Demystifying Redwood Genetics: Tall Trees, Big Genomes

Along the Northern California coast stand real-life giants. Redwood trees are iconic massive conifers that tower over the visitors of the Redwood National and State Parks. Once you see them for yourself, it’s immediately apparent how these incredible photosynthetic organisms draw people from across the globe. After all, humans tend to be captivated by the biggest of anything. But it turns out their height isn't their only massive feature: the redwood genome is approximately eight-times larger than the human genome.

Among those drawn to the giants are a group of geneticists from the University of California, Berkeley. Unlike most visitors whose gaze fixates on the trees’ upper bounds, their interest concerns the giants’ unique genomic structure and its role in helping the species survive an uncertain future. Under the existential threat of climate change, the trees’ genome may already be changing. But, just as it's difficult to see the top of a redwood giant, studying its massive genome is anything but easy.

Standing Tall

California’s state tree, the coast redwood (Sequoia sempervirens), is the world’s tallest growing tree species, readily reaching heights of 90 to 105 meters.¹ The largest amongst them, Hyperion, is aptly named for the Greek Titan of light, whose name means "he who watches from above” or simply "the high one.”² Standing nearly 116 meters, Hyperion is the tallest living organism on the planet and is estimated to be between 600 to 800 years old.³

Need a frame of reference? That’s ~500% older and ~25% taller than the Statue of Liberty from ground to torch. To this day, only two statues on the planet reach higher, both constructed after 2008.

But, if you want to peer at California’s sun titan, you won’t have much luck. Hyperion is located deep within an untrailed area in California's densely forested Northern Coast. Furthermore, the National Park Service carefully protects Hyperion from visitors and destructive tourism to keep the redwood standing tall for years to come. But, even for Hyperion, there’s no hiding from the effects of a changing climate.

A Changing Northern California Climate

Redwoods are only found in a narrow strip of Northern California, occupying a specific and vital niche. As a result, they are particularly threatened by climate change, especially when it leads to a reduction in water access. At their size, each redwood consumes 160 gallons or 605 liters of water every day.⁴ In the summer when it’s drier, they are especially dependent on fog for their water, capturing as much as 40% of their total annual water through their leaves. Lucky for them, Northern California has historically had no shortage of fog. But what happens if—as some have predicted⁵—the region’s emblematic fog patterns change? Are there evolutionary mechanisms that might help these legendary trees survive?

The Redwood Genome Structure and Survival

To understand how redwoods and other plants like them can survive and adapt to changing ecosystems, researchers must study their molecular blueprints and associated genomic diversity. In doing so, they can begin to unravel the relationship between redwood evolution and climate change.

That is exactly what Alexandra “Sasha” Nikolaeva, a graduate student from UC Berkeley, set out to do. Nikolaeva and her team collected samples from across the redwood range to study population structure and explore redwood genomic diversity.

"Redwoods may survive thanks to their unique polyploid genome"

In particular, Nikolaeva was curious to see if there were ploidy differences across the range, given the assumed importance of chromosome copies to redwood survival. “One of the reasons the community thinks [redwoods] can survive in that region is their genome’s unique structure. Redwoods are polyploid conifers with six sets of chromosomes. Though polyploidy is not uncommon in plants, it is very rare for conifers, which are mostly diploid,” says Nikolaeva.

Being a polyploid plant comes with advantages and disadvantages that impact niche adaptation.⁶ For example, polyploid plants “have larger cells, including guard cells, which control evapotranspiration. These cells are basically the plants' breathing elements, helping to capture CO₂ for food synthesis. In redwoods, these cells are larger than the guard cells of its closest diploid relative, giant sequoia."

One form of ploidy variation, aneuploidy, became a core target of their genomic survey. According to Nikolaeva, “aneuploidy describes a change in the number of total chromosomes within a genome. Occasionally, there will be a change where a chromosome is lost or added, leading to either seven or five copies of that chromosome in a redwood.” Adding or dropping chromosomes may provide improved fitness to redwood trees.

To begin understanding how this phenomenon affects adaptation, the team first needed to better clarify to what extent aneuploidy occurs in coast redwoods. However, examining ploidy in a genome this large comes with some considerable challenges that the team had to overcome.

