Like many deep-sea animals, giant isopods (genus Bathynomus) look like they’re ready to star in a B-horror movie. Yet, they’ve become charismatic marine ambassadors in aquariums around the world—in some places, you can even pet one! Now, they’re also helping scientists better understand how species adapt to the dark depths, thanks to a high-quality genome sequence published May 13 in BMC Biology.
The Chinese research team behind the new assembly writes that isopods are great for studying adaptation because representatives of the speciose group (more than 10,000 species have been described to date) can be found all over the world in extremely diverse habitats, from tropical forests to the bottom of the sea. Indeed, the oceanic seafloor is considered an especially demanding habitat, and any organism living there must cope with freezing temperatures, intense pressures, deep darkness, and limited food. Giant isopods are one of the dominant invertebrates in this environment, surviving by scavenging the rare bounties that fall from above in the form of sinking carcasses. A complete genome could allow scientists to probe the genetics underlying the traits that help them thrive in the deep, including their large bodies, oversized stomachs, and remarkable fasting ability (one captive isopod lived for five years without eating).
To sequence the genome of the giant isopod Bathynomus jamesi, the team de novo assembled Pacific Bio long reads rather than using either of the existing two terrestrial isopod genomes as a scaffold. That resulted in a highly contiguous, 5.24 Gb genome—nearly 3.5 times the size of the next largest isopod genome—that, based on a pool of expected crustacean genes, was about 95 percent complete.
NOAA Office of Ocean Exploration and Research, Gulf of Mexico 2017
Notably, roughly 90 percent the genome featured repetitive sequences, a much larger proportion than that observed in other sequenced crustaceans (which are typically less than 60 percent repetitive sequences). The authors speculate that “repeat proliferation might be the major driving force for the genome expansion of B. jamesi,” and that transposable elements, which account for the vast majority of the repetitive sequences, likely have a “profound impact on the plasticity of the whole genome.”
The researchers also detected the expansion of numerous gene families, including ones associated with thyroid and insulin signaling—which are both tied to growth regulation—and lipid metabolism. “The expansion of these gene families may reflect the adaptive evolution of B. jamesi to the deep-sea environment,” they write.
The analyses performed are just the beginning, the authors conclude—the data reported will serve as “a valuable resource for understanding body size evolution and adaptation mechanisms of macrobenthic organisms to deep-sea environments” and “provide powerful tools for broader studies on the ecology, evolutionary biology, and biological conservation of isopods.”
Mycoheterotrophic plants—sometimes referred to as “mycorrhizal cheaters”—steal their sustenance from fungi, allowing them to reduce or ditch photosynthesis altogether. To elucidate how this parasitic relationship evolved, researchers generated high-quality genome assemblies for sister species of orchid: Platanthera zijinensis, which is partially mycoheterotriphic, and P. guangdongensis, which is fully mycoheterotrophic. Analyses of the data published April 21 in Nature Plants suggest that mycoheterotrophy is associated with increased substitution rates across the genome and numerous gene losses, including many photoreceptor genes. Combined, the findings “suggest that the evolution of full mycoheterotrophy in orchids may be an adaptation to occupy specific biological niches without light,” the authors write.
Flying spider-monkey tree fern (Alsophila spinulosa)
Despite being the most speciose group of non-flowering land plants, paltry genomic resources exist for ferns. A chromosome-level assembly of the 6.23 Gb genome of the flying spider-monkey tree fern, published May 09 in Nature Plants, is only the third fern genome sequenced to date, and the first for the order Cyatheales (tree ferns). The researchers behind the sequence write that it “provides a unique reference for inferring the history of genetic diversity, secondary metabolite biosynthesis, and evolution of tree ferns for better protection and application of tree ferns in the future.” Indeed, thanks to genomic comparisons with other plants, the team was able to probe the plant’s evolutionary history—which may have included two genetic bottlenecks—and begin to investigate how it builds the vascular tissues that support its tree-like physiology.
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.