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

Butano State Park
Butano State Park

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. This five-year effort will sequence the coast redwood and giant sequoia genomes and develop tools to assess genetic diversity. The tools will inform management plans to help these species thrive in the coming centuries.

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 know the complete genomes of Sequoia sempervirens and Sequoiadendron giganteum. By obtaining this 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. We are now ready to sequence the coast redwood and giant sequoia genomes. Though the technology for conifer genomic sequencing is refined, sequencing these two signature species will remain a challenge, particularly for coast redwoods. To date, all the conifers that have been sequenced are 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:

 

YEAR 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 Dendrome 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 visionary and generous lead gift to support the Redwood Genome Project.


Frequently Asked Questions

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Sequoia National Park
Sequoia National Park
How will genetic information on coast redwood and giant sequoia forests impact restoration and conservation activities?
Why haven’t the genomes for coast redwood and giant sequoia been sequenced yet?
Is genetic research new for the League?
What are the results from past League-sponsored genetic research?
Why is low genetic diversity a major conservation issue?
What is the Redwood Genome Project?
Who will lead the project?
When does the project start?
How much will the project cost?
What will a successful Redwood Genome Project mean for the League?

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. They are principal investigators in the Dendrome Project, a collaborative effort to compile genome databases for forest tree species.

Johns Hopkins University
Johns Hopkins Biomedical Engineering Professor Steven Salzberg and his team will conduct 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.


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