Biology subjects

Corradi, N.

Publications and source records attributed to Corradi, N..

8 recordsLinked to original sources

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↗

bioRxiv2024

Analyses of transposable elements in arbuscular mycorrhizal fungi support evolutionary parallels with fungal plant pathogens

Transposable elements (TEs) are repetitive DNA sequences that excise or create copies that are inserted elsewhere in the genome. Their expansion shapes genome variability and evolution by impacting gene expression and rearrangement rates. Arbuscular mycorrhizal fungi (AMF) are beneficial plant symbionts with large, TE-rich genomes, and recent findings showed these elements vary significantly in abundance, evolution, and regulation among model AMF strains. Here, we aimed to obtain a more comprehensive understanding of TE function and evolution in AMF by investigating assembled genomes from representatives of all known families. We uncovered multiple, family-specific bursts of insertions in different species, indicating variable past and ongoing TE activity contributing to the diversification of AMF lineages. We also found that TEs are preferentially located within and around candidate effectors/secreted proteins, as well as in proximity to promoters. Altogether, these findings support the role of TEs in promoting the diversity in proteins involved in molecular dialogues with hosts and, more generally, in driving gene regulation. The mechanisms of TEs evolution we observed in these prominent plant symbionts bear striking similarities to those of many filamentous plant pathogens.

genomics↗

bioRxiv2023

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

Transposable elements (TEs) are repetitive DNA that can create variability in genome structure and regulation. The genome of Rhizophagus irregularis, a widely studied arbuscular mycorrhizal fungus (AMF), comprises approximately 50% repetitive sequences that include transposable elements. Despite their abundance, two-thirds of TEs remain unclassified, and their regulation among AMF life-stages remains unknown. Here, we aimed to improve our understanding of TE diversity and regulation in this model species by curating repeat datasets obtained from chromosome-level assemblies and by investigating their expression across multiple conditions. Our analyses uncovered new TE superfamilies and families in this model symbiont and revealed significant differences in how these sequences evolve both within and between R. irregularis strains. With this curated TE annotation, we also detected that the number of upregulated TE families in colonized roots is four times higher than in the extraradical mycelium, and their overall expression differs depending on the plant host. This work provides a fine-scale view of TE diversity and evolution in model plant symbionts and highlights their transcriptional dynamism and specificity during host-microbe interactions. We also provide Hidden Markov Model profiles of TE domains for future manual curation of uncharacterized sequences (https://github.com/jordana-olive/TE-manual-curation/tree/main).

genomics↗

bioRxiv2023

Resolving the haplotypes of arbuscular mycorrhizal fungi highlights the role of two nuclear populations in host interactions

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.

genomics↗

bioRxiv2022

A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis

The root systems of most plant species are aided by the soil foraging capacities of symbiotic Arbuscular Mycorrhizal (AM) fungi of the Glomeromycotina subphylum. Despite recent advances in our knowledge of the ecology and molecular biology of this mutualistic symbiosis, our understanding of the AM fungi genome biology is just emerging. Presented here are the most contiguous and highest-quality nuclear and mitochondrial genome assemblies of an arbuscular mycorrhizal fungus to date, achieved through Nanopore long-read DNA sequencing and Hi-C data. This haploid genome assembly of Rhizophagus irregularis, alongside short- and long-read RNA-Sequencing data, was used to produce a comprehensive annotation catalogue of gene models, repetitive elements, small RNA loci, and DNA cytosine methylome. A phylostratigraphic gene age inference framework revealed that the birth of genes associated with nutrient transporter activity and transmembrane ion transport systems predates the emergence of Glomeromycotina. While symbiotic nutrient cycling in AM fungi relies on genes that existed in ancestor lineages, a burst of Glomeromycotina-restricted genetic innovation is also detected. Analysis of the chromosomal distribution of genetic and epigenetic features highlights evolutionarily young genomic regions that produce abundant small RNAs, suggesting active RNA-based monitoring of genetic sequences surrounding recently evolved genes. This chromosome-scale view of the genome of an AM fungus genome reveals previously unexplored sources of genomic novelty in an organism evolving under an obligate symbiotic life cycle. HighlightsO_LIAssembly of 32 highly contiguous chromosomal scaffolds for R. irregularis, with 23 complete and gapless C_LIO_LIGene annotation based on short- and long-read RNA-Seq data from different developmental stages C_LIO_LIComplete annotation set including mitochondrial genes, DNA methylome, small RNAome, repetitive/transposable elements, functional annotation C_LIO_LIIdentification of a burst of lineage-restricted genetic innovation in the Glomeromycotina subphylum C_LI

genomics↗

bioRxiv2021

Long reads and Hi-C sequencing illuminate the two-compartment genome of the model arbuscular mycorrhizal symbiont Rhizophagus irregularis

Chromosome folding links genome structure with gene function by generating distinct nuclear compartments and topologically associating domains (TADs). In mammals, these undergo preferential interactions and regulate gene expression. However, their role in fungal genome biology is unclear. Here, we combine Nanopore (ONT) sequencing with chromatin conformation capture sequencing (Hi-C) to reveal chromosome and epigenetic diversity in a group of obligate plant symbionts; the arbuscular mycorrhizal fungi (AMF). We find that five phylogenetically distinct strains of the model AMF Rhizophagus irregularis carry 33 chromosomes with substantial within species variability in size, as well as in gene and repeat content. Strain-specific Hi-C contact maps all reveal a checkerboard pattern that underline two dominant euchromatin (A) and heterochromatin (B) compartments. Each compartment differs in the level of gene transcription, regulation of candidate effectors and methylation frequencies. The A-compartment is more gene-dense and contains most core genes, while the B-compartment is more repeat-rich and has higher rates of chromosomal rearrangement. While the B-compartment is transcriptionally repressed, it has significantly more secreted proteins and in planta up-regulated candidate effectors, suggesting a possible host-induced change in chromosome conformation. Overall, this study provides a fine-scale view into the genome biology and evolution of prominent plant symbionts, and opens avenues to study the epigenetic mechanisms that modify chromosome folding during host-microbe interactions.

genomics↗

bioRxiv2020

More filtering on SNP calling does not remove evidence of inter-nucleus recombination in dikaryotic arbuscular mycorrhizal fungi

We respond to a recent reanalysis of single nucleus sequence data from Chen et al. 2018 eLife, which indicated that evidence of inter-nuclear recombination in dikaryotic arbuscular mycorrhizal fungi decreases when heterozygous, duplicated sites being supported by less than 5 reads, are removed from the dataset. Here, we show that applying a more stringent methodology for filtering SNP calls that focuses exclusively on single copy and homozygous regions with at least 5 reads supporting a given SNP, still recovers several hundreds putative inter-nucleus recombination events within the same dataset. We also provide evidence for retaining SNPs supported by less than 5 reads for genotyping individual nuclei using the same dataset.

genomics↗