Ferns are weird. They are green and leafy like other forest plants, but they reproduce more like mushrooms, releasing clouds of spores. Many species do not require a partner for fertilization, unlike most of their seed-bearing cousins. Recent studies estimate that ferns separate from seed plants about 400 million years ago.
And fern genomes are incredibly large. Despite the unique physiology of ferns and their relationship to seed plants, these strange genomes have been largely overlooked by researchers. Until recently, only two (relatively small) fern genomes were fully sequenced, compared to more than 200 flowering plant genomes. Now, the first complete tree fern genome has been successfully sequenced – that of the flying tree fern – indicating how these particular plants have accumulated such a massive set of genes.
“If you want to understand the origin of seeds or flowers, ferns are a very important comparison to make,” says Fay-Wei Li, fern biologist at Cornell University’s Boyce Thompson Institute and co-author of the new study, published in Natural plants. “But what I really want to know is why fern genomes are so big.”
Li’s team found that the palm-shaped fern has more than six billion base pairs of DNA, a billion more than the average flowering plant genome (humans, by comparison, have about three billion pairs). The new analysis suggests that more than 100 million years ago, an ancestor of this fern duplicated its entire genome, a common replication error in plants, Li says.
But it’s unclear why tree ferns would retain so much genetic material; most flowering plants revert to thinner genomes after duplications. This species could be accumulating chromosomes, says Li: “I call it the Marie Kondo hypothesis. Chromosomes bring joy to ferns, but they don’t bring joy to seed plants. For plants that reproduce asexually, he says, a large genome can add opportunities for beneficial mutations to occur while buffering undesirables. Ferns are also long-lived, so they evolve more slowly, which may have contributed to conserved genetic material.
Using the fully sequenced genome, the researchers also discovered which genes build the fern’s unusual trunk-like stem – valuable insight into how key traits evolved in stem plants, says biologist Jan de Vries. of Plant Evolution at the University of Göttingen in Germany, which was not involved in the study. “Evolution is a handyman. Shedding light on viable molecular programs that have evolved tells us what is biologically possible and where the constraints are,” he says. “Using this knowledge, we can start tinkering with ourselves for synthetic biological purposes.”