Redwood Genome Project

Forever Forest
Donors to the League’s Forever Forest Campaign are providing $1 million to support this project. Learn more

The Redwood Genome Project is a five-year effort that sequenced the coast redwood and giant sequoia genomes and will develop tools to assess genetic diversity.

Save the Redwoods League has protected nearly all of the ancient redwood groves that exist on the planet following 150 years of wide-scale logging across the natural range of the redwood forest. Now, reflecting upon our ongoing commitment to protection and restoration, we will focus on regenerating the magnificent, mature redwood forest by accelerating old-growth characteristics in the young and vigorous timber stands now flourishing on previously harvested lands. One of the League’s goals is to leave the world better than we found it for generations to come. We will achieve this goal by regenerating mature forests through a variety of advanced management techniques, including selective harvesting — removing specific trees in heavily stocked or overcrowded forests to allow the remaining trees to reach maximum size in as short a time as possible.

But managers working to restore the forests across the redwood range must determine which trees should go, and which should stay. Their task is challenging because redwood trees are not identical; like human beings, they manifest a broad genetic range. Some grow slowly, some rapidly. Some can withstand drought and other stressors better than others. We need to understand our redwoods on the genomic scale if we hope to restore these forests to their rightful grandeur. To ensure resilient old-growth forests for the future, we need to preserve their genetic diversity now. To this end, the League has launched the Redwood Genome Project.

Sequenced Genome Sizes: The coast redwood and giant sequoia genomes were sequenced by Save the Redwoods League, University of California, Davis and Johns Hopkins University.
The coast redwood and giant sequoia genomes were sequenced by Save the Redwoods League, University of California, Davis and Johns Hopkins University.

We began this five-year effort by sequencing the coast redwood and giant sequoia genomes. Both sequences are complex in their own right, but the coast redwood genome is nearly 9 times larger than the human genome. New technologies made mapping its complex code faster and more cost effective.

With both genomes available for study, researchers are now developing tools to assess genetic diversity out in the forest. These tools will inform management plans and help these species thrive in the coming centuries.

The Redwoods Genome Project is made possible by Forever ForestThe Campaign for the Redwoods, a comprehensive campaign launched by Save the Redwoods League in January 2020 to garner support for the organization’s ambitious vision for the next century of redwoods conservation. The League’s goal is to raise $120 million by 2022 to fund the first years of this centennial vision, which includes protecting entire landscapes through large-scale, strategic land acquisitions; restoring young redwood forests to become the old-growth forests of the future; and connecting all people with the beauty and power of the redwoods through transformational park experiences.

Threats to our coast redwood and giant sequoia forests, of course, are many. They include ongoing development pressures, industrial harvest, biologically inappropriate harvest rotations in “working” forests, and inadequate management of harvested lands that currently sustain young redwoods.

Climate change is a particularly tough challenge. We are now living in the Anthropocene, the emerging geological epoch characterized by human impacts. The warming climate already is imposing significant stresses on the West’s wild land systems, including the redwood forests. These changes will continue for millennia, and we must accommodate them in our conservation strategies if we hope to protect and ultimately revitalize our coast redwood and giant sequoia forests.

Restoring these forests through the Anthropocene will require more than established techniques such as road retirement, soil stabilization, prescribed fire and thinning. The coast redwood and giant sequoia forests lost more than mere mass when the ancient trees were felled. It’s likely that genetically unique individuals have been lost with each old tree that was cut. Many reforestation projects further restricted genetic diversity because the trees that were used for replanting had been selected for rapid growth, a policy that risked the loss of genes associated with traits such as disease resistance and drought tolerance. Today’s forests differ from the ancient forests on the macro scale, but they also diverge at the molecular level. And this is a deficiency that must be remedied if we hope to restore and maintain coast redwood and giant sequoia forests for our grandchildren and their grandchildren. Restricted genetics are as great a threat to these forests as logging and development, especially in an era of dramatic climate change.

Sequoia National Park. Photo by Mark Bult
Sequoia National Park. Photo by Mark Bult

To re-establish the genetic diversity of these forests, we must first know the complete genomes of Sequoia sempervirens and Sequoiadendron giganteum. Now that we have these data, we can develop the genetic screening tools that will inform and guide the management techniques that will allow forests to survive — indeed, thrive — in the emerging Anthropocene.