The Complexities of Studying a Massive and Understudied Genome

Investigating redwood ploidy diversity is easier said than done. This is partly due to the fact that the redwood genome is very large, even by conifer standards. Recent estimates indicate the coast redwood genome is approximately three times larger than its closest relatives, the giant sequoia (Sequoiadendron giganteum) and the dawn redwood (Metasequoia glyptostroboides).⁷

Large genomes require greater computational resources to process the sheer volume of data. In addition, the larger a plant genome is, the more repetitive sequences it usually includes, which can make it harder to determine a specific gene’s location and increase the difficulty of accurate assembly.⁸

"It's a lot harder to study aneuploidy in polyploids compared to diploid organisms"

However, raw genome size is only one part of the challenge. Having multiple chromosomal copies itself complicates analyses. “It's a lot harder to study aneuploidy in polyploids compared to diploid organisms. The increases or decreases of chromosome numbers are smaller in polyploids relative to diploids, which lose half of a pair if a chromosome is dropped. In a polyploid, one chromosome copy is only a small fraction of the total number of chromosomes.” In other words, the smaller the relative difference, the harder it is to detect chromosome copy number changes. This makes it difficult to reliably identify chromosome numbers in species with large polyploid genomes, like the coast redwood.

Adding to this complexity, redwoods are not a traditional model organism. Unlike more commonly studied species, like humans and rodents, few tools and reagents are available that are specifically designed to improve the efficiency and quality of experiments in redwoods, including genome sequencing.

Working with Custom NGS Panels From Twist

To help overcome this challenge, Nikolaeva’s collaborator, Lydia Smith (Lab Manager of the Evolutionary Genetics Lab at UC Berkeley), pointed her toward Twist’s next-generation sequencing (NGS) offerings.

Nikolaeva and Smith ultimately applied a custom NGS panel and target enrichment reagents from Twist to explore redwood genomic diversity. “That was really a big game-changer for us because we didn't think we were going to be able to do this using exome sequencing because of the associated costs. We thought we would have to go with restriction site-associated DNA sequencing (RADSeq),” says Nikolaeva.

Twist’s custom offerings and bioinformatics support helped the team develop a method to collect sequencing results capable of resolving and observing ploidy differences across the coast redwood range. As Smith put it, “​​If Sasha had collected RADSeq data, she would have a big data set that she'd be tearing her hair out trying to analyze. Though she would have publishable data from it, being able to get actual target captured sequences makes a huge difference in the rigor of the research, the statistics that can be applied, and the number of directions the data can be taken in later.”

References

1. “The Redwoods of Coast and Sierra.” Nps.gov, 2019, www.nps.gov/parkhistory/online_books/shirley/sec10.htm.
2. Dhar, Rittika. Hyperion: Titan God of Heavenly Light | History Cooperative. 16 July 2022, historycooperative.org/hyperion-titan-god-of-heavenly-light/.
3. Candide. “The Tallest Trees in the World.” Medium, 11 Sept. 2019, medium.com/@candidegardening/the-tallest-trees-in-the-world-4b7e90f7f910
4. “Fog, Redwoods and a Changing Climate (U.S. National Park Service).” Www.nps.gov, www.nps.gov/articles/000/fog-redwoods-and-a-changing-climate.htm.
5. “The Future of Fog.” Public Policy Institute of California, www.ppic.org/blog/the-future-of-fog/.
6. Comai, Luca. “The Advantages and Disadvantages of Being Polyploid.” Nature Reviews Genetics, vol. 6, no. 11, 11 Oct. 2005, pp. 836–846, https://doi.org/10.1038/nrg1711.
7. Neale, David B, et al. “Assembled and Annotated 26.5 Gbp Coast Redwood Genome: A Resource for Estimating Evolutionary Adaptive Potential and Investigating Hexaploid Origin.” G3 Genes|Genomes|Genetics, vol. 12, no. 1, 14 Dec. 2021, https://doi.org/10.1093/g3journal/jkab380.
8. Claros, Manuel Gonzalo, et al. “Why Assembling Plant Genome Sequences Is so Challenging.” Biology, vol. 1, no. 2, 18 Sept. 2012, pp. 439–459, https://doi.org/10.3390/biology1020439.