HiFi based metagenomic assembly strategy provides accuracy near isolated genome resolution in MAG assembly
Feilong Deng, Yanhua Han, Minghui Li, Yunjuan Peng, Jianmin Chai, Guan Yang, Ying Li, Jiangchao Zhao
Abstract
Recovering high-contiguity, circular bacterial genomes from complex microbiomes (e.g., gut) is challenged by limitations of short-read and error-prone long-read sequencing. This study comprehensively compares PacBio High-Fidelity (HiFi) sequencing-based metagenome-assembled genomes (MAGs) against Illumina MAGs, Oxford Nanopore Technologies (ONT) MAGs, and isolate whole-genome sequencing genomes from the same sample. HiFi sequencing yielded 31 high-quality MAGs, including 10 complete circular genomes. HiFi MAGs demonstrated significantly higher completeness, continuity, and lower contamination than Illumina or ONT MAGs (p-adj < 0.05). Crucially, HiFi MAGs exhibited closer genomic proximity to corresponding isolates at both single-nucleotide polymorphism and gene presence/absence levels. This benchmarking establishes HiFi as a robust approach for generating MAGs rivaling isolated genome quality, providing critical insights for accurate microbial genomic studies.