Variability of inverted repeats in all available genomes of bacteria

Otília Porubiaková, Jan Havlík, Indu, Michal Šedý, Veronika Přepechalová, Martin Bartas, Stefan Bidula, Jiří Šťastný, Miroslav Fojta, Václav Brázda

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Noncanonical secondary structures in nucleic acids have been studied intensively in recent years. Important biological roles of cruciform structures formed by inverted repeats (IRs) have been demonstrated in diverse organisms, including humans. Using Palindrome analyser, we analyzed IRs in all accessible bacterial genome sequences to determine their frequencies, lengths, and localizations. IR sequences were identified in all species, but their frequencies differed significantly across various evolutionary groups. We detected 242,373,717 IRs in all 1,565 bacterial genomes. The highest mean IR frequency was detected in the Tenericutes (61.89 IRs/kbp) and the lowest mean frequency was found in the Alphaproteobacteria (27.08 IRs/kbp). IRs were abundant near genes and around regulatory, tRNA, transfer-messenger RNA (tmRNA), and rRNA regions, pointing to the importance of IRs in such basic cellular processes as genome maintenance, DNA replication, and transcription. Moreover, we found that organisms with high IR frequencies were more likely to be endosymbiotic, antibiotic producing, or pathogenic. On the other hand, those with low IR frequencies were far more likely to be thermophilic. This first comprehensive analysis of IRs in all available bacterial genomes demonstrates their genomic ubiquity, nonrandom distribution, and enrichment in genomic regulatory regions.
Original languageEnglish
Article numbere01648-23
JournalMicrobiology Spectrum
Issue number4
Early online date23 Jun 2023
Publication statusPublished - 17 Aug 2023


  • Bacteria domain
  • Bacterial genome analysis
  • Inverted repeats
  • Palindrome analyser

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