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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 #379484
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

Author
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: Cold Spring Harbor Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 10/20/2020
Publication Date: 10/24/2020
Citation: Bickhart, D.M., Koren, S., Kolmogorov, M., Watson, M., Pevzner, P., Phillippy, A.M., Smith, T.P. 2020. Improving metagenome assemblies with long read sequence data. Cold Spring Harbor Meeting. October 20-24, 2020. Virtual Meeting.

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 (127 in total) than our rumen metagenome dataset. We also found that 44 of these contigs were predicted to be closed circles, representing the most closed, single-contig assemblies from a single sample to our knowledge.