Precise genotyping of circular mobile elements from metagenomic data uncovers human-associated plasmids with recent common ancestors.

ABSTRACT: Mobile genetic elements with circular genomes play a key role in the evolution of microbial communities. Their circular genomes correspond to circular walks in metagenome graphs, and yet, assemblies derived from natural microbial communities produce graphs riddled with spurious cycles, complicating the accurate reconstruction of circular genomes. We present DomCycle, an algorithm that reconstructs likely circular genomes based on the identification of so-called "dominant" graph cycles. In the implementation, we leverage paired reads to bridge assembly gaps and scrutinize cycles through a nucleotide-level analysis, making the approach robust to misassembly artifacts. We validated the approach using simulated and real sequencing data. Application of DomCycle to 32 publicly available DNA shot

SUBMITTER: Shalon N 

PROVIDER: S-EPMC9104695 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature