Giant plant genomes are driven by the accumulation of repetitive DNA and its conversion into a „dark matter“
Nuclear genome size, corresponding to the total length of DNA molecules in cell nuclei, varies more than 2,000-fold between different plant species. The genome size is not proportional to the number of genes, complexity, or size of the plant species. For example, the genome of the oak tree is surprisingly 65-fold smaller than the genome of some herbs like Paris quadrifolia (Figure). This herb carries 58.8 billion DNA base pairs in its nuclei, making its giant genome 20-fold larger than that of humans.
It is supposed that a large part of the genome size variation is caused by a differential accumulation of repetitive DNA, which is composed of mobile elements and other sequences that have the ability to translocate and multiply their copies in the genome. On the other hand, these elements are also continually removed from the genome at various rates, and it is believed that it is the ratio of accumulation to removal frequencies acting over long periods of species’ evolution that determines its genome size.
The study recently published in Nature Plants, led by the teams from Biology Centre CAS, Queen Mary University London, and Royal Botanic Gardens Kew, has confirmed this hypothesis and elucidated the emergence of giant plant genomes. Based on their findings, such genome size expansion is caused by less efficient removal of repetitive elements that subsequently persist in the genome for a long time and gradually diversify by acquiring random mutations. The resultant “dark matter”, composed of degraded repetitive sequences that are no longer recognizable to molecular mechanisms facilitating their removal, further contributes to the genome size growth. It is notable that genome size expansion affects plant phenotype by prolonging DNA replication and thus increasing cell cycle time, which generally results in slower growth and long generation time. Thus, it might not be surprising that species with giant genomes are frequently found among critically endangered plants, perhaps due to their slow growth and limited adaptability to changing environment.