PCI Genomics

166

Title

RAREFAN: A webservice to identify REPINs and RAYTs in bacterial genomesuse asterix (*) to get italics

Authors

Frederic Bertels, Julia von Irmer, Carsten Fortmann-GrotePlease use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"

Year

2023

Picture

Abstract

Compared to eukaryotes, repetitive sequences are rare in bacterial genomes and usually do not persist for long. Yet, there is at least one class of persistent prokaryotic mobile genetic elements: REPINs. REPINs are non-autonomous transposable elements replicated by single-copy transposases called RAYTs. REPIN-RAYT systems are mostly vertically inherited and have persisted in individual bacterial lineages for millions of years. Discovering and analyzing REPIN populations and their corresponding RAYT transposases in bacterial species can be rather laborious, hampering progress in understanding REPIN-RAYT biology and evolution. Here we present RAREFAN, a webservice that identifies REPIN populations and their corresponding RAYT transposase in a given set of bacterial genomes. We demonstrate RAREFAN’s capabilities by analyzing a set of 49 Stenotrophomonas maltophilia genomes, containing nine different REPIN-RAYT systems. We guide the reader through the process of identifying and analyzing REPIN-RAYT systems across S. maltophilia, highlighting erroneous associations between REPIN and RAYTs, and providing solutions on how to find correct associations. RAREFAN enables rapid, large-scale detection of REPINs and RAYTs, and provides insight into the fascinating world of intragenomic sequence populations in bacterial genomes. RAREFAN is available at http://rarefan.evolbio.mpg.de.

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Keywords

REPINs, RAYTs, tranposable elements, Stenotrophomonas maltophilia, sequence populations

Methods that require specific expertise (optional)

NonePlease indicate the methods that may require specialised expertise during the peer review process (use a comma to separate various required expertises).

Thematic fields

Bacteria and archaea, Bioinformatics, Evolutionary genomics, Viruses and transposable elements

Suggested reviewers - Suggest up to 10 reviewers (provide names and Email addresses). (Optional)

Lindi Wahl, lwahl@uwo.ca, Sebastien Wielgoss, sebastien.wielgoss@env.ethz.ch, Anne Kupczok, anne.kupczok@wur.nl, Peter Lind, peter.lind@umu.se, Alexander Suh, alexander.suh@ebc.uu.se No need for them to be recommenders of PCI Genomics. Please do not suggest reviewers for whom there might be a conflict of interest. Reviewers are not allowed to review preprints written by close colleagues (with whom they have published in the last four years, with whom they have received joint funding in the last four years, or with whom they are currently writing a manuscript, or submitting a grant proposal), or by family members, friends, or anyone for whom bias might affect the nature of the review - see the code of conduct

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Submission date

2022-06-07 08:21:34

Recommender

Gavin Douglas

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