Tree genome sequencing technologies have advanced greatly in the past two decades. Initially, these were daunting undertakings, especially for conifers, which typically have exceedingly large genomes, making their sequencing both time-consuming and prohibitively expensive. Progress, however, has been steady, and scores of species have been sequenced, including familiar conifers such as Douglas-fir, sugar pine, and Norway spruce.

Though the technology for conifer genomic sequencing is refined, sequencing the coast redwood genome posed a significant challenge. Before its genome was fully mapped, all the conifers that were sequenced were diploid, meaning they have only two sets of chromosomes. Coast redwoods, by contrast, are hexaploid: They have six chromosomal sets, greatly complicating the sequencing task.

The power of cutting-edge genomic technology has led to the capacity to rapidly discover and characterize, at the level of the DNA sequence, the variation in genes that underlie an organism’s ability to adapt to its surrounding environment. The cataloguing of adaptive DNA sequence variations is crucial for redwood conservation, in that it allows researchers to identify specific trees that contribute to the genetic diversity and are well adapted in their particular regions under changing environmental conditions — drought and rising temperatures, for example.

Coast redwoods and giant sequoia harboring genes that may allow them to withstand environmental stresses are planetary treasures and integral to the League’s long-term conservation strategy. Our ability to protect the redwood forests will thus be predicated on our ability to conserve those components of the redwood genomes that contribute to tree health and forests resiliency.

Past League genomic inquiries already have yielded valuable information about coast redwood and giant sequoia genetics that could aid conservation initiatives. By analyzing small sections of DNA called neutral genetic markers, research grantees discovered that giant sequoia groves may be inbred; that coast redwood “fairy rings” (circles of redwoods around stumps or dead trees) are not always clones; and that the southern coast redwood population is genetically distinct from northern populations.

The Redwood Genome Project will add substantively to this critical body of data. It will require five years to complete, and will focus on the following milestones:


One (2017) An annotated reference genome for coast redwood and giant sequoia will be produced. The final quality of this genomic assembly will depend on funding. These completed reference genomes will be available to the public on the project website (external link) and the TreeGenes Project (external link).
Two (2018) The goal for the second year is the full identification of genetic variation in coast redwoods and giant sequoia. This will be accomplished by sequencing a diverse panel of trees for each species; these sequences will then be compared, and their genetic differences recorded. These procedures will yield gigantic datasets that will be analyzed at Johns Hopkins University, a process likely to require several months. The final results will be used to develop technologies to genotype trees that will be employed in the third year of the project.
Three (2019) In the third year of the project, full-genome studies of coast redwoods and giant sequoia will be conducted at the landscape scale. These surveys will utilize the genotyping technologies developed in Year Two, with the genomic information of each tree linked to the environmental variation of its specific site.

These initial field studies will establish the feasibility of our genomic survey techniques and point the way for other research groups conducting their own studies, contributing to an ever-expanding knowledge base that ultimately will be utilized by resource managers as they plan their conservation strategies.

Four (2020) Forest genetic inventories will be compiled as guides for restoration planning.
Five (2021) Initial genetic restoration projects will be implemented.

We thank Ralph Eschenbach and Carol Joy Provan for their generous lead gift to support the Redwood Genome Project.

You too can support this ambitious work to better understand redwood genetic diversity — it all starts with your gift to the Redwoods Genome Project.

Frequently Asked Questions

Expand All | Collapse All

Sequoia National Park
Sequoia National Park

How will genetic information on coast redwood and giant sequoia forests impact restoration and conservation activities?

Forestry decisions made on both public and private lands alter the genetic diversity of coast redwood and giant sequoia populations and can hamper the forests’ ability to adapt to environmental shifts such as climate change. Every timber harvest, reforestation planting and restoration thinning project thus affects the composition of the future forest, ultimately determining the forest’s health and resiliency. With genome sequencing and the genetic screening tools that we will develop, we’ll be able to rapidly assess forest genetic diversity to inform our management plans.

Why weren’t the genomes for coast redwood and giant sequoia been sequenced before now?

Full genome sequencing of conifers has not been possible until recently; however, we now have a reliable methodology for sequencing conifer genomes. Sequences for several California conifers, including Douglas fir and sugar pine, have been concluded by our research partners.

The massive size of the coast redwood genome (nearly 9 times larger than the human genome) posed particular challenges. Coast redwoods have six sets of large chromosomes. (Humans only have two.) In 2014, the University of California, Davis, granted $50,000 in pilot funding to Dr. David Neale to investigate the feasibility of sequencing the coast redwood genome; Neale determined it was indeed possible. This pilot effort produced a preliminary sequence for coast redwoods, pointing the way toward a functional coast redwood genomic sequence.

