Despite being one of the most diverse groups of plants on the planet, ferns were until recently the only major plant group to not have their genomes sequenced.

Now, for the first time ever, biologists have sequenced the genomes of two tiny ferns, Azolla filiculoides and Salvinia cucullata, and their findings have some major implications for agriculture.

The fern experts now hope to sequence other fern genomes and unravel more fern secrets.

For the first time ever, biologists have sequenced the genomes of two tiny ferns, Azolla filiculoides and Salvinia cucullata, and they’ve revealed some interesting secrets.

Despite being one of the most diverse groups of plants on the planet, ferns were the only major plant group to not have their genomes sequenced until now.

“This however is not due to lack of interest, but the fact that fern genomes tend to be humongous,” Fay-Wei Li, a plant biologist at the Boyce Thompson Institute and Cornell University in Ithaca, New York, told Mongabay in an email.

Ferns can have as many as 720 pairs of chromosomes and genomes as big as 148 billion base pairs of DNA sequences (Gb). By contrast, Arabidopsis (Arabidopsis thaliana), the first plant to have its genome sequenced, has only five pairs of chromosomes and a genome size of 0.135 Gb. (For comparison, the human genome has around 3 billion base pairs).

Li and his team, however, found that both Azolla and its sister genus, Salvinia, have extremely small genomes — A. filiculoides is 0.75 Gb while S. cucullata is 0.26 Gb — making them good candidates for genome sequencing. “We were excited about this result, and an international consortium was assembled to sequence these two ferns,” Li said.

But there was a problem. Getting funding for the genome project wasn’t easy, and all their letters of intent were declined, Li said. So the researchers tried to get some funding through a crowdfunding site called Experiment.com.

“We saw our colleagues doing a crowdfunding campaign to support their field expedition, and we thought, hey that’s cool,” Li said. “The first few days of crowdfunding were basically just us (and my mom!) throwing money into the pot. But with lots of social networking (I learned how to tweet for the first time! follow me @fern_way), the news spread…”

With support from around the world, Li and his colleagues were not only able to obtain enough funds to sequence both species of fern, but they also connected with other researchers who then became involved in the genome project.

Four years later, the researchers have published their results in Nature Plants.

Tiny ferns with “super” powers

The ferns that the team selected have some very interesting traits. Azolla, for instance, is believed to have played a major role in cooling down the planet several million years ago, earning it the title of “super-plant.” In what geologists call the “Azolla event,” huge blooms of Azolla covered the Artic Sea some 50 million years ago, removing large amounts of carbon dioxide from the atmosphere, turning a greenhouse Earth with warm temperatures at the poles into today’s planet with polar ice caps.

Azolla is also used as a “green manure” in rice farms in Asia. The fern, sometimes called the mosquito fern or fairy moss, harbors a nitrogen-fixing cyanobacterium called Nostoc azollae within its leaves that captures nitrogen from the atmosphere and converts it into forms that the ferns and rice plants can use. But unlike most other plant-microbe symbiotic partnerships, N. azollae is associated with Azolla throughout its life cycle and transfers from a parent to offspring every time the fern reproduces. In most other plants, each generation has to get its symbiotic microbes from the environment.

Li and his colleagues identified several genes that are specific to Azolla’s interactions with its symbiont bacteria, whose genomes have been sequenced previously.

“Now that we have genomes available for both the fern and cyanobacterium, there is great promise for tapping into the secrets of this natural biofertilizer that may help lead to future sustainable agricultural practices,” Kathleen Pryer, a professor at Duke University, U.S., said in a statement.

Ferns are also good at fending off insects. “When you walk into a forest, it’s usually very striking to find that ferns show little to no sign of insect damage,” Li said.

But when the researchers tracked down the gene responsible for the insecticidal proteins in S. cucullata, also known as the Asian watermoss, they were surprised to find that the gene had likely come not from its plant ancestors, but from bacteria.

“The finding that the fern insecticidal protein coming from bacteria was a big surprise,” Li said. “An important implication [of this] is that genes move around naturally among organisms, and perhaps GMOs” —genetically modified organisms — “are not as ‘unnatural’ as people tend to think. It’s a naturally modified gene, and now that we’ve found it, it could have huge implications for agriculture.”

The fern experts now hope to sequence other fern genomes.

“We are going fernatic to sequence more ferntastic genomes!” Li said. “Obviously the current two fern genomes do not give us the complete picture of fern genome structure and evolution. We want to eventually address why fern genomes can be so big… Currently we have about 10 fern species in the sequencing pipeline.”

Citation:

Li, F. W., Brouwer, P., Carretero-Paulet, L., Cheng, S., de Vries, J., Delaux, P. M., … & Simenc, M. (2018). Fern genomes elucidate land plant evolution and cyanobacterial symbioses. Nature plants, 1. http://dx.doi.org/10.1038/s41477-018-0188-8.