New research reveals the very first complete genome sequences of ferns. The report published in the journal Nature Plants uncovers some real oddities and tells a story of the persistence of scientists – and the good will of the public.
Lead author Fay-Wei Li, of the Boyce Thompson Institute in Ithaca, New York, US, first became interested in ferns during his PhD, which was supervised by the paper’s last author, Duke University biologist, Kathleen Pryer.
The first plant genome was sequenced in 2000. Subsequently all major plant groups have been sequenced.
This may in part be due to their ridiculously large genomes, which average twelve billion base pairs but can range up to 148 billion. (In contrast, the human genome contains three billion.) Nonetheless, Pryer had been working for years to address this hole in scientific knowledge and Li became fascinated.
The pair, leading an international team, focussed on a unique, floating water fern called Azolla filiculoides. It was selected because, for a fern, it has a peculiarly small genome, amounting to only 750 million base pairs. (That of a banana comprises 523 million.) Sequencing Azolla should have been a breeze.
Except no one wanted to fund the research, fobbing it off as odd or of little interest.
Where to turn when traditional sources of funding dry up?
The internet, of course.
Through a science crowdfunding site called experiment.com they managed to quickly raise more than their goal. With some free sequencing from the Beijing Genomics Institute in Shenzhen, China, the project was up and running.
Despite the obstacles, it was worth the effort.
“Azolla has a really cool biology and evolutionary history,” says Li. “Azolla engages in symbiosis with cyanobacteria for nitrogen fixation, and for this reason it has been used as a green manure for rice paddies in Asia for hundreds of years.”
The partner bacterium, Nostoc azollae, was also sequenced in the research. It is partly what makes Azolla unique, because it passes down the fern’s generations during reproduction.
The genetics behind this symbiotic relationship helped to uncover the origins of another curious trait of ferns.
“When you walk into a forest, it’s usually very striking to find that ferns show little to no sign of insect damage,” says Li.
The plants, it turns out, have a very effective insecticidal gene that helps to protect them from the ravening bug hordes. The gene, the research reveals, probably came into plant lineages, millions of years earlier, via horizontal gene transfer from another symbiotic bacteria much like Nostoc.
Azolla also grows incredibly quickly and for that reason is of interest as a carbon sink. Indeed, the fossil record shows a vast proliferation fifty million years ago, the “Azolla event”, that may well be associated with a period of dramatic global cooling.
Not only does this research help us understand the evolutionary history of a major plant group, it also holds the promise of practical application.
“Now that we have genomes available for both the fern and cyanobacterium, there is great promise for tapping into the secrets of this natural biofertiliser that may help lead to future sustainable agricultural practices,” says Pryer.
Stephen Fleischfresser is a lecturer at the University of Melbourne's Trinity College and holds a PhD in the History and Philosophy of Science.
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