Ferns are the second-most successful clade of vascular plants, outnumbered only by their flowering kin. Yet genomic resources for the group have remained scarce, with no whole genome sequences for any of the 10,000 or so homosporous ferns—species with only one kind of spore—that account for more than 99 percent of fern diversity. That changed this year with the publication of three fern genomes in Nature Plants.
See “Why Did Ferns Persist When All Other Plants Perished?”
Researchers have long struggled to construct fern genomes due to their immense size and complexity. In general, the plants boast genomes that are 12 Gb long on average—larger than most flowering plants and nearly four times the length of the human genome. And these massive genomes are split into dozens of chromosomes. For instance, it’s estimated that the adder’s-tongue fern (Ophioglossum reticulatum) has 720 pairs of chromosomes. While ferns in general average about 40 pairs, that still considerably exceeds our mere 23.
Why ferns have such gigantic genomes isn’t clear, but scientists have long hypothesized that the answer lies in rounds of whole-genome duplications—which, unfortunately for bioinformaticians, makes assembling a genome even trickier. Still, three independent research teams recently succeeded in assembling high-quality genomes of the C-fern (Ceratopteris richardii; 7.46 Gb, 39 pairs of chromosomes), the flying spider-monkey tree fern (Alsophila spinulosa; 6.23 Gb, 69 pairs of chromosomes), and the southern maidenhair fern (Adiantum capillus-veneris; 4.8 Gb, 30 pairs of chromosomes). All three, published in recent months, employed similar tactics, including PacBio long-read sequencing along with Illumina short-reads for assembly polishing and Hi-C chromosome capture to elucidate genome structure.
Surprisingly, evidence for whole-genome duplications was hard to find. “In fact, there’s only the evidence for potentially two duplications in this whole lineage, that go back hundreds of millions of years,” Florida Museum of Natural History botanist Pamela Soltis, who was a member of the C-fern genome team, tells The New York Times. Instead, fern genomes appear to have grown because of transposable elements and repetitive sequences, she says.
See “Adapting with a Little Help from Jumping Genes”
The sequence of the C-fern in particular, a model organism, also revealed an apparent penchant for incorporating DNA from other species obtained via horizontal gene transfer. The researchers found numerous putative bacterial genes that were not only incorporated into the ferns’ DNA but also expressed in diverse tissues, likely acting as defensive toxins. “The mechanisms behind horizontal gene transfer remain one of the least investigated areas of land plant evolution,” Doug Soltis, also with the Florida Museum of Natural History, explains in an institutional news release. “Over evolutionary timescales, it’s a bit like winning the lottery. Any time a plant is wounded, its interior is susceptible to invasion from microbes, but for their DNA to be incorporated into the genome seems amazing.”
See “Horizontal Gene Transfer Happens More Often Than Anyone Thought”
Further analyses of the sequences, especially comparative ones, will likely shed light on longstanding questions in genome and plant biology, experts say. The C-fern genome, for instance, contains genes involved in flowering and seed development in angiosperms, while the maindenhair fern genome contains ones used by other plants for pollen development. These putative flower-related genes seem to be expressed in reproductive structures, though exactly what they do in flowerless, pollenless ferns remains unclear. Additional work to understand their functions may shed light on the early evolution of flowering. “To understand how anything works in any organism, including ourselves, you need to look at where it came from and what its context was prior to taking on whatever function it has now,” Pamela Soltis tells the Times.
University of Washington botanist Verónica Di Stilio expresses similar sentiments to Science. “Having reference genomes representative of each of the major plant lineages opens up so many possibilities,” she says. “Genomes are tools, the tip of the iceberg.”
Wild yak (Bos mutus)
Although not the first yak genomes ever published, chromosome-level assemblies for both wild and domesticated yak (Bos grunniens) published September 6 in Nature Communications yield novel insights into how the animals adapted to their high-altitude, low-oxygen environment. Specifically, the genome sequences allowed researchers to perform single-cell whole-genome sequencing and transcriptomics, which uncovered specialized immune cells in yak lungs. These cells express numerous genes differently than their counterparts in cattle, a member of the same genus as yaks. These differences in expression levels, including in two genes previously linked to high-altitude adaptation, may be driven by hundreds of structural variants identified in the yak genomes. “These findings provide new insights into the high-altitude adaptation of yak and have important implications for understanding the physiological and pathological responses of large mammals and humans to hypoxia,” the authors write.
Oriental dobsonfly (Neoneuromus ignobilis)
More than 6 percent of all insects are aquatic, and all stem from previously terrestrial creatures. Indeed, it’s thought that insects evolved aquatic phases or lifestyles on more than 50 different occasions, making the adaptation of insects to freshwater habitats one of the most bountiful examples of convergent evolution. Researchers have now begun to explore the genetics of this evolutionary convergence, thanks in part to a chromosome-scale genome assembly for the Oriental dobsonfly (Neoneuromus ignobilis) published in the September issue of Genomics. By comparing the dobsonfly’s genome with those of 41 other insects (11 of which were aquatic insects from other groups), researchers uncovered convergent expansions in genes coding for long-wavelength-sensitive and blue-sensitive opsins, TRP channels that respond to thermal stress, and enzymes that transfer sulfate groups, all of which may be involved in adapting to an underwater life. Intriguingly, the team also found a higher-than-expected number of convergent amino acid substitutions, which appeared to be especially common in sequences that steer protein modifications. “Our comparative genomic analysis revealed the evidence of molecular convergences in aquatic insects during both gene family evolution and convergent amino acid substitution, and these molecular convergences may contribute to the ecological adaptation of aquatic insects,” the team concludes in the paper.
Genome Spotlight is a monthly column for The Scientist’s Genetics & Genomics newsletter that highlights recently published genome sequences and the mysteries of life they may reveal.