Johns Hopkins teams up with U.C. Davis and Save the Redwoods League to sequence the first coast redwood genome

Steven Salzberg, Bloomberg Distinguished Professor of biomedical engineering, computer science, and biostatistics at Johns Hopkins University, collaborated with researchers from the University of California, Davis and Save the Redwoods League to successfully sequence the coast redwood and giant sequoia genomes. This marks the first major milestone of a five-year project to develop the tools needed to study the genomic diversity of these forest species.

At nearly nine times the size of the human genome, the coast redwood genome is now the second largest ever sequenced, with six sets of chromosomes (hexaploid) and 27 billion base pairs of DNA. The genome of the giant sequoia is roughly three times that of the human genome. The largest genome sequenced to date belongs to the axolotl, a North American salamander whose genome of 28.4 billion base pairs was completed in 2018. Like the human genome, the axolotl genome contains two sets of chromosomes (diploid).

“We pushed the boundaries of genome sequencing technology to take on the redwood and sequoia mega-genomes,” said Salzberg. “After using our specially developed algorithms to assemble these enormous and complex genome sequences, we have gained a new appreciation for how difficult it is to put together a hexaploid genome, especially one as large as the coast redwood’s.”

Over the last 150 years, 95 percent of the ancient coast redwood range and about one-third of the giant sequoia range have been logged. With this unprecedented loss of old trees and the addition of redwood clones often planted in their place, conservationists have grown concerned that the forests’ genomic diversity has fundamentally changed, which could leave the redwoods vulnerable to drought, fire, and other stressors related to climate change.

The redwood genome project was launched in late 2017, with a projected five-year timeline. By the end of the project, the genome sequences and the screening tools developed will allow field crews to quickly assess adaptive genomic diversity in redwood forests to inform management plans that restore the health and resilience of these forests throughout their natural ranges. With the genomes sequenced, the League will work to inventory diversity across the landscapes and identify both “hot spots” of genomic diversity for enhanced protection and areas of low diversity for restoration.

“Sequencing the coast redwood and giant sequoia genomes for the first time opens a new scientific frontier for our restoration projects,” said Sam Hodder, president and CEO of Save the Redwoods League. “This work will reveal the forests’ genetic identity so that we can protect the diversity that’s left, and in some areas, restore what was lost.”

During the next stage of the project, researchers will create a database capturing range-wide genomic variation within each species; develop genotyping tools that will allow resource managers to identify coast redwood and giant sequoia genetic variation while in the field; compile forest genetic inventories; and launch pilot restoration projects based on the accrued data.

“Our goal is to provide Save the Redwoods League and forest resource managers modern genomic tools to assist with the restoration of the redwood forest,” said David Neale, professor in the Department of Plant Sciences at the University of California, Davis. “Completing the sequences of the coast redwood and giant sequoia genomes is the first step and the foundation upon which everything gets built. In the next phase of our research, we’ll begin to uncover the amount of genetic variation that exists in redwood populations and associate that variation to the environments to which they’re adapted.”

The coast redwood and giant sequoia sequence data is now available to the scientific community at large.