RAREFAN: A webservice to identify REPINs and RAYTs in bacterial genomes

Fortmann-Grote, Carsten; Balk, Julia; Bertels, Frederic

doi:10.1101/2022.05.22.493013

Cited by 3 publications

(2 citation statements)

References 28 publications

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“…REP and REPIN sequences were identified within bacterial species using a specific program that is available through a webserver (http://rarefan.evolbio.mpg.de). [ 64 ]…”

Section: Methodsmentioning

confidence: 99%

“…REP and REPIN sequences were identified within bacterial species using a specific program that is available through a webserver (http:// rarefan.evolbio.mpg.de). [64] REP sequence groups were identified using a previously described procedure. [19] First, we extracted all 21 bp long sequences that occurred more than 55 times in the genome (P. chlororaphis TAMOak81, and Neisseria meningitidis 2594).…”

Section: Identifying Repins In Bacterial Genomesmentioning

confidence: 99%

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Ancient Darwinian replicators nested within eubacterial genomes

Bertels

Rainey

2022

BioEssays

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Integrative mobile genetic elements (MGEs), such as transposons and insertion sequences, propagate within bacterial genomes, but persistence times in individual lineages are short. For long-term survival, MGEs must continuously invade new hosts by horizontal transfer. Theoretically, MGEs that persist for millions of years in single lineages, and are thus subject to vertical inheritance, should not exist. Here we draw attention to an exception -a class of MGE termed REPIN. REPINs are nonautonomous MGEs whose duplication depends on non-jumping RAYT transposases. Comparisons of REPINs and typical MGEs show that replication rates of REPINs are orders of magnitude lower, REPIN population size fluctuations correlate with changes in available genome space, REPIN conservation depends on RAYT function, and REPIN diversity accumulates within host lineages. These data lead to the hypothesis that REPINs form enduring, beneficial associations with eubacterial chromosomes. Given replicative nesting, our hypothesis predicts conflicts arising from the diverging effects of selection acting simultaneously on REPINs and host genomes. Evidence in support comes from patterns of REPIN abundance and diversity in two distantly related bacterial species. Together this bolsters the conclusion that REPINs are the genetic counterpart of mutualistic endosymbiotic bacteria.

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“…REP and REPIN sequences were identified within bacterial species using a specific program that is available through a webserver (http://rarefan.evolbio.mpg.de). [ 64 ]…”

Section: Methodsmentioning

confidence: 99%

Section: Identifying Repins In Bacterial Genomesmentioning

confidence: 99%

Ancient Darwinian replicators nested within eubacterial genomes

Bertels

Rainey

2022

BioEssays

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Ancient Darwinian replicators nested within eubacterial genomes

Bertels

Rainey

2021

Preprint

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Relationships among organisms, in which one lives inside of another, with benefits accruing to both partners, are referred to as endosymbiotic. Such relationships are common in the biological world, yet descriptions are confined to organismal life. Here we argue that short sequence repeats known as REPINs – whose replication is dependent on a non-jumping RAYT transposase – form a similar facultative symbiotic relationship with the bacterial chromosome. Evidence stems from distribution patterns across the eubacteria: persistence times of many millions of years, exceedingly rare duplication rates, vertical transmission, and population biology typical of living organisms, including population size fluctuations that correlate with available genome space. Additional analysis of patterns of REPIN evolution conform with theoretical predictions of conflict (and resolution) arising from the effects of selection operating simultaneously on REPINs and host cells. A search for similar kinds of genomic symbionts suggests that the REPIN-RAYT system is not unique.

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REPORTH: Determining orthologous locations of repetitive sequences between genomes

Bharadwaj,

van Dijk,

Bertels

2024

Preprint

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Repetitive sequences are a common feature of bacterial genomes. Some repetitive sequences such as REPINs are mobile within the genome but inherited only vertically from mother to daughter across bacterial genomes. Selfish elements in contrast are mobile within the genome but also travel horizontally from genome to genome. Yet, no matter the nature of the association between the repetitive elements and the host, it is difficult to study the evolutionary dynamics of repetitive sequences across genomes. If it is unclear whether two sequences in two different genomes are in orthologous positions, it is difficult to infer parameters like the replication rate, horizontal transfer rate and rate of loss. Here we present a tool to facilitate these analyses called REPORTH. REPORTH determines whether repetitive sequences in different but closely related bacterial genomes occur in orthologous genomic positions. Whether a position is orthologous or not depends on the orthology of flanking sequences. Flanking sequences are deemed orthologous if they are bidirectional best hits. All repetitive sequences that are found in orthologous positions across different genomes are grouped together. Analyses of these groups can be used to study the evolutionary dynamics of selfish repetitive elements such as insertion sequences, but also for mutualistic repetitive elements such as REPINs.

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RAREFAN: A webservice to identify REPINs and RAYTs in bacterial genomes

Cited by 3 publications

References 28 publications

Ancient Darwinian replicators nested within eubacterial genomes

Ancient Darwinian replicators nested within eubacterial genomes

Ancient Darwinian replicators nested within eubacterial genomes

REPORTH: Determining orthologous locations of repetitive sequences between genomes

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