Decision letter: Comment on 'Single nucleus sequencing reveals evidence of inter-nucleus recombination in arbuscular mycorrhizal fungi'

Comment on 'Single nucleus sequencing reveals evidence of inter-nucleus recombination in arbuscular mycorrhizal fungi'

eLife ◽

10.7554/elife.47301 ◽

2019 ◽

Vol 8 ◽

Cited By ~ 2

Author(s):

Benjamin Auxier ◽

Anna Bazzicalupo

Keyword(s):

Arbuscular Mycorrhizal Fungi ◽

Mycorrhizal Fungi ◽

Arbuscular Mycorrhizal ◽

Single Nucleus ◽

Low Coverage

Chen et al. recently reported evidence for inter-nucleus recombination in arbuscular mycorrhizal fungi (Chen et al., 2018a). Here, we report a reanalysis of their data. After filtering the data by excluding heterozygous sites in haploid nuclei, duplicated regions of the genome, and low-coverage depths base calls, we find the evidence for recombination to be very sparse.

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Author response: Comment on 'Single nucleus sequencing reveals evidence of inter-nucleus recombination in arbuscular mycorrhizal fungi'

10.7554/elife.47301.015 ◽

2019 ◽

Author(s):

Benjamin Auxier ◽

Anna Bazzicalupo

Keyword(s):

Arbuscular Mycorrhizal Fungi ◽

Mycorrhizal Fungi ◽

Arbuscular Mycorrhizal ◽

Author Response ◽

Single Nucleus

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Single nucleus sequencing reveals evidence of inter-nucleus recombination in arbuscular mycorrhizal fungi

eLife ◽

10.7554/elife.39813 ◽

2018 ◽

Vol 7 ◽

Cited By ~ 18

Author(s):

Eric CH Chen ◽

Stephanie Mathieu ◽

Anne Hoffrichter ◽

Kinga Sedzielewska-Toro ◽

Max Peart ◽

...

Keyword(s):

Genetic Diversity ◽

Arbuscular Mycorrhizal Fungi ◽

Mycorrhizal Fungi ◽

Direct Evidence ◽

Life Stage ◽

Primary Source ◽

Arbuscular Mycorrhizal ◽

Genetic Exchange ◽

Average Similarity ◽

Single Nucleus

Eukaryotes thought to have evolved clonally for millions of years are referred to as ancient asexuals. The oldest group among these are the arbuscular mycorrhizal fungi (AMF), which are plant symbionts harboring hundreds of nuclei within one continuous cytoplasm. Some AMF strains (dikaryons) harbor two co-existing nucleotypes but there is no direct evidence that such nuclei recombine in this life-stage, as is expected for sexual fungi. Here, we show that AMF nuclei with distinct genotypes can undergo recombination. Inter-nuclear genetic exchange varies in frequency among strains, and despite recombination all nuclear genomes have an average similarity of at least 99.8%. The present study demonstrates that AMF can generate genetic diversity via meiotic-like processes in the absence of observable mating. The AMF dikaryotic life-stage is a primary source of nuclear variability in these organisms, highlighting its potential for strain enhancement of these symbionts.

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Decision letter: Single nucleus sequencing reveals evidence of inter-nucleus recombination in arbuscular mycorrhizal fungi

10.7554/elife.39813.057 ◽

2018 ◽

Author(s):

Rene Geurts ◽

Peter Young ◽

Michael Seidl

Keyword(s):

Arbuscular Mycorrhizal Fungi ◽

Mycorrhizal Fungi ◽

Arbuscular Mycorrhizal ◽

Single Nucleus

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

10.1101/2020.01.15.906412 ◽

2020 ◽

Cited By ~ 1

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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