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Coalescent framework for prokaryotes undergoing interspecific homologous recombination

Heredityvolume 120pages474484 (2018) | Download Citation


Coalescent process for prokaryote species is theoretically considered. Prokaryotes undergo homologous recombination with individuals of the same species (intraspecific recombination) and with individuals of other species (interspecific recombination). This work particularly focuses on interspecific recombination because intraspecific recombination has been well incorporated in coalescent framework. We present a simulation framework for generating SNP (single-nucleotide polymorphism) patterns that allows external DNA integration into host genome from other species. Using this simulation tool, msPro, we observed that the joint processes of intra- and interspecific recombination generate complex SNP patterns. The direct effect of interspecific recombination includes increased polymorphism. Because interspecific recombination is very rare in nature, it generates regions with exceptionally high polymorphism. Following interspecific recombination, intraspecific recombination cuts the integrated external DNA into small fragments, generating a complex SNP pattern that appears as if external DNA was integrated multiple times. The insight gained from our work using the msPro simulator will be useful for understanding and evaluating the relative contributions of intra- and interspecific recombination events in generating complex SNP patters in prokaryotes.

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The authors very much thank the three reviewers for their useful and kind comments that improved the manuscript. This work was supported in part by the Japan Society for the Promotion of Science (JSPS).

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  1. Graduate University for Advanced Studies, Hayama, Kanagawa, 240-0193, Japan

    • Tetsuya Akita
    • , Shohei Takuno
    •  & Hideki Innan
  2. National Research Institute of Far Seas Fisheries, Fisheries Research Agency, Yokohama, Kanagawa, 236-8648, Japan

    • Tetsuya Akita


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The authors declare that they have no competing interests.

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Correspondence to Hideki Innan.

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