Intraisolate Mitochondrial Genetic Polymorphism and Gene Variants Coexpression in Arbuscular Mycorrhizal Fungi

annisa firdayani;

Arbuscular my corrhizal 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 use daconventional poly merasechain reaction-based approach on selected mitochondrial regions with a high-fidelityDNA polymerase, followed by cloningand Sanger sequencing. Two isolates of Rhizophagus irregularis were used, one cultivate dinvitro for several generations(DAOM-197198) and the other recently isolated from the field(DAOM-242422). At different loci in both isolates, we found intra isolate allelic variation within them tDNA and in a single copy nuclear marker, which highlighted the presence of several non synonymous mutations in protein codinggenes. We confirmed that some of this variation persisted in the trans criptome, giving rise to ateast four distinct nad4 trans cripts in DAOM-197198. We also detected the presence of numerous mitochondrial DNA copies within nuclear genomes (numts), providing insights to understand this important evolutionary processin 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.