Mugambi, K. M. | Search bioRxiv

bioRxiv2026

The 3D Genome of Gigaspora margarita Unveils Stable Chromatin and Nucleolar Organization and Symbiont-Dependent Genome Dynamics

Arbuscular mycorrhizal fungi (AMF) are widespread plant symbionts that enhance nutrient acquisition and influence ecosystem productivity. Previous chromosome-level assemblies of a model species revealed a two-compartment genome architecture (active A and repressed B chromatin compartments), yet its conservation across evolutionarily distant AMF lineages remains unresolved. Here, we present a chromosome-scale and 3D genome assembly of Gigaspora margarita isolate BEG34--the largest and most repeat-rich AMF genome to date--alongside that of its obligate endobacterium, Candidatus Glomerobacter gigasporarum (CaGg), using PacBio HiFi and Hi-C sequencing. The G. margarita genome comprises 43 chromosomes (792 Mb) organized into stable A/B compartments and Topologically Associating Domains structures, irrespective of the presence of endobacteria. We uncover 21 divergent rDNA operons distributed across six chromosomes and show that these physically interact, suggesting conserved nucleolar organization. We also reveal that the CaGg genome is tripartite and mobilome-rich, encoding prophages, an orphan CRISPR array, and complete pathways for many novel and essential cofactors, including heme, which may enhance host bioenergetics. We also find that the endobacteriums presence regulates transposable elements in G. margarita. These findings reveal conserved principles of chromatin architecture in AMF symbionts and highlight the tight molecular interplay between fungal hosts and their endosymbionts, offering new insights into genome evolution and symbiotic adaptation.

genomics↗

bioRxiv2024

Arbuscular mycorrhizal fungal genotype and nuclear organization as driving factors in host plant nutrient acquisition and stable carbon capture

O_LIArbuscular mycorrhizal fungi (AMF) are obligate root symbionts of most plants that improve plant growth by transferring nutrients into plant roots through networks of soil hyphae. These hyphal networks represent a carbon sink in soil; thus, it has been suggested that these fungi can also boost atmospheric carbon storage, highlighting their potential role in managing greenhouse emissions. In this study, we aimed to determine whether certain AMF genotypes and nuclear organizations (homokaryons vs heterokaryons) are associated with higher rates of host plant yield and carbon storage. C_LIO_LIWe compared Sudan-grass (Sorghum x drummondii) AMF inoculation across eight strains of Rhizophagus irregularis: four homokaryotic and four heterokaryotic strains. Sudan-grass was grown in a growth chamber, which included 13C-CO2 pulse labeling to track plant carbon into AMF. C_LIO_LIAMF inoculation increased total and belowground biomass, as well as phosphorous, magnesium, and manganese uptake in the host. Heterokaryons led to greater belowground biomass, as well as less variable increases in shoot phosphorous. Mycorrhizal inputs to soil mineral-associated organic carbon - a highly persistent carbon pool with slow turnover - were overall greater in heterokaryons than in homokaryons but varied significantly among strains. C_LIO_LIThis indicates that the potential for carbon storage by mycorrhizal carbon inputs varies based on fungal genomic identity and nuclear organization. Overall, inoculation improved the yield of Sudan-grass and resulted in significant inter-strain variation in persistent carbon contributions to the soil. This work highlights the importance of considering genotype and nuclear identity in assessments of AMF as bio-stimulants and drivers of carbon storage. C_LI Societal Impact StatementIt is crucial to develop strategies for reducing our continued excessive global increases in fertilizer applications and to offset CO2 emissions. The pervasive underground hyphal networks of arbuscular mycorrhizal fungi (AMF) present an enticing bio-stimulant and carbon sink. We inoculated Sudan-grass plants with eight genotypically distinct strains of a model AMF species to determine if strain identity affects plant growth and carbon storage. We found that plant biomass, nutrient acquisition and stable soil carbon inputs varied among strains, emphasizing the importance of AMF strain identity in the selection of AMF inoculants for optimizing crop yield and carbon storage.

microbiology↗