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bioRxiv · 10.1101/2020.01.15.906412

More filtering on SNP calling does not remove evidence of inter-nucleus recombination in dikaryotic arbuscular mycorrhizal fungi

Chen, E.·Mathieu, S.·Hoffrichter, A.·Ropars, J.·Dreissig, S.·Fuchs, J.·Brachmann, A.·Corradi, N.
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Abstract

We respond to a recent reanalysis of single nucleus sequence data from Chen et al. 2018 eLife, which indicated that evidence of inter-nuclear recombination in dikaryotic arbuscular mycorrhizal fungi decreases when heterozygous, duplicated sites being supported by less than 5 reads, are removed from the dataset. Here, we show that applying a more stringent methodology for filtering SNP calls that focuses exclusively on single copy and homozygous regions with at least 5 reads supporting a given SNP, still recovers several hundreds putative inter-nucleus recombination events within the same dataset. We also provide evidence for retaining SNPs supported by less than 5 reads for genotyping individual nuclei using the same dataset.

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Chen, E., Mathieu, S., Hoffrichter, A., Ropars, J., Dreissig, S., Fuchs, J., Brachmann, A., Corradi, N.. 2020-01-15. More filtering on SNP calling does not remove evidence of inter-nucleus recombination in dikaryotic arbuscular mycorrhizal fungi. https://doi.org/10.1101/2020.01.15.906412

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