Is genetic research new for the League?

The genome project is our most ambitious genetic research program to date, but Save the Redwoods League has invested in genomic research since the 1990s. Genetic research will continue as a priority because genetics are fundamental to coast redwood and giant sequoia conservation.

What are the results from past League-sponsored genetic research?

Past League research grantees analyzed small sections of DNA called neutral genetic markers that enabled important early progress toward understanding the coast redwood and giant sequoia genomes. Through this method, our grantees discovered that small giant sequoia groves appear to be inbred; coast redwood tree “fairy rings” (circles of young redwoods around dead trees) are not always clones; and the southern coast redwood population is genetically distinct from the northern population.

Recent grantee Lakshmi Narayan of the University of California, Berkeley, uncovered a startling result during her doctoral research into coast redwood genetic clones in old-growth forests. Scanning the redwood trees at Big Basin Redwoods State Park for shared genetic markers, she discovered that genetic diversity was lowest in an old-growth stand where partial timber harvest occurred decades before.

Why is low genetic diversity a major conservation issue?

Low genetic diversity in a population of any species may be less resilient to stress caused by diseases, environmental changes, and other likely results of climate change. In such cases, there may not be enough individuals that can survive adverse events. In genetically diverse populations, however, individuals range significantly in their response to stress; the likelihood that tolerant individuals exist in the population increases. Therefore, a prime conservation objective for coast redwoods and giant sequoia is the protection — and if necessary, the enhancement — of forest genetic diversity.

What is the Redwood Genome Project?

The Redwood Genome Project will develop modern forest inventory tools based on genetic sequences that can be used by forest managers for the conservation and restoration of coastredwood (Sequoia sempervirens) and giant sequoia (Sequoiadendron giganteum) forests. The project has produced public reference genome sequences for coast redwood and giant sequoia; and will produce a database of genetic variation for the entire coast redwood and giant sequoia genomes; develop genotyping tools, including single nucleotide polymorphism (SNP) chips that can be used by resource managers to accurately, rapidly and inexpensively measure adaptive genetic variation in forest populations; compile forest genetic inventories for the guidance of restoration planning; and implement genetic restoration projects.

Who is leading the project?

Under the direction of League Science Director Dr. Emily Burns, this five-year project will be advanced by Dr. David Neale at the University of California, Davis, Dr. Steven Salzberg at Johns Hopkins University, and their research teams. A Science Advisory Board (composed of Science Committee members, forest geneticists and park managers), will provide guidance to ensure that the results benefit the conservation and restoration of coast redwood and giant sequoia forests.

How much will the project cost?

Costs over the five-year course of the project will total $2.6 million.

What will a successful Redwood Genome Project mean for the League?

This project along with other League-supported research programs will continue to educate and inform our community about redwoods and help us protect these natural wonders forever. Additionally, after the project is complete, we will have the tools in hand to answer many critical questions about the redwood forest, including:

  • Have past timber harvests inadvertently removed redwoods that may have been particularly well-suited for an era of climate change?
  • Where have plantings of industrial clones replaced natural genetic diversity with low-diversity redwood groves?
  • Which redwoods harbor “survival” genes for drought, disease or pest resistance, and thus warrant a targeted conservation effort?

About the Partners

Save the Redwoods League
League Science Director Emily Burns took her PhD from the University of California, Berkeley, and has been studying the redwood forest since 2004. Her doctoral studies focused on the physiological influence of fog on the plants of the redwood forest. Currently, much of her research centers on ferns, which she has determined are prime early markers for changing environmental conditions in redwood biomes.

University of California, Davis
David Neale and Alison Scott of UC Davis’ Department of Plant Sciences specialize forest tree genome sciences. Their research includes genome sequencing and genetic diversity studies related to breeding and conservation.

Johns Hopkins University
Johns Hopkins Biomedical Engineering Professor Steven Salzberg and his team conducted computational analyses of redwood and giant sequoia DNA for the Redwood Genome Project. During his career, Salzberg has developed software for a wide range of applications in the genomics field, including gene identification, genome assembly, sequencing, comparative genomics and evolutionary genomics. Hopkins Biomedical Engineering Professor Winston Timp is an expert on sequencing technology with particular expertise in nanopore sequencing methods.

Tags: , , , , , , , , , ,