The Quiet Branches

In what are now the Northern coastal oceans started getting greener ~65 million years ago, around the time when most dinosaurs went extinct. A distant relative of grasses was put on the evolutionary path to colonize the oceans. This new colonizer may have been the result of something plants routinely do to form new species: duplicating their entire genomes. A mass extinction had just occurred. There were fewer herbivores. Likely fewer pathogens. And seagrasses took advantage of an open niche in the environment. Today, the coasts of the North Atlantic and Pacific Oceans are all home to a species of seagrass: Zostera marina, common name, eelgrass (seagrasses are, evolutionarily speaking, monocots and part of the order Alismatales, fairly distant from true grasses in order Poales. Probably the most well-known monocots are the true grasses and orchids). Zostera meadows are now the base of a productive ecosystem under the sea.

In what are now the Northern coastal oceans started getting greener ~65 million years ago, around the time when most dinosaurs went extinct. A distant relative of grasses was put on the evolutionary path to colonize the oceans.

I spoke with Jeremy Shmutz of the Hudsonalpha Institute, one of the authors of the Zostera marina genome paper sequenced by the Department of Energy’s Joint Genome Institute (DOE-JGI). The DOE has a division dedicated to sequencing plant genomes. Like many projects in science, putting together a proposal for why any given plant genome should be sequenced is required (it’s akin to requesting time on the Hubble Space Telescope). Genomes are big undertakings, even in an era of cheap sequencing and high computing power.

One humorous thing he said is that grasses are ‘simplified dicots’. I think I know what he means; grasses tend to be very recognizable plants– thin-leaved, fast growing and lacking in showy flowers (most are wind pollinated). And grasses- at least crop grasses, tend to have genomes that align well with one another (i.e. the order of the DNA sequences in their genomes can be lined up to one another in large uninterrupted chunks). Though they are still complex and unique plants in their own right. With 10,000 some species, grasses are a successful group of plants and have been able to transform landscapes. Think of savannahs, prairies, most farm fields, lawns, veldt, and all the other words we use to describe many expansive, open, landscapes and these environments are defined by grasses. Bamboo forests are made up of grasses too. And eelgrass, still a monocot like true grasses, but distantly related to terrestrial grasses, also defines an entire ecosystem. Grasses are the grains that are the staple of our diets. There are genome sequences for many grasses including maize, rice, and wheat– and they can be a good source of biofuels, something else DOE is interested in exploring. Converting biomass to useable fuel is not an easy task, however.

Few species of plants have recolonized fresh water. Many float on the surface of freshwater lakes or live in bogs, though a few live completely under the water. From there, even fewer plants have adapted back to life in the oceans, like Zostera. This requires— as salmon do annually— moving from fresh back to salt water, including a period in estuarial waters where salinity can vary wildly (not to mention adapting to ocean currents and tides)— physiology and phenotype had to change to make the transition. Zostera, over time, was able to make that transition. It’s the plant equivalent of ancient land-dwelling whales adapting to life in the oceans again over evolutionary time. Some of Zostera’s ancestors evolved the traits necessary for life under water.

Why a reference genome and Why Zostera?

In genomics, one of the best things to have on hand to inform further work is a reference genome. Population surveys, high-throughput gene expression analyses (measuring the expression of entire genome’s worth of genes at one time), evolutionary history studies and more are all made easier with a reference genome. As I’ve talked about before, knowing the genome sequence helps us know what genes and what variants of genes exist and that is a critical part of the legacy of life on Earth. A useful gene for application could come from anywhere.

When the human genome was sequenced/published in 2000, that was not the sum total of all human variation but was an overall structure of what all human genomes look like– the location, structure, and the approximate number of genes present. A gene is a sequence of DNA that carries the information for some trait when it’s expressed and they are usually located in one specific place in a genome. With a reference in hand, figuring out just how individual genes vary in a population is a lot easier– some genes vary little over a population, others can vary a lot. The DOE really started the genomics era when it took on the Human Genome Project in the 1980’s.

When I spoke with Dr. Schmutz about the sequencing Zostera sequencing, he told me it started in 2009. Even in an era where genome sequencing has advanced a lot, it is anything but a trivial process– there are technical and computational challenges that have to be resolved and some genomes are just hard to sequence (or certain regions are hard to sequence). Zostera, for instance has some places where DNA is quite repetitive, in the from of “jumping genes” (aka transposons) that are hard to sequence over and assemble into a single sequence. How do you know what order those repeats go in? And exactly how many there are?

Schmutz underscored the importance of the Zostera project saying that with the Zostera genome, whole new avenues of research open up. Ecological and population studies can be done and include genetic/genomic information as a part of it. Zostera is part of a vast and productive ecosystem that has implications for climate change models. After all, one things plants do is sequester carbon. Zostera’s adaptations to ocean life may also yield genes that particularly suit it to marine life that might be co-opted for use in salt or drought stress in terrestrial plants. And there are other genomics projects that can add onto this project, like Jonathan Eisen’s seagrass microbiome project, exploring the microbes that colonize aquatic plants. Having the Zostera genome may yield insights into its interactions with the microbial world. As with many scientific projects though, it will take time to see the full result of having the genomic resource available, but just with the genome recently published, there’s a lot to be learned.

