Conserving genetic diversity of ancient, towering California trees

ALEXA FONTANILLA / AGGIE

Coast redwood, giant sequoia tree genomes to be fully sequenced by UC Davis, Johns Hopkins research partnership

Scientists are going to learn much more about the coast redwood and giant sequoia trees over the next five years. Save the Redwoods League is partnering with UC Davis and Johns Hopkins University to fully sequence the genome of these two colossal California trees. The completed genome would be the longest assembled.

Coast redwood groves stretch along much of the Pacific coast of California. These trees are the tallest organisms in the world, with some individuals reaching over 100 meters in height. Giant sequoias live in much smaller habitats in the western portions of the Sierra Nevada mountain range. They are considered the largest trees by measure of mass or volume, with heights over 75 meters and diameters over 7 meters. Both live long lifespans and can thrive for centuries, with some remarkable trees known to have lived for over 2,500 years.

The two trees under study are close relatives among the order Pinales, comprised of conifer trees like pines which produce cones for reproductive purposes. Although the coast redwood is present in greater numbers than the giant sequoia, both are considered endangered species. Conservation efforts are being made to restore the old-growth forests which were cut down to create wooden structures for human civilization, especially in San Francisco.

“For conservation of the redwood forest, protecting genetic diversity is key and the sequences generated through this partnership will provide a new perspective that will enable us to ensure we are protecting genetic diversity throughout the forest ecosystems,” said Dr. Emily Burns, the director of science at Save the Redwoods League and one of the research project partners, in an email interview.

The initial phase of the project is to sequence the genome of an individual redwood and sequoia to serve as a representative model.

“The first reference sequence will come from leaves and seeds from one giant sequoia (from Sequoia National Park) and one coast redwood (from Butano State Park),” Burns said. “In the second year of the project, 10 more sequences will be generated of each species from trees ranging in seed origin and physical traits. These trees have not been selected yet.”

The best reference trees will be healthy and actively producing cones and seeds for collection purposes. Trees showing evidence of disease or insect damage would be avoided.

“We can look for genes, but figuring out variants which are drought tolerant or disease resistant is really the next step — where we use the reference genome, then just sample specific potential target areas in many different trees to see what variation there is in the genome and how it’s associated with these phenotypes,” said Dr. Winston Timp, a professor of biomedical engineering at Johns Hopkins and one of the research project partners, in an email interview.

Working with a complete genome of the coast redwood and giant sequoia will help the researchers plan and maintain diverse groves when planting or culling trees.

“Having a genome sequence of an organism is essentially the parts list,” said Dr. David Neale, a professor of plant science at UC Davis and one of the research project partners. “Why do we sequence the human genome? Now we have the parts list. We understand all the genes that make up life. The more you understand, the better you can do in terms of treating this organism.”

The initial sequencing will be completed at UC Davis. Johns Hopkins researchers will be performing other types of sequencing work, compiling millions of genetic puzzle pieces together to form the full genome assembly.

“The team at Hopkins, their specialty is bioinformatics, and they do what is called the genome assembly,” Neale said. “We take DNA, we put it in a machine, we generate sequences, but it’s all these little pieces that have to be put together to get a continuous structure. This is a big computationally heavy exercise that they’re some of the best at the world at.”

Only recently has the technology existed to perform such complicated analyses. Nanopore sequencing feeds DNA strands through pores on the scale of a nanometer in size to analyze genetic sequences. Illumina sequencing uses dyes and fluorescent lighting to identify each base pair. Depending on the sequencing technique used, the scale of the genetic puzzle can be drastically different.

“If the redwood genome is ~39Gb, or 39 billion bases, and we break it into pieces about 10,000 bp long to sequence on the nanopore, we need about 4 million fragments to cover it even once!” Timp said. “But it’s even worse when you use the more conventional Illumina sequencing where the reads are only on the order of 100 bases long — there it’s ~400 million pieces”

Just 10 years ago, the redwood and sequoia genomes would be too tough to tackle. Improved automation of sequence methods have made this project more reasonable.

“Prof. David Neale at UC Davis and his colleagues are the world’s experts on sequencing conifer genomes and were bold enough to tackle the large coast redwood genome – no small task given it’s 10x larger than the human genome and will be the largest genome sequenced once done,” Burns said.

Although redwoods and sequoias are now only found in restricted habitats in California, physical evidence shows these trees were more widespread in previous millennia.

“If you look at fossils, you can see there was once a great diversity of redwoods, and that redwoods used to live all over the Northern Hemisphere,” said Dr. Alison Scott, a postdoctoral researcher in plant science at UC Davis working on this project. “But over time, their ranges have shifted, and those lineages have shrunk to the point that now there’s only one representative species and three lineages.”

Complete sequences will be needed for the next phases of the project, which involve identifying small differences in genetic structure which may have beneficial effects in the trees.

“In theory, we’d be able to not only look at the genetic diversity, but we’d be able to also say something about, ‘this genotype is more drought tolerant than this one,’” Scott said.

The end goal of the project is to use the completed coast redwood and giant sequoia genome to better understand how to boost genetic diversity and help preserve the forests for the future.

 

Written by: George Ugartemendia — science@theaggie.org