26 letters. If you set a dullard and a genius the task of devising a form of writing the dullard would produce Chinese characters and the genius the alphabet.  Another analogy. The more exotic versions of the Swiss Army knife have  several dozen implements, most of which are never used. The Swiss Army knife would be a much more efficient item if it had far fewer implements which were designed to be dual purpose, for example, a double edged blade with different types of edge on the two edges or a blade  with a file on its non-cutting surfaces.

Those two analogies  could explain why homo sapiens has such a small genome. Our genome may be comparatively small because it has reduced the number of components in the cause of efficiency.  The question then arises why would natural selection work to make some genomes more efficient than others.  Three likely candidates put themselves forward. The first is the innate capacities of the ancestral organism, the second, the environment in which an organism evolves. The third, the existential imperative to pass on the organism’s genes.

It is noticeable that the largest genomes are attached to organisms which are relatively low on the evolutionary scale.  It could be that they simply do not have the capacity to refine their genomes to become more efficient while  those higher up the evolutionary scale have the capacity in varying degrees. (I would bet that mammals have smaller genomes on average  than reptiles and amphibians).  This would mean that instead of refining their genomes towards efficiency every time a favourable or at least non-harmful mutation occurs this gets added to the genome which gets ever larger.   

As for environment, it is noticeable that the organisms which have the very large genomes tend to be in environments which have probably  been stable.  Paris japonica comes from a very restricted  mountain landscape which was on an island ; catfish wallow around in murky water.  Natural selection would not be directed towards improving genetic efficiency because the organisms were doing very nicely thank you.  Conversely, homo sapiens and his evolutionary forebears had immense selection pressure on them to survive because they were widespread enough to experience a  considerable range of environments both geographical and over time.  It may also be that living on land is a more demanding environment than water.  To that can be added the high intelligence, self-awareness  and language  of  homo sapiens which produces unique  selective choices because the mental environment is rich and varied in a way that it cannot be for any other animal.  Such environmental pressures were  probably the prime or sole  driver  for greater efficiency, although of course the flexibility of the genome could be dependent on mutations which were independent of environment.    If so, then the efficiency of our genomes is simply a lucky chance.  

If the prime directive of existence is to pass on genes, there would be a strong selective pressure to reduce the size of the genome to increase  reproductive capacity.  For such a large animal  (we are in the top 5% of land animals by size) homo sapiens has become a most fantastically successful breeder, no other animal of comparable size comes close to our breeding success.  A very large genome would have greatly  restricted such reproduction both in terms of time taken to reproduce and the increased likelihood of genetic defects (more genes, more potential  defects).  

* The team’s findings are already available online and will be printed in an upcoming issue of the Botanical Journal of the Linnean Society. The paper can be downloaded from

http://onlinelibrary.wiley.com/doi/10.1111/j.1095-8339.2010.01072.x/abstract

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Comments

  • Chris  On December 15, 2010 at 8:21 pm

    It would also depend on the organism’s susceptibility to viruses. Every time a virus infects a cell, there is a small possibility that it will enter what is known as the lysogenic cycle, and insert itself into your DNA for later emergence under preset conditions (Takes HIV or the chickenpox virus for prime examples). However, sometimes this goes horribly wrong, and the virus is unable to excise itself. The virus is now rendered harmless but is stuck in your DNA.

    This is normally not a problem, but if this were to happen in the testes or ovaries, and a gamete were infected, then all the cells in the offspring’s body will contain genomes with the virus in it (often becoming the parts of DNA known as introns, non-coding parts of dna that must be snipped out every single time the DNA is read, surely slowing the actual growth of the organism).
    Over time, these mutate to unrecognisability and simply become what is known as ‘junk’DNA. Or perhaps humans are marginally better at cleaning up our own genomes than the catfish, but worse than the microbe?

    Another possibility is that large tracts of DNA are based around repeated sequences. These have no coding function whatsoever, but serve as marker points for the molecular machinery in the cell. A less efficient ‘navigation’ system would account for more of these.

    So it could be you are right, that genome size is related to efficiency, but its more likely that this is the work of viruses.

    Just thought you might like these thoughts form a biology student 🙂

  • Robert Henderson  On December 16, 2010 at 9:34 am

    That is an avenue worth exploring because the immune systems of mammals are more efficient than those of cold blooded animals. It could be that only with the development of mammalian immune systems could the process of reducing redundant parts of the genome reach its present level, if that is indeed what has happened.

    Without such an efficient immune system, it could pay an orgnism to evolve a larger and larger genome simply to deal with infections by isolating them individually, which would go back to my analogy with Chinese characters and the alphabet.

  • Jaume Pellicer  On December 19, 2010 at 3:38 pm

    The bigger genome, the less efficient? This is a good question, but when we are thinking about genomes, what do we understand by efficiency? Just a genome size reduction? In this case, maybe we should call into caution some comparisons between plants and humans. At first sight, if we compare the size of the human genome with that of Paris japonica it is easy to think that maybe our genome is relatively smaller due to a reduction in the number of components in the cause of efficiency. But this is an exceptional case, as most angiosperms have small genomes – the modal genome size for plants is just 600 Mb of DNA – thus most plants have genomes much smaller than Homo sapiens (N.B. the smallest actually belongs to a carnivorous plant with just 63 Mb DNA compared with 300,000Mb in humans!). Furthermore, if we consider ourselves at the higher end of the evolutionary scale, why is it that up to 40% of our genome is composed of just non-coding, repetitive and possibly redundant DNA? Is this really a sign of efficiency?

    It is true that plants (or organisms in general) with big genomes must make a bigger energetic effort, and need extra time to perpetuate themselves as the amount of DNA they need to replicate in each cell division is much larger than in plants with small genomes, but those such as Paris japonica have developed “efficient” strategies to undergo reproduction and growth just in time during the favorable season and at a time when most species with small genomes do not grow. Species with large genomes tend to grow either in northern temperate woodlands early in the year when it is cold and before the trees grow and shade out the light, or in the Mediterranean during the cool spring before it gets too hot and dry during the summer. They have optimized their life strategy to occupy these niches and in such conditions having a large genome is an advantage. What happens is that they have divided their ‘growth’ into two phases (i) in the preceeding summer they replicate their DNA, this takes a long time because they have so much DNA but they are in no hurry. (ii) In the following spring when it it too cold for species to replicate their DNA (because this process is temperature sensitive) those species with large genomes now start to ‘grow’ by cell expansion’ (this is temperature insensitive). They are actually pumping water to expand their cells, and because the rate of cell expansion is positively correlated with genome size, those species with very big genomes can expand their cells and hence ‘grow’ very rapidly. Thus while someone might think that some geophytes, such as Paris japonica and other lilies, which grow in their gardens, do not seem to take more time than other plants, even when they have big genomes. Actually, this observation must be reconsidered since what we may be watching at is actually a cell expansion arising following the slow replication of DNA in the preceeding season. That is, they have optimized the growth cycle by splitting it into two phases: cell division and cell expansion and it enables them to grow during a time of year when most other species are still dormant.

    Even so, it is true that genome size obesity has been suggested in different published studies to be maladaptative. Given the consequences associated with having a large genome (longer cell divisions, restricted to being perennial, more sensitive to pollution and radiation, etc.), and the fact that we live in a constantly changing environment, these consequences associated with larger genomes does increase the likelihood of these ‘obese’ plants (or organisms) becoming extinct.

    In relation to the immense diversity of genome sizes in organisms, the fact that there is no direct correlation between genome size and organism complexity is what researchers called the ‘C-value paradox’, or more recently, ‘C-value enigma’. It is true that the genome size of humans is small, but we should not forget that although Paris japonica has a very large genome, as I noted above, most flowering plants have small genomes, many of them are similar or smaller than the human genome. The difference is that in plants the range of variation is much larger, about 2400-fold in angiosperms In contrast the range in many other groups is much narrower. In mammals it is only 5-fold, and the same is found in reptiles, while in birds genome size vary even less, with values ranging only about 2.4-fold in birds (all them with small genomes). So, the real question is why are some genomes are so big, so variable, and how are they organized and function? And why have some organisms evolved larger genomes than their relatives when most of the evidence suggests that having big genomes is associated with so many negative consequences? All these questions have currently no answer, and that is what we are trying to do in the Jodrell Laboratory at Kew.

  • Robert Henderson  On December 20, 2010 at 10:29 am

    Many thanks for your contribution, Dr Pellicer. Efficiency must surely involve simplicity because (1) the more complex a dynamic system the more opportunity for something to go wrong – that is why we find Heath-Robinson cartoons funny – and (2) the more complex a system is, the more energy it needs. It is also true that the increase in energy use may grow disproportionately with an increase in complexity as connectivity has to increase not merely between any new component and the old but between old components to support new functions.

    On the question of the “junk” DNA I would say two things: first, as yet we do not know why junk DNA exists or if it has any useful purpose – my own guess is that it is redundant but survives simply because there is insufficient selectional pressure to remove it – and second, don’t expect perfection from natural selection which is eternally a work in progress and invariably leaves rough edges – think of the crude reshaping of a flatfish such as plaice for example or the chronic back pain many humans suffer because of the imperfect anatomical shift from an ape-like to an upright posture.

    A few thoughts on genetic plasticity which may explain why the variation in plants is greater. Fungi and plants are vastly more plastic than animals. That could be the simple explanation for the difference. However, that cannot be the whole story because mammals are much less plastic than cold blooded animals (which may why there are only approximately a miserly 4,500 mammal species.)

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