DNAnexus, the global leader in genome informatics and data management, today announced details of its collaboration with Dawe lab from University of Georgia, Hufford lab from Iowa State University, and Ware lab from Cold Spring Harbor Laboratory and the United States Department of Agriculture (USDA), to successfully complete de novo genome assembly for the maize population, which involves 26 cultivars found in the United States. DNAnexus provided a turnkey service that overcame challenges created by the complex nature of the maize genome and the need for scalability, delivering a 350-fold reduction in assembly time and 10-fold improvement in contiguity of reference genome quality.
This collaboration is significant because, by the end of this century it is estimated more than 11 billion people will inhabit the planet. The impacts of climate change, along with growing population, requires genetic-enabled agricultural improvements, similar to precision medicine in human health. Maize, being the world’s most important grain based on production volume, makes it a particularly critical crop to understand in order to support growing global demands.
“We leveraged DNAnexus and their xVantage Group to help us complete a population-level genome assembly for maize,” said Doreen Ware, PhD, Scientist & Adjunct Professor, USDA ARS and Cold Spring Harbor Laboratory. “The team really pushed the frontiers forward for us, allowing us to scale and optimize this particularly complex genome and utilize multiple technologies to deliver an exceptionally high-quality reference assembly. Leveraging this new knowledge of the maize genome, researchers can further improve maize yields, nutritional content and the plant’s resistance to negative effects of climate change, pests, and disease.”
Genome assembly for maize is particularly complex because of the plant’s repetitive and transposable elements that are constantly in flux. Similar in size to the human genome, two thirds of the maize genome is comprised of repeat regions, which requires heavy computational resources for accurate de novo assembly. Leveraging DNAnexus on Microsoft Azure, a variety of sequencing and assembly technologies were used in this collaboration, including PacBio SMRT long-read technology, Illumina short-reads, and BioNano optical mapping.
“This maize assembly project is a powerful example of how DNAnexus is being used to accelerate scientific discovery,” said Richard Daly, CEO at DNAnexus. “The next Green Revolution is going to be data-driven. And we’re proud to be the leading provider for genome assembly services in the world.”
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Data from the maize assembly will be presented at the International Plant and Animal Genome conference taking place January 12-16, 2019 in San Diego, California