Arbuscular mycorrhizal fungi heterokaryons have two nuclear populations with distinct roles in host–plant interactions

Abstract

Arbuscular mycorrhizal fungi (AMF) are prominent root symbionts with a multinucleate cytoplasm that can carry thousands of nuclei deriving from two parental strains and varying in relative abundance in a large syncytium. Here, we set out to improve our understanding of such remarkable genetics by resolving the nuclear genomes of all publicly available AMF heterokaryons using PacBio HiFi and Hi-C sequencing. We find that all AMF heterokaryons carry two sets of homologous chromosomes, where genes associated with plant colonization reside in gene-sparse, repeat-rich compartments. The co-existing nuclear genomes are phylogenetically related but differ significantly in content and epigenetics, resulting in nucleus-specific regulatory programs during mycorrhizal interactions. AMF heterokaryons carry signatures of past genetic exchange indicative of sexual reproduction, followed by clonal haplotype evolution. This work uncovers the contribution and origin of nuclear genomes present in AMF heterokaryons and opens avenues for improvement and environmental application of these strains..

The mycorrhizal symbiosis: research frontiers in genomics, ecology, and agricultural application

“…The combination of Hi‐C and HiFi PacBio sequencing identified two sets of homologous chromosomes among thousands of coexisting nuclei in AMF heterokaryons. These two sets of related genomes differ in content, gene expression, and epigenetic regulation, and the abundance of each set varies depending on the host plant and environmental conditions (Sperschneider et al ., 2023).…”

A journey into the world of small RNAs in the arbuscular mycorrhizal symbiosis

“…Chromosome‐level genome sequencing coupled to Hi‐C analyses of R. irregularis strains showed that nuclei are organized in a euchromatic compartment, containing many genes with core functions, and a heterochromatic and heavily methylated compartment, rich in repetitive sequences but also in genes for predicted secreted proteins highly expressed in planta (Yildirir et al ., 2022; Sperschneider et al ., 2023). This suggests that during the symbiotic phase the chromatin condensation in AM fungi could be, to some extent, under the control of the host plant.…”

Strain-specific evolution and host-specific regulation of transposable elements in the model plant symbiontRhizophagus irregularis

“…Using RepeatModeler and RepeatMasker, recent analyses of R. irregularis chromosomelevel datasets indicated that strains of this species carry an average of 50% of TE 9,12 .…”

“…However, only one third of their repeat content could be classified, and thus on average 30% of all available genomes are composed by unclassified TE sequences 9,12,19,21 . To address this, we used five chromosome-assembly level from homokaryon and four heterokaryon strains to generate curated repeat libraries.…”

“…Furthermore, despite their longevity, no sexual reproduction has been formally observed in these organisms. However, evidence has now shown that AMF strains can either carry one (AMF homokaryons) or two nuclear (AMF heterokaryons) genotypes in their cells, a genetic characteristic found in sexually multinucleated strains of ascomycetes and basidiomycetes, suggesting that sexual reproduction does exist in these prominent symbionts 8,9 .…”