Two years ago, scientists announced that they'd discovered the largest genome yet seen in an unlikely source: the New Caledonian fork fern . Every cell in the small fern native to the South Pacific contains a staggering 160 billion base pairs of DNA, and most ferns also have high chromosome numbers, including the world record holder with more than 1,400 chromosomes. (For comparison, humans have 3.2 billion base pairs on 46 chromosomes.) To find out why, scientists at the University of New Hampshire (UNH) and Cornell University took a counterintuitive approach by focusing on members of the fern genus Salvinia, which have some of the smallest fern genomes.
Their research, published in Proceedings of the National Academy of Sciences , revealed unexpectedly dynamic fern genomes, linked differences in chromosome numbers to differences in reproduction, and may provide clues into how the aquatic invasive species Salvinia molesta is able to overrun ponds and other bodies of water with frightening speed.
The research team was led by UNH's Erin Sigel, research scientist and collections manager for the Albion R. Hodgdon Herbarium , in collaboration with Fay-Wei Li, associate professor with the Boyce Thompson Institute and Cornell's School of Integrative Plant Science, and Yanã Rizzieri, doctoral student in the Li lab. They took a detailed look at the genome of Salvinia cucullata, the fern with the smallest known genome at a mere 250 million base pairs. For comparison, they also investigated the genome of Salvinia molesta, one of the top 100 invasive plant species in the world.
To their surprise, they found that S. cucullata had nearly four times as many chromosomes—68—as originally expected despite its minuscule genome size. Salvinia molesta also defied expectations. While its genome size was 10 times larger than that of S. cucullata, it had fewer chromosomes, and S. molesta was revealed to be a hybrid between two other Salvinia species that are unknown to science.
"Our findings show that the evolution of Salvinia genomes is very dynamic, more like that in flowering plants than in most ferns that have large genomes," says Sigel. "The discoveries we made about Salvinia molesta's genome also provides insight into what makes it such a successful invasive species."
More than a blueprint
A genome is much more than just a blueprint for cellular functions. Rapid advances in DNA sequencing technology have revealed a huge amount about biology beyond the strings of ACGTs. Ferns, which have been around for hundreds of millions of years, have some of the largest and most stable genomes around.
What makes fern genomes so big? Ferns, like all plants, duplicate their entire genomes on occasion. Compared to most plants, though, ferns are inefficient at shrinking their genomes after doubling. Their inefficient downsizing is likely a consequence of their distinct reproductive biology: Most ferns only produce a single type of bisexual spore, which enables inbreeding and offers fewer opportunities for rearranging and shedding chromosomes.
A small number of ferns including Salvinia produce separate male and female spores that are similar to reproduction in flowering plants, providing greater opportunities for chromosome rearrangement and loss. The whole-genome sequencing in the study showed that S. cucullata and S. molesta have undergone extensive chromosome fissions and fusions, underscoring their dynamic genome evolution relative to other ferns. The differences in reproduction between Salvinia and most ferns likely shapes genome size and structure.
Commonly known as giant salvinia or Kariba weed, S. molesta is native to Brazil and is now spreading in the southern United States. It can double its biomass in as few as three days and continues until it completely covers water surfaces and overwhelms native plants and animals. The researchers found that because S. molesta was formed by hybridization between two species with different chromosome numbers, it cannot reproduce sexually, relying instead on clonal reproduction. In environments to which it is well adapted, it can quickly and vigorously grow and break off genetically identical offspring. The low genetic variability of S. molesta could provide an opening for its control as treatments that inhibit its growth will likely work similarly throughout its invasive range.
