Salzberg and Timp among research collaboration to sequence the Redwood genome
September 27, 2017
Steven Salzberg, Bloomberg Distinguished Professor of Biomedical Engineering, and Winston Timp, assistant professor of biomedical engineering, are among the researchers from Johns Hopkins collaborating with the University of California, Davis, and the Save the Redwoods League in 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 genomes of these two species. The tree genomes will help to inform efforts to restore the health and resilience of these forests throughout their natural ranges as they face environmental stressors such as climate change.
“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 Salzberg.
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 when it is finished. Though initial research from David Neale at the University of California, Davis, determined that sequencing the redwood genome is feasible, in the case of coast redwoods, the research will be especially demanding because their genome is hexaploid. This means that it has six sets of chromosomes, unlike almost all other animals and plants, which have only two.
Researchers will tackle this complex task by using the nanopore technology to sequence large sections of the genome at once. “It’s a bit like putting together a puzzle,” says Timp. “It’s the difference between putting together a complex jigsaw puzzle with tiny little pieces versus a puzzle with big pieces.”
Learn more on Johns Hopkins Medicine.
Learn more about Salzberg’s genome work in JHU Engineering.