Substitutions of short heterologous DNA segments of intragenomic or extragenomic origins produce clustered genomic polymorphisms

Research output: Contribution to journalArticleScientificpeer-review


  • Klaus Harms
  • Asbjørn Lunnan
  • Nils Hülter
  • Tobias Mourier
  • Lasse Vinner
  • Cheryl P. Andam
  • Pekka Marttinen
  • Helena Fridholm
  • Anders Johannes Hansen
  • William P. Hanage
  • Kaare Magne Nielsen
  • Eske Willerslev
  • Pal Jarle Johnsen

Research units

  • University of Copenhagen
  • Arctic University of Norway
  • Kiel University
  • Oslo Metropolitan University
  • Statens Serum Institut
  • Boston University
  • GenØk-Center for Biosafety


In a screen for unexplained mutation events we identified a previously unrecognized mechanism generating clustered DNA polymorphisms such as microindels and cumulative SNPs. The mechanism, short-patch double illegitimate recombination (SPDIR), facilitates short single-stranded DNA molecules to invade and replace genomic DNA through two joint illegitimate recombination events. SPDIR is controlled by key components of the cellular genome maintenance machinery in the gram-negative bacterium Acinetobacter baylyi. The source DNA is primarily intragenomic but can also be acquired through horizontal gene transfer. The DNA replacements are nonreciprocal and locus independent. Bioinformatic approaches reveal occurrence of SPDIR events in the gram-positive human pathogen Streptococcus pneumoniae and in the human genome.


Original languageEnglish
Pages (from-to)15066-15071
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number52
Publication statusPublished - 27 Dec 2016
MoE publication typeA1 Journal article-refereed

    Research areas

  • Illegitimate recombination, Microindels, Mutation

ID: 10357806