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Mobile introns shape the genetic diversity of their host genes

Jelena Repar, Tobias Warnecke
doi: https://doi.org/10.1101/092585
Jelena Repar
1Molecular Systems Group, MRC Clinical Sciences Centre (CSC), Du Cane Road, London W12 0NN, United Kingdom
2Molecular Systems Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, United Kingdom
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Tobias Warnecke
1Molecular Systems Group, MRC Clinical Sciences Centre (CSC), Du Cane Road, London W12 0NN, United Kingdom
2Molecular Systems Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, United Kingdom
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Abstract

Self-splicing introns populate several highly conserved protein-coding genes in fungal and plant mitochondria. In fungi, many of these introns have retained their ability to spread to intron-free target sites, often assisted by intron-encoded endonucleases that initiate the homing process. Here, leveraging population genomic data from Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Lachancea kluyveri, we expose non-random patterns of genetic diversity in exons that border self-splicing introns. In particular, we show that, in all three species, the density of single nucleotide polymorphisms increases as one approaches a mobile intron. Through multiple lines of evidence we rule out relaxed purifying selection as the cause of uneven nucleotide diversity. Instead, our findings implicate intron mobility as a direct driver of host gene diversity. We discuss two mechanistic scenarios that are consistent with the data: either endonuclease activity and subsequent error-prone repair have left a mutational footprint on the insertion environment of mobile introns or non-random patterns of genetic diversity are caused by exonic co-conversion, which occurs when introns spread to empty target sites via homologous recombination. Importantly, however, we show that exonic co-conversion can only explain diversity gradients near intron-exon boundaries if the conversion templates comes from outside the population. In other words, there must be pervasive and ongoing horizontal gene transfer of self-splicing introns into extant fungal populations.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted December 08, 2016.
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Mobile introns shape the genetic diversity of their host genes
Jelena Repar, Tobias Warnecke
bioRxiv 092585; doi: https://doi.org/10.1101/092585
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Mobile introns shape the genetic diversity of their host genes
Jelena Repar, Tobias Warnecke
bioRxiv 092585; doi: https://doi.org/10.1101/092585

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