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.

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

eLife ◽  
2019 ◽  
Vol 8 ◽  
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.

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

eLife ◽  
2018 ◽  
Vol 7 ◽  
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.

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 High-Level Molecular Diversity of Copper-Zinc Superoxide Dismutase Genes among and within Species of Arbuscular Mycorrhizal Fungi

2009 ◽  
Vol 75 (7) ◽  
pp. 1970-1978 ◽  
Author(s):  
Nicolas Corradi ◽  
Beat Ruffner ◽  
Daniel Croll ◽  
Alexandre Colard ◽  
Ales Horák ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Amino Acid ◽  
Arbuscular Mycorrhizal Fungi ◽  
Natural Population ◽  
Mycorrhizal Fungi ◽  
Molecular Diversity ◽  
Glomus Intraradices ◽  
Arbuscular Mycorrhizal ◽  
Single Copy ◽  
Acid Sites

ABSTRACT In the ecologically important arbuscular mycorrhizal fungi (AMF), Sod1 encodes a functional polypeptide that confers increased tolerance to oxidative stress and that is upregulated inside the roots during early steps of the symbiosis with host plants. It is still unclear whether its expression is directed at scavenging reactive oxygen species (ROS) produced by the host, if it plays a role in the fungus-host dialogue, or if it is a consequence of oxidative stress from the surrounding environment. All these possibilities are equally likely, and molecular variation at the Sod1 locus can possibly have adaptive implications for one or all of the three mentioned functions. In this paper, we analyzed the diversity of the Sod1 gene in six AMF species, as well as 14 Glomus intraradices isolates from a single natural population. By sequencing this locus, we identified a large amount of nucleotide and amino acid molecular diversity both among AMF species and individuals, suggesting a rapid divergence of its codons. The Sod1 gene was monomorphic within each isolate we analyzed, and quantitative PCR strongly suggest this locus is present as a single copy in G. intraradices. Maximum-likelihood analyses performed using a variety of models for codon evolution indicated that a number of amino acid sites most likely evolved under the regime of positive selection among AMF species. In addition, we found that some isolates of G. intraradices from a natural population harbor very divergent orthologous Sod1 sequences, and our analysis suggested that diversifying selection, rather than recombination, was responsible for the persistence of this molecular diversity within the AMF population.

scholarly journals Correction: Single nucleus sequencing reveals evidence of inter-nucleus recombination in arbuscular mycorrhizal fungi

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Eric CH Chen ◽  
Stephanie Mathieu ◽  
Kinga Sedzielewska-Toro ◽  
Max Peart ◽  
Adrian Pelin ◽  
...  
Keyword(s):  
Arbuscular Mycorrhizal Fungi ◽  
Mycorrhizal Fungi ◽  
Arbuscular Mycorrhizal ◽  
Single Nucleus

scholarly journals Author response: Single nucleus sequencing reveals evidence of inter-nucleus recombination in arbuscular mycorrhizal fungi

2018 ◽  
Author(s):  
Eric CH Chen ◽  
Stephanie Mathieu ◽  
Anne Hoffrichter ◽  
Kinga Sedzielewska-Toro ◽  
Max Peart ◽  
...  
Keyword(s):  
Arbuscular Mycorrhizal Fungi ◽  
Mycorrhizal Fungi ◽  
Arbuscular Mycorrhizal ◽  
Author Response ◽  
Single Nucleus
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