Slightly beneficial genes are retained by evolving Horizontal Gene Transfer despite selfish elements

Dijk, Bram van; Hogeweg, Paulien; Doekes, Hilje M.; Takeuchi, Nobuto

doi:10.1101/2020.02.13.947077

Cited by 2 publications

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“…Whether HGT is a continuous process on evolutionary time scales or instead occurs in bursts has been a matter of debate (Rivera et al, 1998;Jain et al, 1999;Wolf and Koonin, 2013), and bursts of transfer events at some point in the past might explain some of the deviations from the −3 power-law behaviour we observe (Figure 5). In addition to HGT bursts, other complex evolutionary mechanisms that we do not consider in our model could in theory explain those deviations, including mechanisms of gene loss that allow bacteria to eliminate detrimental genes, or selfish genetic elements (van Dijk et al, 2020). Finally, the RefSeq database is expected to contain misclassifications of contigs.…”

Section: Discussionmentioning

confidence: 99%

Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain

Sheinman

Arkhipova

Arndt

et al. 2021

eLife

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Horizontal Gene Transfer (HGT) is an essential force in microbial evolution. Despite detailed studies on a variety of systems, a global picture of HGT in the microbial world is still missing. Here, we exploit that HGT creates long identical DNA sequences in the genomes of distant species, which can be found efficiently using alignment-free methods. Our pairwise analysis of 93 481 bacterial genomes identified 138 273 HGT events. We developed a model to explain their statistical properties as well as estimate the transfer rate between pairs of taxa. This reveals that long-distance HGT is frequent: our results indicate that HGT between species from different phyla has occurred in at least 8% of the species. Finally, our results confirm that the function of sequences strongly impacts their transfer rate, which varies by more than 3 orders of magnitude between different functional categories. Overall, we provide a comprehensive view of HGT, illuminating a fundamental process driving bacterial evolution.

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Section: Discussionmentioning

confidence: 99%

Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain

Sheinman

Arkhipova

Arndt

et al. 2021

eLife

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show abstract

“…5). In addition to HGT bursts, other complex evolutionary mechanisms that we do not consider in our model could in theory explain those deviations, including mechanisms of gene loss that allow bacteria to eliminate detrimental genes, or selfish genetic elements [72]. Finally, misclassifications of contigs as well as errors in genome assembly could bias the estimation of the effective HGT rate A.…”

Section: Discussionmentioning

confidence: 99%

Long identical sequences found in multiple bacterial genomes reveal frequent and widespread exchange of genetic material between distant species

Sheinman

Arkhipova

Arndt

et al. 2020

Preprint

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Horizontal transfer of genomic elements is an essential force that shapes microbial genome evolution. This process occurs via various mechanisms and has been studied in detail for a variety of biological systems.However, a coarse-grained, global picture of horizontal gene transfer (HGT) in the microbial world is still missing. One reason is the difficulty to process large amounts of genomic microbial data to find and characterize HGT events, especially for highly distant organisms. Here, we exploit that HGT between distant species creates long identical DNA sequences in distant species, which can be found efficiently using alignment-free methods. We analyzed over 90, 000 bacterial genomes and thus identified over 100, 000 events of HGT. We further develop a mathematical model to analyze the statistical properties of those long exact matches and thus estimate the transfer rate between any pair of taxa. Our results demonstrate that long-distance gene exchange (across phyla) is very frequent, as more than 8% of the bacterial genomes analyzed have been involved in at least one such event. Finally, we confirm that the function of the transferred sequences strongly impact the transfer rate, as we observe a 3.5 order of magnitude variation between the most and the least transferred categories. Overall, we provide a unique view of horizontal transfer across the bacterial tree of life, illuminating one fundamental process driving bacterial evolution.Microbial genomes are subject to loss and gain of genetic material from other organisms [5, 59], via 2 a variety of mechanisms: conjugation, transduction, and transformation, collectively known as horizontal 3 gene transfer (HGT) [69, 26]. The exchange of genetic material is a key driver of microbial evolution that 4 allows rapid adaptation to local niches [6]. Gene acquisition via HGT can provide microbes with adaptive 5 traits, conferring a selective advantage in particular conditions [34, 42] and eliminate deleterious mutations, 6 resolving Muller's ratchet paradox [70]. 7Since the discovery of HGT more than 50 years ago [24] many cases of HGT have been intensively 8 studied. Several methods to infer HGT rely on identifying shifts in (oligo-)nucleotide compositions along 9 genomes [62]. Other methods are based on discrepancies between gene and species distances, i.e., sur-10 prising similarity between genomic regions belonging to distant organisms that cannot be satisfactorily 11 explained by their conservation [38, 49, 35, 51, 18, 19, 9]. For example, genomes from different genera are 12 typically up to 60 − 70% identical, meaning that one in every three base pairs is expected to differ. The 13 presence of regions in different genomes that are significantly more similar than expected can, therefore, be 14 interpreted as recent HGT events. Using such methods the transfer of drug-and metal-resistance genes [31], 15 toxin-antitoxin systems [72] and virulence factors [22, 50] have been observed numerous times. It is also 16 known that some bacterial taxa, such as members of t...

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Slightly beneficial genes are retained by evolving Horizontal Gene Transfer despite selfish elements

Cited by 2 publications

References 79 publications

Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain

Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain

Long identical sequences found in multiple bacterial genomes reveal frequent and widespread exchange of genetic material between distant species

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