title: Population genomics reveals that within-fungus polymorphism is common and maintained in populations of the mycorrhizal fungus Rhizophagus irregularis.
abstract: Arbuscular mycorrhizal (AM) fungi are symbionts of most plants, increasing plant growth and diversity. The model AM fungus Rhizophagus irregularis (isolate DAOM 197198) exhibits low within-fungus polymorphism. In contrast, another study reported high within-fungus variability. Experiments with other R. irregularis isolates suggest that within-fungus genetic variation can affect the fungal phenotype and plant growth, highlighting the biological importance of such variation. We investigated whether there is evidence of differing levels of within-fungus polymorphism in an R. irregularis population. We genotyped 20 isolates using restriction site-associated DNA sequencing and developed novel approaches for characterizing polymorphism among haploid nuclei. All isolates exhibited higher within-isolate poly-allelic single-nucleotide polymorphism (SNP) densities than DAOM 197198 in repeated and non-repeated sites mapped to the reference genome. Poly-allelic SNPs were independently confirmed. Allele frequencies within isolates deviated from diploids or tetraploids, or that expected for a strict dikaryote. Phylogeny based on poly-allelic sites was robust and mirrored the standard phylogeny. This indicates that within-fungus genetic variation is maintained in AM fungal populations. Our results predict a heterokaryotic state in the population, considerable differences in copy number variation among isolates and divergence among the copies, or aneuploidy in some isolates. The variation may be a combination of all of these hypotheses. Within-isolate genetic variation in R. irregularis leads to large differences in plant growth. Therefore, characterizing genomic variation within AM fungal populations is of major ecological importance.
authors.affiliation: Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
authors.forename: Tania
authors.initials: T
authors.lastname: Wyss
authors.affiliation: Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.|Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: Frédéric G
authors.initials: FG
authors.lastname: Masclaux
authors.affiliation: Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
authors.forename: Pawel
authors.initials: P
authors.lastname: Rosikiewicz
authors.affiliation: Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: Marco
authors.initials: M
authors.lastname: Pagni
authors.affiliation: Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
authors.forename: Ian R
authors.initials: IR
authors.lastname: Sanders
mesh_terms: D056915:DNA Copy Number Variations; D014644:Genetic Variation; D023281:Genomics; D005838:Genotype; D055137:Glomeromycota / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D056186:Metagenomics; D038821:Mycorrhizae / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D010802:Phylogeny; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA