title: Intraisolate mitochondrial genetic polymorphism and gene variants coexpression in arbuscular mycorrhizal fungi.
abstract: Arbuscular mycorrhizal fungi (AMF) are multinucleated and coenocytic organisms, in which the extent of the intraisolate nuclear genetic variation has been a source of debate. Conversely, their mitochondrial genomes (mtDNAs) have appeared to be homogeneous within isolates in all next generation sequencing (NGS)-based studies. Although several lines of evidence have challenged mtDNA homogeneity in AMF, extensive survey to investigate intraisolate allelic diversity has not previously been undertaken. In this study, we used a conventional polymerase chain reaction -based approach on selected mitochondrial regions with a high-fidelity DNA polymerase, followed by cloning and Sanger sequencing. Two isolates of Rhizophagus irregularis were used, one cultivated in vitro for several generations (DAOM-197198) and the other recently isolated from the field (DAOM-242422). At different loci in both isolates, we found intraisolate allelic variation within the mtDNA and in a single copy nuclear marker, which highlighted the presence of several nonsynonymous mutations in protein coding genes. We confirmed that some of this variation persisted in the transcriptome, giving rise to at least four distinct nad4 transcripts in DAOM-197198. We also detected the presence of numerous mitochondrial DNA copies within nuclear genomes (numts), providing insights to understand this important evolutionary process in AMF. Our study reveals that genetic variation in Glomeromycota is higher than what had been previously assumed and also suggests that it could have been grossly underestimated in most NGS-based AMF studies, both in mitochondrial and nuclear genomes, due to the presence of low-level mutations.
authors.affiliation: Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada.
authors.forename: Denis
authors.initials: D
authors.lastname: Beaudet
authors.affiliation: Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada.
authors.forename: Ivan Enrique
authors.initials: IE
authors.lastname: de la Providencia
authors.affiliation: Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada.
authors.forename: Manuel
authors.initials: M
authors.lastname: Labridy
authors.affiliation: Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada.
authors.forename: Alice
authors.initials: A
authors.lastname: Roy-Bolduc
authors.affiliation: Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada.
authors.forename: Laurence
authors.initials: L
authors.lastname: Daubois
authors.affiliation: Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada mohamed.hijri@umontreal.ca.
authors.forename: Mohamed
authors.initials: M
authors.lastname: Hijri
mesh_terms: D000483:Alleles; D002466:Cell Nucleolus / Q000235:genetics*; D019143:Evolution, Molecular; D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal; D054629:Genome, Mitochondrial; D059014:High-Throughput Nucleotide Sequencing; D008928:Mitochondria / Q000235:genetics; D038821:Mycorrhizae / Q000235:genetics*; D010802:Phylogeny; D011110:Polymorphism, Genetic
keywords: NGS and Sanger sequencing; arbuscular mycorrhizal fungi; gene variants coexpression; heteroplasmy; mitochondria; polymorphism