The largest known genome belongs to a tiny fern

Big things can sometimes come in small packages. 

A small fern has broken the record for the largest genome yet known, researchers report May 31 in iScience. The plant’s full set of genetic instructions is over 50 times the size of the human genome. And it’s about 7 percent larger than the genome of the previous record holder, a Japanese flower dubbed Paris japonica.

Most plants have relatively small genomes, says Jaume Pellicer, an evolutionary biologist at the Botanical Institute of Barcelona. But some groups of plants are exceptions, possessing immense genomes that are some of the largest yet discovered across the tree of life. Pellicer and his colleagues were interested in studying these giant genomes to better understand how they evolve and function in the organisms that wield them.

Previous work suggested that some fork ferns (Tmesipteris) had particularly big genomes. So, the team embarked on a detailed survey of the six fork fern species found in the South Pacific islands of New Caledonia. The researchers took cells from the ferns’ leaves and isolated their nuclei, which contain the genome. By staining the nuclei’s DNA with a fluorescent dye and comparing how much these nuclei fluoresced relative to those from multiple plants with smaller genomes, the researchers calculated the size of each fork fern’s genome. 

One species — T. oblanceolata — has the largest genome of any organism yet measured. The fern mainly grows on larger forest plants and is up to only 15 centimeters long. But its genome has a length of 160 billion nucleobases, the paired chemical rungs bridging the two sides of the DNA double helix.

Pellicer and colleagues had also identified the previous record holder — at about 150 billion nucleobases — in 2010. Because it’s taken so long for the team to break their own record, Pellicer wonders if T. oblanceolata is at or near the biological limit of genome size. Maintaining such a cumbersome spool of genetic material can get complicated at such extreme sizes and it’s not yet clear how these genomes function, he says.

“You have to replicate over 100 meters of DNA every time a cell divides,” Pellicer says, which requires the organism to expend a great deal of energy. “To me, it’s very puzzling.”

Plant genomes vary greatly in size, with the largest genomes being 2,500 times as big as the smallest (SN: 2/10/21). One way plants can dramatically bloat their genomes is by inheriting extra copies of entire chromosomes. Another process, Pellicer says, is accumulating long sections of repetitive DNA sequences. Analyzing and sequencing T. oblanceolata’s vast genome in detail could reveal more about how it grew so large.

Plant evolutionary scientist Liming Cai wonders if some plants with giant genomes, like this fork fern, might have a history of repeated genetic bottlenecks, where the species went through multiple rounds of population shrinking and loss of genetic diversity.

“During a process like this, a lot of the deleterious mutations would accumulate. And that would include a lot of the junk DNA that may play a role in creating such [large] genomes,” says Cai, of the University of Texas at Austin.

Cai is also curious how the abundance of gene copies in the fork fern’s huge genome compares to those in the far smaller genomes of some aquatic ferns. Such research might help reveal how and why extremes in genome size evolve.

Pellicer says the findings highlight the importance of cataloging biodiversity using genome data and targeting those studies on less obvious species. The fork fern may not be an iconic, showy plant with beautiful flowers, but its cells harbor a biological marvel.

“It would never get the attention of anyone walking by,” he says. “It’s a small plant, you wouldn’t even bother to look at it. But the beauty of this plant is inside.”