RAREFAN: A webservice to identify REPINs and RAYTs in bacterial genomes
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 RA...
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2023-02-01
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| Online Access: | https://peercommunityjournal.org/articles/10.24072/pcjournal.244/ |
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| author | Fortmann-Grote, Carsten Irmer, Julia von Bertels, Frederic |
| author_facet | Fortmann-Grote, Carsten Irmer, Julia von Bertels, Frederic |
| author_sort | Fortmann-Grote, Carsten |
| collection | DOAJ |
| description | 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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| format | Article |
| id | doaj-art-c3b6db9d5ba047179ebfd355e6e80d26 |
| institution | Kabale University |
| issn | 2804-3871 |
| language | English |
| publishDate | 2023-02-01 |
| publisher | Peer Community In |
| record_format | Article |
| series | Peer Community Journal |
| spelling | doaj-art-c3b6db9d5ba047179ebfd355e6e80d262025-02-07T10:16:49ZengPeer Community InPeer Community Journal2804-38712023-02-01310.24072/pcjournal.24410.24072/pcjournal.244RAREFAN: A webservice to identify REPINs and RAYTs in bacterial genomesFortmann-Grote, Carsten0https://orcid.org/0000-0002-2579-5546Irmer, Julia von1Bertels, Frederic2https://orcid.org/0000-0001-6222-4139Max-Planck-Institute for Evolutionary Biology, Department of Microbial Population Biology, Plön, GermanyMax-Planck-Institute for Evolutionary Biology, Department of Microbial Population Biology, Plön, GermanyMax-Planck-Institute for Evolutionary Biology, Department of Microbial Population Biology, Plön, GermanyCompared 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. https://peercommunityjournal.org/articles/10.24072/pcjournal.244/sequence analysis, mobile genetic elements, bacterial genomes, Stenotrophomonas maltophilia |
| spellingShingle | Fortmann-Grote, Carsten Irmer, Julia von Bertels, Frederic RAREFAN: A webservice to identify REPINs and RAYTs in bacterial genomes Peer Community Journal sequence analysis, mobile genetic elements, bacterial genomes, Stenotrophomonas maltophilia |
| title | RAREFAN: A webservice to identify REPINs and RAYTs in bacterial genomes |
| title_full | RAREFAN: A webservice to identify REPINs and RAYTs in bacterial genomes |
| title_fullStr | RAREFAN: A webservice to identify REPINs and RAYTs in bacterial genomes |
| title_full_unstemmed | RAREFAN: A webservice to identify REPINs and RAYTs in bacterial genomes |
| title_short | RAREFAN: A webservice to identify REPINs and RAYTs in bacterial genomes |
| title_sort | rarefan a webservice to identify repins and rayts in bacterial genomes |
| topic | sequence analysis, mobile genetic elements, bacterial genomes, Stenotrophomonas maltophilia |
| url | https://peercommunityjournal.org/articles/10.24072/pcjournal.244/ |
| work_keys_str_mv | AT fortmanngrotecarsten rarefanawebservicetoidentifyrepinsandraytsinbacterialgenomes AT irmerjuliavon rarefanawebservicetoidentifyrepinsandraytsinbacterialgenomes AT bertelsfrederic rarefanawebservicetoidentifyrepinsandraytsinbacterialgenomes |