Earth Day 2019: How 10x Genomics technology is helping to “Protect Our Species”
Each year on April 22, we celebrate Earth Day, the largest civic-minded day of action in the world, with more than one billion people in 192 countries participating. A different theme is chosen for each Earth Day, and this year—the 49th celebration—the campaign is “Protect Our Species.”
According to Earth Day Network, “the world is facing the greatest rate of extinction since we lost the dinosaurs more than 60 million years ago. But unlike the fate of the dinosaurs, the rapid extinction of species in our world today is the result of human activity.” The 2019 campaign urges us all to work together to protect endangered and threatened species including bees, coral reefs, elephants, giraffes, whales, and others.
We are doing our part in this worldwide conservation effort, with Linked-Read technology that turns standard short reads into long-range information, helping researchers make the most out of even very limited samples from endangered and threatened species. For example, our de novo Assembly Solution, powered by Supernova 2.0 software, enables high quality, cost-effective de novo assemblies at scale for plants and animals using as little as 1 ng of input DNA.
Our tools are being used in several exciting new sequencing studies that focus on genetic diversity and conservation among plants and animals. Last year, we partnered with the CanSeq 150 Initiative, an effort led by Canada’s Genomics Enterprise (CGEn) that aims at sequencing 150 new genomes. The initiative was launched in honor of Canada’s 150th birthday and will focus on groundbreaking conservation and biodiversity research. Through the partnership, CGEn plans to produce high quality de novo assemblies of genetically unexplored genomes using data generated by 10x Genomics’ Linked-Reads technology and the Chromium de novo Assembly Solution. Our de novo Assembly Solution is also a part of the Genome 10K (G10K) Consortium’s Vertebrate Genome Project. The project’s goal is to create reference quality genome assemblies of 260 species that represent all vertebrate orders, creating a significant resource for life sciences research and worldwide conservation efforts.
We also joined the Sanger Institute’s 25 Genomes Project last year. Our technology will help as they sequence the genomes of 25 UK species and gain a better understanding of biodiversity in the country. Further, the resulting research will allow biologists to discover better ways to protect the sequenced species, aiding in future conservation efforts. The DNA sequences of these animals, birds, fish, insects, and plants will be made available to all scientists for use in their research at no cost.
Endangered species research efforts are similarly using our tools. In late 2017, it was announced that researchers had used our Chromium System to create the first assembly of the African wild dog genome, a threatened species. Critical to the work was linked long-read technology, and the team of researchers (including scientists from Stanford University, the country of Zimbabwe, and 10x Genomics) used the 10x Genomics Chromium system and Supernova Assembler to create assemblies for three individual African wild dogs. The authors concluded that with the availability of reference genomes, they can improve genetic monitoring of threatened species. The genomes can also help researchers and conservationists to better understand the ecology and adaptability of those species in a changing environment.
And this post would not be complete without mentioning Benny the monk seal. Using a blood sample from this celebrity marine mammal, Alan F. Scott and David Mohr of the John Hopkins School of Medicine, Genetic Resources Core Facility, sequenced Benny’s DNA using the 10x de novo Assembly Solution. The Supernova Assembler was applied to the sequence data, producing remarkably long scaffold lengths (N50s of nearly 30 Mb) and providing new insights into the endangered monk seal population of Hawaii.
Last year we also reported on the fruitful collaboration between Canadian scientists and the Vancouver Aquarium to construct beluga whale and Northern sea otter reference genomes. As with monk seals, these arctic sea mammals are designated at-risk, so assembly of their genomes are valuable contributions to conservation efforts. The project relied on our Linked-Read sequencing solutions and Supernova Assembler, and it was published in the December 2017 issue of Genes (Jones et al. 2017; Jones et al. 2017). As the authors explained, availability of these genomes may allow them to more quickly identify genetic factors that provide disease resistance in rapidly changing habitats.
We are so happy to be a part of these genome sequencing and assembly projects that are taking steps to Protect Our Species this Earth Day. Next year, Earth Day will celebrate its 50th anniversary, and we look forward to reporting on even more progress. Big plans are in place for this milestone celebration, and there’s no doubt 10x Genomics will continue to play a valuable role in conservation biology efforts.