2022 Progress Report: Model fern reveals insight into DNA thievery in ferns

Open Green Genomes hits milestone with C. richardii

The Science

Fern genomes are huge, and incredibly complex — making it difficult to grasp a deeper understanding of fundamental aspects of fern biology and, more broadly, land plant evolution. Recent findings in Ceratopteris richardii show a long history of dynamic evolution and rapid changes in both genome content and structure following a genome duplication event that occured some 60 million years ago. Massive gene loss, rampant gene duplications, and even more ancient gene transfers from bacteria have all armed the plant with an array of defense mechanisms.

The Impact

There are over 10,400 species of ferns alive today. Boasting adaptations in order to protect themselves from environmental stresses, ferns’ secondary metabolites and associated genes are great resources for bioremediation, new agricultural applications or life-saving drugs. A better understanding of its genetic complexities will illuminate the evolutionary history of a pivotal plant as well as the evolution of seed plants, the fern’s distant cousin. Ceratopteris richardii, or C-fern, specifically has been studied in plant research laboratories and plant biology courses across the globe for insights into reproductive, space and genome biology.

The undeniable power of plants, and the lessons they can teach us, are why the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility located at Lawrence Berkeley National Laboratory (Berkeley Lab) took on the Open Green Genome Initiative in 2018 as part of its Community Science Program. The OGG has set out to generate high-quality genome assemblies and annotations for 35 species representing all major evolutionary lineages in the land plant tree of life. Ultimately, the resulting comparative framework can inform the efficient production of plant-based biofuels and bioproducts. 

Summary

A recent paper published in Nature Communications on Ceratopteris richardii marks the first published manuscript of a genome sequence generated through the OGG. For a long time, C-fern has served as a model for studying ferns and for teaching plant biology. It is typical of most ferns in many ways, including its large genome with numerous chromosomes.

For a long time, this immense size and chromosomal hoarding had been thought to be the result of multiple whole-genome duplications. The process of genome-doubling, where an extra set of chromosomes is passed along to offspring supplying it with raw genetic materials and increased genome complexity, made sense. The problem with that theory was that the handful of documented WGDs in ferns could not explain the massive size of most fern genomes.

A team of researchers put together a chromosomal genome assembly and associated methylome, transcriptome and metabolome analyses for C-fern that was able to shed some light on the mystery. They found over seven million repetitive elements that account for 85.2% of the C-fern assembly. While they did identify a couple WGD events, these events could not fully account for the size and complexity of the C-fern’s genome.

Instead, it seems many of the fern’s defense-related gene families were snatched from bacteria. The insertion of transposable elements — also known as “jumping genes” because they can change position within a genome — into certain DNA segments has led the fern to its gene hoarding and those long genes. And gene family analysis showed that genes directing development of reproductive structures in seed plants were essentially co-opted from those directing spore development in the last common ancestor of seed plants and ferns.

The genome is available on the JGI’s plant portal, Phytozome. Researchers hope to have demonstrated the potential of ferns as sources of novel genetic material with applications including ecological remediation and bioprospecting — paving the way for C-fern to expand its role as a key plant system for teaching next-generation plant biology.