scholarly journals More Filtering on SNP Calling Does Not Remove Evidence of Inter-Nucleus Recombination in Dikaryotic Arbuscular Mycorrhizal Fungi

2020 ◽  
Vol 11 ◽  
Author(s):  
Eric C. H. Chen ◽  
Stephanie Mathieu ◽  
Anne Hoffrichter ◽  
Jeanne Ropars ◽  
Steven Dreissig ◽  
...  
Keyword(s):  
Arbuscular Mycorrhizal Fungi ◽  
Mycorrhizal Fungi ◽  
Arbuscular Mycorrhizal ◽  
Snp Calling

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

2020 ◽  
Author(s):  
Eric C.H. Chen ◽  
Stephanie Mathieu ◽  
Anne Hoffrichter ◽  
Jeanne Ropars ◽  
Steven Dreissig ◽  
...  
Keyword(s):  
Arbuscular Mycorrhizal Fungi ◽  
Mycorrhizal Fungi ◽  
Sequence Data ◽  
Arbuscular Mycorrhizal ◽  
Single Copy ◽  
Snp Calling ◽  
Single Nucleus

AbstractWe 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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