Genome evolution in the modern fern

Defying all expectations, a fern no larger than a dinner plate currently holds the title for highest chromosome count, with a whopping 720 pairs crammed into each of its nuclei. This penchant of ferns for hoarding DNA has stumped scientists, and the intractable size of their genomes has made it difficult to sequence, assemble and interpret them.

Two new papers published in the journal Nature Plants are rewriting history with the first full-length genomes for homosporous ferns, a large group that contains 99% of all modern fern diversity.

Analysis of the Ceratopteris genome provides hints for solving the long-standing mystery of why ferns, on average, retain more DNA than other plants. Comparisons to genomes from other groups also led to the surprise discovery that ferns stole the genes for several of their anti-herbivory toxins from bacteria.

Since the 1960s, the most favored explanation for why ferns contain so much DNA invoked rampant whole-genome duplications, in which an extra set of chromosomes is accidentally passed on to an organism’s offspring. This can sometimes be beneficial, as all the extra genes can then be used as raw material for the evolution of new traits. In fact, whole-genome duplication has been implicated in the origin of nearly all crop plants.

Whole-genome duplication is common in plants and even some animals, but most organisms tend to jettison the extra genetic baggage over time, slimming back down to smaller genomes that are metabolically easier to maintain.

"Ceratopteris richardii, aka C-Fern, has long been the preeminent model species for understanding molecular aspects of fern development and helping students in introductory biology course learn about plant life cycles," said James Leebens-Mack, UGA professor of plant biology and co-author on the study. "The Open Green Genomes Initiative has sequenced and assembled its massive genome, revealing a dynamic evolutionary history including genome duplications, rampant chromosomal rearrangements, and transfer of functional genes from microbes into fern genomes.  The publicly available genome sequence will greatly enhance the utility of C-Fern as a model species for both teaching and research."

Continue reading the September 1 media release.

Image: Ceratopteris richardii BY MARCHANT ET AL., 2022 IN NATURE PLANTS