The adaptive acquisition of single DNA segments drives metabolic evolution across<i>E. coli</i>lineages

Pang, Tin Yau; Lercher, Martin J.

doi:10.1101/148460

Cited by 2 publications

(1 citation statement)

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“…Defining microbial species is challenged by microbial diversity. Microbial diversity is attributable to the need of microorganisms to rapidly mutate to adapt to the environment under different environmental conditions [1]. Horizontal gene transfer is also a factor that affects microbial diversity, and as long as it is beneficial to survival, a transferred gene is retained [2].…”

Section: Introductionmentioning

confidence: 99%

A New Genome-to-Genome Comparison Approach for Large-Scale Revisiting of Current Microbial Taxonomy

et al. 2019

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Microbial diversity has always presented taxonomic challenges. With the popularity of next-generation sequencing technology, more unculturable bacteria have been sequenced, facilitating the discovery of additional new species and complicated current microbial classification. The major challenge is to assign appropriate taxonomic names. Hence, assessing the consistency between taxonomy and genomic relatedness is critical. We proposed and applied a genome comparison approach to a large-scale survey to investigate the distribution of genomic differences among microorganisms. The approach applies a genome-wide criterion, homologous coverage ratio (HCR), for describing the homology between species. The survey included 7861 microbial genomes that excluded plasmids, and 1220 pairs of genera exhibited ambiguous classification. In this study, we also compared the performance of HCR and average nucleotide identity (ANI). The results indicated that HCR and ANI analyses yield comparable results, but a few examples suggested that HCR has a superior clustering effect. In addition, we used the Genome Taxonomy Database (GTDB), the gold standard for taxonomy, to validate our analysis. The GTDB offers 120 ubiquitous single-copy proteins as marker genes for species classification. We determined that the analysis of the GTDB still results in classification boundary blur between some genera and that the marker gene-based approach has limitations. Although the choice of marker genes has been quite rigorous, the bias of marker gene selection remains unavoidable. Therefore, methods based on genomic alignment should be considered for use for species classification in order to avoid the bias of marker gene selection. On the basis of our observations of microbial diversity, microbial classification should be re-examined using genome-wide comparisons.

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Section: Introductionmentioning

confidence: 99%

A New Genome-to-Genome Comparison Approach for Large-Scale Revisiting of Current Microbial Taxonomy

et al. 2019

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Assessing the benefits of horizontal gene transfer by laboratory evolution and genome sequencing

2018

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BackgroundRecombination is widespread across the tree of life, because it helps purge deleterious mutations and creates novel adaptive traits. In prokaryotes, it often takes the form of horizontal gene transfer from a donor to a recipient bacterium. While such transfer is widespread in natural communities, its immediate fitness benefits are usually unknown. We asked whether any such benefits depend on the environment, and on the identity of donor and recipient strains. To this end, we adapted Escherichia coli to two novel carbon sources over several hundred generations of laboratory evolution, exposing evolving populations to various DNA donors.ResultsAt the end of these experiments, we measured fitness and sequenced the genomes of 65 clones from 34 replicate populations to study the genetic changes associated with adaptive evolution. Furthermore, we identified candidate de novo beneficial mutations. During adaptive evolution on the first carbon source, 4-Hydroxyphenylacetic acid (HPA), recombining populations adapted better, which was likely mediated by acquiring the hpa operon from the donor. In contrast, recombining populations did not adapt better to the second carbon source, butyric acid, even though they suffered fewer extinctions than non-recombining populations. The amount of DNA transferred, but not its benefit, strongly depended on the donor-recipient strain combination.ConclusionsTo our knowledge, our study is the first to investigate the genomic consequences of prokaryotic recombination and horizontal gene transfer during laboratory evolution. It shows that the benefits of recombination strongly depend on the environment and the foreign DNA donor.Electronic supplementary materialThe online version of this article (10.1186/s12862-018-1164-7) contains supplementary material, which is available to authorized users.

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The adaptive acquisition of single DNA segments drives metabolic evolution acrossE. colilineages

Cited by 2 publications

References 17 publications

A New Genome-to-Genome Comparison Approach for Large-Scale Revisiting of Current Microbial Taxonomy

A New Genome-to-Genome Comparison Approach for Large-Scale Revisiting of Current Microbial Taxonomy

Assessing the benefits of horizontal gene transfer by laboratory evolution and genome sequencing

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