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You wouldn’t know it to look at it, but some plants have much more DNA than others. And perhaps even more mind-boggling, some have far more than most animals – including humans. Now scientists are unveiling increasingly extreme examples of this giant genome phenomenon, even though their existence remains a mystery.
New research has identified the largest known genome of any living organism in an unassuming fern found in New Caledonia, an island chain in the South Pacific. According to the research, the rare plant contains 160 billion base pairs, the linked units that make up DNA strands. By comparison, the human genome consists of only 3 billion.
“Small humble things can hide some of the most amazing secrets,” says evolutionary biologist Jaume Pellicer, a researcher at the Spanish Botanical Institute of Barcelona and corresponding author of the study published May 31 in the journal Cell.
Huge genomes are also rare. According to Pellicer, of the approximately twelve thousand documented plant genomes, all but half a dozen are at least an order of magnitude smaller than that of the fork fern, called Tmesipteris oblanceolata, described in the paper.
“The limits of biology must be discovered,” says Pellicer. He should know, he keeps discovering them.
Before this study, the largest known genome of any fungus, plant or animal belonged to the Paris japonica flower, holder of 149 billion base pairs (gigabase pairs or Gbp).
Pellicer was part of the team that revealed the discovery of P. japonica in a September 2010 study. He also co-authored a paper in May 2017 that hypothesized why 150 Gbp could be the upper limit for genome sizes. Now he has been proven wrong.
“The main goal of this project is not to find a record for plant genome size, to be honest,” Pellicer said. “We want to investigate several cases of genomic gigantism.”
Ferns are known to have extremely repetitive genomes. After analyzing related samples from New Zealand and Tasmania, Pellicer focused on the New Caledonian fork fern as a potentially interesting target for research.
In May 2023, he and his team collected samples of the small plant in the wild and brought them back to the laboratory, where they compared the fern’s genome to species of known genome size.
The amount of DNA in the fork fern’s giant genome may be more than 50 times greater than that of a human, but that doesn’t make the fern more complex or mean it has more genes. Only about 1% of the genome consists of genes that code for proteins, Pellicer estimates. The rest consists of non-functional, repetitive sequences long considered “junk DNA,” although scientists now know it’s not actually junk DNA. A lot of that genetic gibberish can affect the way genes function.
How exactly the fern accumulated so many base pairs is still an unsolved puzzle. What could be at play, according to Pellicer, is a combination of rampant polyploidy – or having more than two sets of chromosomes, which is common in plants but not animals – and the accumulation of non-coding DNA sequences that can replicate themselves . and move through the genome.
“The more interesting question that the study is inherently unable to answer is why (the genome) grows so large, and how ferns in particular can deal with the consequences of having such an unnecessarily large genome,” says fern expert Eric Schuettpelz, research botanist and curator in the Department of Botany at the Smithsonian Institution. He did not cooperate in this investigation. “Ferns seem to be very bad at getting rid of repetitive DNA and extra chromosomes.”
It turns out that super-large genomes are not advantageous. Genome gigantism, or genome obesity, is extremely inefficient, the experts explain. It takes a lot of energy and nutrients to make that much DNA. Most plants have a much smaller genome, which allows them to reproduce faster, produce more offspring and adapt to the environment more quickly. Having to copy such a large amount of genetic material every time a cell divides “is just insane,” Schuettpelz said.
How plants with such unwieldy genomes can continue to survive is a mystery, says David Baum, a professor of botany at the University of Wisconsin-Madison, who was not involved in the study.
Pellicer and his colleagues believe that the size of the genome can influence a plant’s likelihood of extinction. The team is currently focusing on research that suggests plant species with large genomes are overrepresented on the International Union for Conservation of Nature’s Red List of Threatened Flora, and analyzing whether genome size could help conservationists identify plants that may be threatened.
Could there exist a plant with an even larger genome than the fork fern? Maybe.
“I’m not going to play with biological boundaries anymore,” Pellicer said. “They are meant to be broken.”
Amanda Schupak is a science and health journalist in New York City.