To Dereplicate or Not To Dereplicate?

ABSTRACT 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...

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Autores principales:	Jacob T. Evans, Vincent J. Denef
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	MAG binning dereplication metagenomics population genomics software Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/59970f89bc9b44a7abe2121e3000f68c
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id	oai:doaj.org-article:59970f89bc9b44a7abe2121e3000f68c
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spelling	oai:doaj.org-article:59970f89bc9b44a7abe2121e3000f68c2021-11-15T15:30:14ZTo Dereplicate or Not To Dereplicate?10.1128/mSphere.00971-192379-5042https://doaj.org/article/59970f89bc9b44a7abe2121e3000f68c2020-06-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00971-19https://doaj.org/toc/2379-5042ABSTRACT 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.Jacob T. EvansVincent J. DenefAmerican Society for MicrobiologyarticleMAGbinningdereplicationmetagenomicspopulation genomicssoftwareMicrobiologyQR1-502ENmSphere, Vol 5, Iss 3 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	MAG binning dereplication metagenomics population genomics software Microbiology QR1-502
spellingShingle	MAG binning dereplication metagenomics population genomics software Microbiology QR1-502 Jacob T. Evans Vincent J. Denef To Dereplicate or Not To Dereplicate?
description	ABSTRACT 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.
format	article
author	Jacob T. Evans Vincent J. Denef
author_facet	Jacob T. Evans Vincent J. Denef
author_sort	Jacob T. Evans
title	To Dereplicate or Not To Dereplicate?
title_short	To Dereplicate or Not To Dereplicate?
title_full	To Dereplicate or Not To Dereplicate?
title_fullStr	To Dereplicate or Not To Dereplicate?
title_full_unstemmed	To Dereplicate or Not To Dereplicate?
title_sort	to dereplicate or not to dereplicate?
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/59970f89bc9b44a7abe2121e3000f68c
work_keys_str_mv	AT jacobtevans todereplicateornottodereplicate AT vincentjdenef todereplicateornottodereplicate
_version_	1718427886574108672

To Dereplicate or Not To Dereplicate?

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