23andMe for Trees
January 4, 2018
Johns Hopkins researchers, in partnership with the University of California, Davis, and the Save the Redwoods League, have embarked on an ambitious plan to fully sequence the coast redwood and giant sequoia genomes for the first time.
Using a new genetic sequencing technology called the Oxford Nanopore MinION device, researchers hope to sequence and annotate the species’ genomes to help inform efforts to restore the health and resilience of the world’s forests.
“These trees can live for 2,000 to 3,000 years while the environment is changing around them. We want to understand what special genetic traits allow them to live so long and to grow so large,” says Steven Salzberg, Bloomberg Distinguished Professor of Biomedical Engineering, Computer Science, and Biostatistics at the Johns Hopkins University and director of the Center for Computational Biology in the McKusick-Nathans Institute of Genetic Medicine.
The coast redwood genome, estimated to contain 33 billion bases of DNA, is more than 10 times larger than the human genome and will be the largest ever sequenced. In the case of coast redwoods, the research will be especially demanding because their genome is hexaploid—it has six sets of chromosomes, unlike almost all other animals and plants, which have only two.
Researchers will use new nanopore technology to sequence large sections of the genome at once. “It’s a bit like putting together a puzzle,” says Winston Timp, assistant professor of biomedical engineering. “It’s the difference between putting together a complex jigsaw puzzle with tiny little pieces versus a puzzle with big pieces.”
Studies confirm that some trees are better at surviving drought, fire, pests, and diseases than others. By identifying the genes responsible for these adaptations, scientists can compile databases for entire forests that will aid resource managers as they plan long-term conservation strategies. “We want a 23andMe for trees,” explains Timp.