Largest known genome is within this plain plant on the forest floor, study says

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You wouldn’t know it by looking at them, but some plants have a lot more DNA than others. And perhaps even more baffling, some have a lot more than most animals — including humans. Now, scientists are revealing ever more extreme examples of this giant-genome phenomenon even as 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 Ocean. The rare plant contains 160 billion base pairs, the coupled units that make up strands of DNA, according to the study. By comparison, the human genome consists of a mere 3 billion.

“Little humble things can hide one of the most amazing secrets inside,” said evolutionary biologist Jaume Pellicer, a researcher at Spain’s Botanical Institute of Barcelona and corresponding author of the study published May 31 in the journal Cell.

Massive genomes are also rare. According to Pellicer, of 12,000 or so documented plant genomes, all but a half dozen are at least an order of magnitude smaller than that of the fork fern, named Tmesipteris oblanceolata, that’s described in the paper.

“The limits of biology are out there to be uncovered,” Pellicer said. He should know — he keeps uncovering 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 P. japonica finding in a September 2010 study. He also coauthored a paper in May 2017 hypothesizing why 150 Gbp could be the upper limit for genome sizes. Now, he has proved himself wrong.

“The main interest of this project is not to find a record for genome size in plants, to be honest,” Pellicer said. “We want to investigate different cases of genomic gigantism.”

Ferns are known to have massively repetitive genomes. After analyzing related samples from New Zealand and Tasmania, Pellicer homed in on the New Caledonian fork fern as a potentially interesting target for study.

In May 2023, he and his team collected samples of the diminutive plant in the wild and brought them back to the lab, where they compared the fern’s genome with species of known genome size.

The amount of DNA in the fork fern’s gigantic genome may be more than 50 times greater than that of a human’s, but that doesn’t make the fern more complex or mean that it has more genes. Only about 1% of its genome are genes that encode for proteins, Pellicer estimated. The rest are nonfunctional repetitive sequences long deemed “junk DNA,” though scientists now know that it’s not actually junk. A lot of that genetic gibberish can affect how genes function.

Exactly how the fern has racked up so many base pairs is still an unsolved puzzle. What could be at play, according to Pellicer, is some combination of rampant polyploidy — or having more than two sets of chromosomes, which is common in plants, though not in animals — and the accumulation of noncoding DNA sequences that are able to replicate themselves and move around the genome.

“The more interesting question that the study isn’t inherently able to get at is why (the genome) gets that big, and how ferns, specifically, are able to deal with the consequences of having such an unnecessarily large genome,” said fern expert Eric Schuettpelz, a research botanist and curator in the Smithsonian Institution’s department of botany. He did not collaborate on this research. “Ferns seem to be really bad at getting rid of the repetitive DNA and extra chromosomes.”

Supersize genomes aren’t advantageous, as it turns out. Genome gigantism, or genome obesity, is extremely inefficient, the experts explain. It takes a lot of energy and nutrients to make so much DNA. Most plants have much smaller genomes, which allows them to reproduce faster, produce more offspring and adapt more quickly to the environment. Having to copy such a large amount of genetic material every time a cell divides, “it’s just insane,” Schuettpelz said.

It’s mystifying how plants with such unwieldy genomes can keep surviving, said 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 genome size may influence a plant’s chances of extinction. The team is currently focused on research that suggests plant species with large genomes are overrepresented on the International Union for Conservation of Nature Red List of threatened flora and analyzing whether genome size could help conservationists identify plants potentially under threat.

Could there be a plant with an even bigger genome than the fork fern? Perhaps.

“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.

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