Abstract
Assembling complete or near complete genomes from complex microbial communities remains a significant challenge in metagenomic studies. Recent developments in single cell amplified genomes (SAGs) have enabled the sequencing of individual draft genomes representative of uncultivated microbial populations. SAGs suffer from incomplete and uneven coverage due to artifacts that arise from multiple displacement amplification techniques. Conversely, metagenomic sequence data does not suffer from the same biases as SAGs, and significant improvements have been realized in the recovery of draft genomes from metagenomes. Nevertheless, the inherent genomic complexity of many microbial communities often obfuscates facile generation of population genome assemblies from metagenomic data. Here we describe a new method for metagenomic-guided SAG assembly that leverages the advantages of both methods and significantly improves the completeness of initial SAGs assemblies. We demonstrate that SAG assemblies of two cosmopolitan marine lineages–Marine Group 1 Thaumarchaeota and SAR324 clade bacterioplankton–were substantially improved using this approach. Moreover, the improved assemblies strengthened biological inferences. For example, the improved SAR324 clade genome assembly revealed the presence of many genes in phenylalanine catabolism and flagellar assembly that were absent in the original SAG.
Highlights
An enormous amount of microbial biodiversity on Earth is comprised of lineages that cannot be cultivated using traditional techniques and have been largely inaccessible to laboratory analysis (Staley and Konopka, 1985; Pace, 1997; Hugenholtz et al, 1998)
Single-cell genomics can be leveraged to produce partial genome assemblies from microbial cells collected from complex environments, but assembling near-complete genomes is complicated by highly biased genome coverage resulting from multiple displacement amplification (MDA; Hedlund et al, 2014)
The success of our method varied across the three SAR324 improved SAG (iSAG) (SAG) analyzed, and overall our results provide useful examples of the advantages and limitations of using metagenomic data for the improvement of assemblies generated from single-cell sequencing
Summary
An enormous amount of microbial biodiversity on Earth is comprised of lineages that cannot be cultivated using traditional techniques and have been largely inaccessible to laboratory analysis (Staley and Konopka, 1985; Pace, 1997; Hugenholtz et al, 1998). To facilitate the integration of these methods we developed a workflow for the combination of single-cell genomic and metagenomic data that can be used to assemble improved draft genomes from environmental samples.
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