PT  - JOURNAL ARTICLE
AU  - Eric C.H. Chen
AU  - Stephanie Mathieu
AU  - Anne Hoffrichter
AU  - Jeanne Ropars
AU  - Steven Dreissig
AU  - Jörg Fuchs
AU  - Andreas Brachmann
AU  - Nicolas Corradi
TI  - More filtering on SNP calling does not remove evidence of inter-nucleus recombination in dikaryotic arbuscular mycorrhizal fungi
AID  - 10.1101/2020.01.15.906412
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.01.15.906412
4099  - http://biorxiv.org/content/early/2020/01/15/2020.01.15.906412.short
4100  - http://biorxiv.org/content/early/2020/01/15/2020.01.15.906412.full
AB  - 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.