To Dereplicate or Not To Dereplicate?

Metagenome-assembled genomes (MAGs) expand our understanding of microbial diversity, evolution, and ecology. Concerns have been raised on how sequencing, assembly, binning, and quality assessment tools may result in MAGs that do not reflect single populations in nature. Here, we reflect on another i...

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Bibliographic Details
Published in:mSphere 2020-05, Vol.5 (3)
Main Authors: Evans, Jacob T, Denef, Vincent J
Format: Article
Language:English
Subjects:
binning
dereplication
Ecological and Evolutionary Science
Editor's Pick
MAG
metagenomics
Opinion/Hypothesis
population genomics
software
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Summary:Metagenome-assembled genomes (MAGs) expand our understanding of microbial diversity, evolution, and ecology. Concerns have been raised on how sequencing, assembly, binning, and quality assessment tools may result in MAGs that do not reflect single populations in nature. Here, we reflect on another issue, i.e., how to handle highly similar MAGs assembled from independent data sets. Obtaining multiple genomic representatives for a species is highly valuable, as it allows for population genomic analyses; however, when retaining genomes of closely related populations, it complicates MAG quality assessment and abundance inferences. We show that (i) published data sets contain a large fraction of MAGs sharing >99% average nucleotide identity, (ii) different software packages and parameters used to resolve this redundancy remove very different numbers of MAGs, and (iii) the removal of closely related genomes leads to losses of population-specific auxiliary genes. Finally, we highlight some approaches that can infer strain-specific dynamics across a sample series without dereplication.
ISSN:2379-5042
2379-5042
DOI:10.1128/mSphere.00971-19