title: Studying genome heterogeneity within the arbuscular mycorrhizal fungal cytoplasm.
abstract: Although heterokaryons have been reported in nature, multicellular organisms are generally assumed genetically homogeneous. Here, we investigate the case of arbuscular mycorrhizal fungi (AMF) that form symbiosis with plant roots. The growth advantages they confer to their hosts are of great potential benefit to sustainable agricultural practices. However, measuring genetic diversity for these coenocytes is a major challenge: Within the same cytoplasm, AMF contain thousands of nuclei and show extremely high levels of genetic variation for some loci. The extent and physical location of polymorphism within and between AMF genomes is unclear. We used two complementary strategies to estimate genetic diversity in AMF, investigating polymorphism both on a genome scale and in putative single copy loci. First, we used data from whole-genome pyrosequencing of four AMF isolates to describe genetic diversity, based on a conservative network-based clustering approach. AMF isolates showed marked differences in genome-wide diversity patterns in comparison to a panel of control fungal genomes. This clustering approach further allowed us to provide conservative estimates of Rhizophagus spp. genomes sizes. Second, we designed new putative single copy genomic markers, which we investigated by massive parallel amplicon sequencing for two Rhizophagus irregularis and one Rhizophagus sp. isolates. Most loci showed high polymorphism, with up to 103 alleles per marker. This polymorphism could be distributed within or between nuclei. However, we argue that the Rhizophagus isolates under study might be heterokaryotic, at least for the putative single copy markers we studied. Considering that genetic information is the main resource for identification of AMF, we suggest that special attention is warranted for the study of these ecologically important organisms.
authors.affiliation: Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Quebec, Canada eric.bapteste@snv.jussieu.fr mohamed.hijri@umontreal.ca.
authors.forename: Eva
authors.initials: E
authors.lastname: Boon
authors.affiliation: Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Quebec, Canada.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Halary
authors.affiliation: CNRS, UMR7138, Institut de Biologie Paris-Seine, Paris, France Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), Paris, France eric.bapteste@snv.jussieu.fr mohamed.hijri@umontreal.ca.
authors.forename: Eric
authors.initials: E
authors.lastname: Bapteste
authors.affiliation: Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Quebec, Canada eric.bapteste@snv.jussieu.fr mohamed.hijri@umontreal.ca.
authors.forename: Mohamed
authors.initials: M
authors.lastname: Hijri
mesh_terms: D000483:Alleles; D001483:Base Sequence; D016000:Cluster Analysis; D003198:Computer Simulation; D003593:Cytoplasm / Q000235:genetics*; D019143:Evolution, Molecular; D018628:Gene Dosage; D005819:Genetic Markers; D014644:Genetic Variation; D059646:Genome Size; D016681:Genome, Fungal; D055137:Glomeromycota / Q000235:genetics* / Q000302:isolation & purification; D058977:Molecular Sequence Annotation; D009154:Mutation / Q000235:genetics; D038821:Mycorrhizae / Q000235:genetics* / Q000302:isolation & purification; D011110:Polymorphism, Genetic; D060888:Real-Time Polymerase Chain Reaction; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D015203:Reproducibility of Results
chemical_list: D005819:Genetic Markers
keywords: arbuscular mycorrhizal fungi; genome evolution; genome heterogeneity; network analysis; next generation sequencing; symbiosis