To say that the eukaryotes have large genomes, one should be comparing them to organisms with much smaller genomes, the prokaryotes. It is the analysis between these organisms that will give conclusive evidence as to why the eukaryotes have large genomes.
Immediately one jumps to the idea that the eukaryotes are more complex and therefore they should have a much bigger genome, where would inevitably produce more genes. That is needless to say true, however the complexity of the genome doesn’t directly match an increase in genome size. Wheat includes a far larger genome than ours however, you might hesitate to call them more complex. Геном Therefore, there has to be more subtle underlying reasons why the eukaryotes have such large genomes.
Transposable elements enhance the size of genomes by copying and inserting into different parts of the genome. However, transposable elements also occur in the prokaryotes and the affect of the transposons on eukaryotes in increasing how big the genome might be negligible. One reason why the affect of transposons isn’t always detrimental to the organism is due to the introns within a eukaryote. The gene rich DNA of the prokaryotes is in sharp contrast to genes scattered around eukaryotic genomes. The introns in the eukaryotic genome cause them to become much, much larger than in the prokaryotes. The gene number difference in eukaryotes is about 10 fold whereas the base pair number could be 1000 fold bigger. The question therefore lies within the introns of the eukaryotes. Why is there so many introns in the eukaryotic genome; giving rise to its ‘large size’?
As the eukaryotes evolved from the prokaryotes one must elucidate the goal of the introns in the eukaryotes as, say a stream (against transposons, mutation etc). However, this could also be construed to have the same equally beneficial properties in prokaryotes. A better approach is to analyse the energy output. Prokaryotes use 25% of these energy production in DNA copying and maintenance (the other 75% being that of protein production). Therefore, any upsurge in size of the DNA in prokaryotes will be too costly for the organisms to keep up and replicate and thus the DNA is stripped down seriously to an extremely gene rich molecule. Eukaryotes are profligate in pouring energy into their genomes (due for their greater energy production capacity as a primary consequence of getting specific organelles devoted to this purpose) and consequently they are able to be so disgracefully inefficient and allow accumulation of introns.
Another and probably the most crucial consequence of being able to pour large levels of energy to the genome is that eukaryotes can allow gene duplication events, which produce proteins that differ very slightly. Not merely this, but in plants especially, entire duplication of genomes and addition of different divergent genomes are commonplace within that kingdom. Giving these organisms such huge genomes.