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ARS Home » Midwest Area » Madison, Wisconsin » U.S. Dairy Forage Research Center » Cell Wall Biology and Utilization Research » Research » Publications at this Location » Publication #374286

Research Project: Investigating Microbial, Digestive, and Animal Factors to Increase Dairy Cow Performance and Nutrient Use Efficiency

Location: Cell Wall Biology and Utilization Research

Title: Improving metagenome assemblies with long read sequence data

item Bickhart, Derek
item KOREN, SERGEY - National Institutes Of Health (NIH)
item KOLMOGOROV, MIKHAIL - University Of California, Davis
item WATSON, MICK - Roslin Institute
item PEVZNER, PAVEL - University Of California, Davis
item PHILLIPPY, ADAM - National Institutes Of Health (NIH)
item Smith, Timothy - Tim

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 4/27/2020
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Metagenome assembly is a nascent field that still requires heavy investment in new technologies and algorithms. Prior state of the art used high depths of coverage of shorter, lower error sequence reads as a basis; however, this approach left the user with highly fragmented microbial genome assemblies. In this presentation, we pioneer the use of longer sequence reads in metagenome assembly and demonstrate that this new technology provides better resolution of genomes and new biological insights into complex communities. For example, we identified 188 novel bacterial-viral interactions in a rumen metagenome dataset. We also demonstrate one of the first uses of high fidelity (HiFi) PacBio circular consensus sequencing reads in a sheep hind-gut sample. HiFi reads appear to better resolve this community and this assembly contained 14-fold more near-complete microbial genomes (140 in total) than our rumen metagenome dataset. We are still investigating the use of this new technology for future applications, but the current results suggest that it will help resolve genomes for low abundance strains in the community.