KU team plans US network for high-quality reference genome sequencing

LAWRENCE — In the United States, a mere sliver of the nation’s biodiversity has been recorded using high-quality reference genomes. Beyond giving a better understanding of biodiversity and ecosystems, data from high-quality reference genomes can enable scientific advances in conservation, agriculture, pest and disease control, medicine and biotechnology.

Now, investigators from the University of Kansas — where genomics are prioritized as a research focus — are making detailed plans for a national reference genome infrastructure with support from the National Science Foundation. Teaming with lead institution Rockefeller University and partner institution Arizona State University, the three-year, $11.9 million planning grant will enable researchers to envision and assemble new American genomic infrastructure.

The project is called Scalable Community Infrastructure for Biodiversity Genomics (SCIBG).

“This project advances creating a library of life on Earth that’s comprehensive and thorough at the genomic level,” said Nico Franz, Krishtalka Director of the KU Biodiversity Institute and Natural History Museum, and professor of ecology & evolutionary biology, who is leading KU's contribution to the project.

Franz’s KU collaborators are Lena Hileman, professor and chair of the Department of Ecology & Evolutionary Biology, and Paulyn Cartwright, Baumgartner Professor of Biology in the Department of Ecology & Evolutionary Biology. The KU team will contribute heavily to the project’s specimen-collection and biodiversity data systems. Its primary focus will be on regionally occurring species of plants, fungi, insects and other invertebrate groups.

According to Franz, the vast majority of biodiversity lacks reference genomes — detailed, high-quality records of an organism’s genetic material. These genomes, typically produced using both DNA and RNA from fresh biological samples, give researchers across a range of disciplines and industries far more information than partial genomic sequences.

The KU team will help envision a nationwide pipeline providing the U.S. scientific community the opportunity to nominate species for sequencing at much lower costs and under a transparent, ethical species selection and governance structure.

“Generating reference genomes remains a moving goal, especially for the broader diversity of species or biodiversity,” Franz said. “In the U.S., depending on certain counts, there are hundreds of thousands of species that could potentially be sequenced and for which a reference genome could be produced.”

The KU researcher said today efforts to produce reference genomes can be costly and fragmented, with inconsistencies in sampling, preservation, and sample and data management practices.

“This project requires a high level of coordination between the lead institutions but also a level of access for national research communities that just hasn't been there so far,” Franz said.

The NSF support for the design phase will result in plans for a scalable, coordinated nationwide system, with a potential five-year implementation phase to follow. Franz said the project aims to build the capacity to produce reference genomes at a vastly larger scale, with a long-term goal of 60 genomes each week.

“More than 25 years ago, there were major efforts to produce a first complete human genome,” he said. “Today, we have 100-200 reference genomes for bee species, for example — but there are more than 21,000 bee species documented worldwide.”

The end result would be a much broader and more representative sampling of biodiversity, according to Franz.

KU’s team will collect specimens primarily at Konza Prairie Biological Station near Manhattan and the KU Field Station, Franz added. KU will produce more than half the samples in the project's internally prioritized sequencing pipeline.

Another role for the KU researchers will involve making the high-quality reference genomes broadly accessible to researchers and the public. The team will produce a public-facing digital tool based on an existing biodiversity specimen-data platform called Symbiota, a KU-housed project.

“The future SCIBG Symbiota portal will display species and samples that have already been sequenced alongside others that are prioritized for new sequencing and publication. There will be high-quality photos, descriptions and other information that promotes the high standards of our biodiversity collections community,” Franz said.

Franz said an eventual national infrastructure producing high-quality reference genomes would boost research into evolution, species conservation, agriculture, medicine and biotechnology.