Cracking the Case of the Giant Fern Genome

Humans, like many complex organisms, have large genomes, which contain the codes for our lives. Want to explain your dark hair, thin bones and existential dread? Look to your 46 chromosomes and three billion nucleotide base pairs.

But those numbers are nothing compared to the genome of another organism, which contains twice as many base pairs and three times as many chromosomes. Is it an octopus? An elephant? An orca? No, it’s the flying spider monkey tree fern.

The flying spider monkey tree fern, a hardy plant found in Southeast Asia, has flat leaves that fan out in a circle at the top of its trunk, and it is just one of many spore-releasing plants with a huge genome. What accounts for, or requires, so much DNA is what Fay-Wei Li, a botanist at the Boyce Thompson Institute, calls “the biggest question in fern genomics.”

In May, Dr. Li led a team that sequenced the full genome of the flying spider monkey tree fern, to try to get an answer. It was only the third time a fern’s DNA had been completely mapped, and the first time that a fern with a genome so large was sequenced. Last week two more papers were published, in Nature Plants, revealing that the maidenhair fern and the “C-Fern” — Ceratopteris richardii, a fern often used as a model organism in the lab — had genomes comparable in their vastness to the flying spider monkey tree fern.

This burst of research, years in the making, challenges a half-century-old hypothesis about fern genes. And although it doesn’t close the case of the fern genome, it might “inform us a lot about genome evolution as a whole,” said Blaine Marchant, a botanist at Stanford University who led the sequencing of the C-Fern.

“It’s been decades that we’ve been begging, ‘Hey, ferns, we need to make this happen!’” said Eric Schuettpelz, a botanist at the Smithsonian Institution who was not involved in the recent research. “These are really exciting times.”

Why some organisms have larger genomes or more chromosomes than others is not entirely clear; plants and animals with lots of genes aren’t necessarily physically or behaviorally more complex. The current record-holder for most base pairs — 149 billion — is a flowering plant with the scientific name Paris japonica; the record-holder for most chromosomes — 1,440 — is the adder’s-tongue fern. Both plants are small and, as organisms go, simple.

One widely held explanation for large genomes is called polyploidy, or whole genome duplication. Typically during reproduction, two gametes — cells with half the number of original chromosomes — come together to create a zygote, with a full suite of genes. But when these gametes first form, it may be that pairs of chromosomes do not fully separate, leading to a zygote with a genome that is twice as large as its parents’. This appears to have happened early in the evolution of flowering plants, but most of the duplicated genes have been stripped out after tens of millions of years of natural selection.

Ferns are closely related to flowering plants, but they have roughly 20 percent more base pairs in their genome. For years, scientists wondered why this was so. Then in 1966, a paper was published in Science claiming that ferns, many of which reproduce asexually, gained an evolutionary advantage from genome duplication. Essentially, the authors argued, the extra genes provided backup chromosomes that helped prevent hereditary diseases.

It was a “really influential and highly creative paper,” said Pamela Soltis, a botanist at the Florida Museum of Natural History who helped sequence the C-Fern. But did fern genomes actually contain signs of mass duplication, or were they simply big? To confirm the theory required sequencing some of these large genomes.

Finally, this year, it happened — and the sequences showed no evidence of polyploidy. “None of that came through,” Dr. Soltis said. “In fact, there’s only the evidence for potentially two duplications in this whole lineage, that go back hundreds of millions of years.”

The C-Fern appears to have gained its large genome primarily from repetitive DNA and transposable elements — “jumping genes” that often move around in chromosomes, with a function that is poorly understood. For Dr. Soltis, the sequencing offered closure for the longstanding hypothesis of fern polyploidy. “We think this is the nail in the coffin for that,” she said.

But Dr. Li was not so convinced. The DNA of the flying spider monkey tree fern contained evidence of a whole genome duplication around 100 million years ago, and the genome has remained remarkably stable since then. It’s a solitary case, but it seems to bolster the idea that polyploidy provided the plant with an evolutionary leg up. “One genome kind of supports this hypothesis, the other one doesn’t,” he said.

Dr. Schuettpelz said: “We don’t have a firm grasp on what these things are doing, but I’ve just been amazed. As we accumulate more and more genomes, and genomes that are more representative of ferns as a whole, things are going to get really exciting really fast.”

Here was something that all of the fern scientists agreed on. “The publication of more and more fern genome assemblies to compare will make inferences much more informative,” Dr. Marchant said.

Dr. Soltis said: “If we want to understand aspects of flowering plants, for instance, we need to be able to compare them in their historical, evolutionary context. And there was really no reference until these two big fern genomes were published.”

Dr. Soltis has been involved in a recent effort to sequence the genome of every known form of life on Earth. The project is ambitious, she acknowledged, but so is science. “To understand how anything works in any organism, including ourselves, you need to look at where it came from and what its context was prior to taking on whatever function it has now,” she said.

Dr. Li added: “So, what do we need? We need more genomes.”