RT Journal Article
SR Electronic
T1 Generation of lineage-resolved complete metagenome-assembled genomes by precision phasing
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.05.04.442591
DO 10.1101/2021.05.04.442591
A1 Derek M. Bickhart
A1 Mikhail Kolmogorov
A1 Elizabeth Tseng
A1 Daniel M. Portik
A1 Anton Korobeynikov
A1 Ivan Tolstoganov
A1 Gherman Uritskiy
A1 Ivan Liachko
A1 Shawn T. Sullivan
A1 Sung Bong Shin
A1 Alvah Zorea
A1 Victòria Pascal Andreu
A1 Kevin Panke-Buisse
A1 Marnix H. Medema
A1 Itzik Mizrahi
A1 Pavel A. Pevzner
A1 Timothy P.L. Smith
YR 2021
UL http://biorxiv.org/content/early/2021/05/04/2021.05.04.442591.abstract
AB Microbial communities in many environments include distinct lineages of closely related organisms which have proved challenging to separate in metagenomic assembly, preventing generation of complete metagenome-assembled genomes (MAGs). The advent of long and accurate HiFi reads presents a possible means to address this challenge by generating complete MAGs for nearly all sufficiently abundant bacterial genomes in a microbial community. We present a metagenomic HiFi assembly of a complex microbial community from sheep fecal material that resulted in 428 high-quality MAGs from a single sample, the highest resolution achieved with metagenomic deconvolution to date. We applied a computational approach to separate distinct haplotype lineages and identified haplotypes of hundreds of variants across hundreds of kilobases of genomic sequence. Analysis of these haplotypes revealed 220 lineage-resolved complete MAGs, including 44 in single circular contigs, and demonstrated improvement in overall assembly compared to error-prone long reads. We report the characterization of multiple, closely-related microbes within a sample with potential to improve precision in assigning mobile genetic elements to host genomes within complex microbial communities.Competing Interest StatementET and DMP are employees of Pacific Biosciences. GU, IL and STS are employees of Phase Genomics. All other authors have no competing interests.