Taking the plunge

Organisms that live in the ocean have a different relationship to their environment. On land, hanging onto water in our bodies is important and it needs to be replenished constantly. Plants on land have to forage for water and maintain a constant column of water through their roots up to the pores in their leaves where water escapes as carbon dioxide is absorbed (the other strategy plants use is to adapt to the amount of water present– like mosses and so-called resurrection plants, that seem to come to life with even a small amount of water added). In the ocean, water is everywhere. Hanging onto water becomes less essential, but maintaining proper levels of fresh water (i.e. managing salt content) becomes the most critical. In the ocean under most conditions, salt in the ocean makes retaining salt-free water harder, it will tend to draw it out of most organisms unless they compensate, or have ways to constantly take in and filter water even as it’s lost. Balancing electrolytes while remaining hydrated is the compensatory goal.

Zostera has compensated. The genome sequence reveals several adaptations to life in the ocean. Zostera regained a component of their cell walls common in algae, but lost in land plants: that of adding sulfur to the sugars that make up their cell walls, making maintaining an equilibrium possible. And what is really cool is that Zostera has achieved the sulfur modification trait through enzymes originally involved in sulfinating other molecules in land plants– a novel solution to what algae have done for billions of years. Zostera has also lost most of the genes needed to have guard cells on their leaves. In land plants, guard cells are all but essential as they are what draw water up from the ground into the plant and into the atmosphere (called transpiration). They also allow for gas exchange; as in it’s the path that carbon dioxide takes to getting into the plant so it can build itself.

I confess I don’t know how Zostera takes in carbon dioxide (presumably dissolved in the water) to do gas exchange. It must do it somehow though because it is still a photosynthetic organism. The carbon dioxide has to get in somehow to get incorporated into sugar that can then go on to be metabolized.

Other oddities about Zostera is that is has lost the ethylene signaling pathway. Ethylene signaling did evolve in algal ancestors of plants, but in Zostera, the enzymes responsible for synthesizing ethylene, the receptors that perceive it and the signaling pathway that gets triggered are absent in the Zostera genome. Plants do rely on diffusion to get rid of ethylene. Without guard cells, ethylene could accumulate to high levels and therefore inhibit growth; this might have been the evolutionary pressure to ditch ethylene as a hormone. The targets of the ethylene pathway do exist, suggesting that their function may still be needed for growth and development, but it’s still an open question as to whether there is an alternative input into those downstream components of the pathway. Did another hormone take over the job of the ethylene signaling pathway? Or is it a biologically unique input?

The Zostera genome is just one stop along the ongoing trek of science.

As with all the lost genes in Zostera, another question is if all marine seagrasses have lost similar genes in their genomes. There is some evidence that other aquatic plants lack some of the ethylene pathway (link to paywalled Trends in Plant Science Article).

There are some other interesting things about Zostera, including the fact that it has lost a UV light receptor as well as a reduced set of phytochrome genes that perceive red/far-red light in plants, suggesting that there is less need for responsiveness to light (or just a lack of some wavelengths of light) under the ocean.

And last, Zostera flowers produce pollen, and that pollen has to find an open flower (specifically the stigma) on another Zostera plant. This all has to happen under water. The seeds of Zostera also have to be adapted to life under the sea. Like many grasses, Zostera can also vegetatively propagate (essentially cloning itself). In fact, that is the Zostera that was sequenced in the Nature paper, a clonal clump from off the coast of Finland.

Genomes are literally a wealth of information. And Zostera is just the latest one to reveal some of its secrets. As Dr. Schmutz noted, this genome opens up new avenues of exploration. The Zostera genome is just one stop on the ongoing trek of science.

[Update: This post was updated to reflect the fact that Zostera and other seagrasses are part of the order Alistamatales, a distant relative of true grasses that are part of the order Poales. March 9, 2016]

References

1. Jeanine L. Olsen, Pierre Rouzé, Bram Verhelst, Yao-Cheng Lin, Till Bayer, Jonas Collen, Emanuela Dattolo, Emanuele De Paoli, Simon Dittami, Florian Maumus, Gurvan Michel, Anna Kersting, Chiara Lauritano, Rolf Lohaus, Mats Töpel, Thierry Tonon, Kevin Vanneste, Mojgan Amirebrahimi, Janina Brakel, Christoffer Boström, Mansi Chovatia, Jane Grimwood, Jerry W. Jenkins, Alexander Jueterbock, Amy Mraz, Wytze T. Stam, Hope Tice, Erich Bornberg-Bauer, Pamela J. Green, Gareth A. Pearson, Gabriele Procaccini, Carlos M. Duarte, Jeremy Schmutz, Thorsten B. H. Reusch & Yves Van de Peer. The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea. 2016. Nature 530: 331-335. (open access).
2. Mary Williams, Mel Oliver,Stephen Pallardy. Water Relations 1: Uptake and Transport. 2014. Plant Cell Teaching Tool in Plant Biology (paywall).
3. Laurentius A.C.J. Voesenek, Ronald Pierik, and Rashmi Sasidharan. Plant Life Without Ethylene. 2015. Trends in Plant Science 20: 783-786.(paywall).

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