RESUMEN
Geosiphon pyriformis, a representative of the fungal sub-phylum Glomeromycotina, is unique in its endosymbiosis with cyanobacteria within a fungal cell. This symbiotic relationship occurs in bladders containing nuclei of G. pyriformis, Mollicutes-like bacterial endosymbionts (MRE), and photosynthetically active and dividing cells of Nostoc punctiforme. Recent genome analyses have shed light on the biology of G. pyriformis, but the genome content and biology of its endosymbionts remain unexplored. To fill this gap, we gathered and examined metagenomic data from the bladders of G. pyriformis, where N. punctiforme and MRE are located. This ensures that our analyses are focused on the organs directly involved in the symbiosis. By comparing this data with the genetic information of related cyanobacteria and MREs from other species of Arbuscular Mycorrhizal Fungi, we aimed to reveal the genetic content of these organisms and understand how they interact at a genetic level to establish a symbiotic relationship. Our analyses uncovered significant gene expansions in the Nostoc endosymbiont, particularly in mobile elements and genes potentially involved in xenobiotic degradation. We also confirmed that the MRE of Glomeromycotina are monophyletic and possess a highly streamlined genome. These genomes show dramatic differences in both structure and content, including the presence of enzymes involved in environmental sensing and stress response.
Asunto(s)
Metagenoma , Simbiosis , Filogenia , Cianobacterias/genética , Cianobacterias/clasificación , Cianobacterias/metabolismo , Nostoc/genética , Nostoc/metabolismo , Metagenómica , Genoma Fúngico , Genoma BacterianoRESUMEN
Arbuscular mycorrhizal fungi (AMF) are obligate mutualists that can enhance nutrition and growth of their plant hosts while providing protection against pathogens. AMF produce spores and hyphal networks that can carry thousands of nuclei in a continuous cytoplasm, with no evidence of sexual reproduction. This review examines the impact of genomic technologies on our view of AMF genetics and evolution. We highlight how the genetics, nuclear dynamics, and epigenetics of these prominent symbionts follow trends preserved in distant multinucleate fungal relatives. We also propose new avenues of research to improve our understanding of their nuclear biology and their intricate genetic interactions with plant hosts.
RESUMEN
Transposable elements (TEs) are repetitive DNA that can create genome structure and regulation variability. The genome of Rhizophagus irregularis, a widely studied arbuscular mycorrhizal fungus (AMF), comprises â¼50% repetitive sequences that include TEs. 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 found that the number of upregulated TE families in colonized roots is 4 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).
Asunto(s)
Elementos Transponibles de ADN , Evolución Molecular , Hongos , Simbiosis , Simbiosis/genética , Micorrizas/genética , Genoma Fúngico , Glomeromycota/genética , Raíces de Plantas/microbiología , Raíces de Plantas/genética , Regulación Fúngica de la Expresión Génica , Anotación de Secuencia Molecular , Especificidad de la EspecieRESUMEN
Arbuscular mycorrhizal fungi (AMF) are prominent root symbionts that can carry thousands of nuclei deriving from two parental strains in a large syncytium. These co-existing genomes can also vary in abundance with changing environmental conditions. Here we assemble the nuclear genomes of all four publicly available AMF heterokaryons using PacBio high-fidelity and Hi-C sequencing. We find that the two co-existing genomes of these strains are phylogenetically related but differ in structure, content and epigenetics. We confirm that AMF heterokaryon genomes vary in relative abundance across conditions and show this can lead to nucleus-specific differences in expression during interactions with plants. Population analyses also reveal signatures of genetic exchange indicative of past events of sexual reproduction in these strains. This work uncovers the origin and contribution of two nuclear genomes in AMF heterokaryons and opens avenues for the improvement and environmental application of these strains.
Asunto(s)
Micorrizas , Micorrizas/genética , PlantasRESUMEN
Optimizing agroecosystems and crops for micronutrient uptake while reducing issues with inorganic contaminants (metal(loid)s) is a challenging task. One promising approach is to use arbuscular mycorrhizal fungi (AMF) and investigate the physiological, molecular and epigenetic changes that occur in their presence and that lead to changes in plant metal(loid) concentration (biofortification of micronutrients or mitigation of contaminants). Moreover, it is important to understand these mechanisms in the context of the soil microbiome, particularly those interactions of AMF with other soil microbes that can further shape crop nutrition. To address these challenges, a two-pronged approach is recommended: exploring molecular mechanisms and investigating microbiome management and engineering. Combining both approaches can lead to benefits in human health by balancing nutrition and contamination caused by metal(loid)s in the agro-ecosystem.
RESUMEN
Arbuscular mycorrhizal fungi (AMF) are obligate plant symbionts of most land plants. In these organisms, thousands of nuclei that are either genetically similar (homokaryotic) or derived from two distinct parents (dikaryotic) co-exist in a large syncytium. Here, we investigated the impact of these two nuclear organizations on the mycorrhizal response of potatoes (Solanum tuberosum) by inoculating four potato cultivars with eight Rhizophagus irregularis strains individually (four homokaryotic and four dikaryotic). By evaluating plant and fungal fitness-related traits four months post inoculation, we found that AMF genetic organization significantly affects the mycorrhizal response of host plants. Specifically, homokaryotic strains lead to higher total, shoot, and tuber biomass and a higher number of tubers, compared to dikaryotic strains. However, fungal fitness-related traits showed no clear differences between homokaryotic and dikaryotic strains. Nucleotype content analysis of single spores confirmed that the nucleotype ratio of AMF heterokaryon spores can shift depending on host identity. Together, these findings continue to highlight significant ecological differences derived from the two distinct genetic organizations in AMF.
Asunto(s)
Micorrizas , Solanum tuberosum , Micorrizas/genética , Fenotipo , Plantas/microbiología , Biomasa , HongosRESUMEN
Rhizophagus irregularis is the model species for arbuscular mycorrhizal fungi (AMF) research and the most widely propagated species for commercial plant biostimulants. Using asymbiotic and symbiotic cultivation systems initiated from single spores, advanced microscopy, Sanger sequencing of the glomalin gene, and PacBio sequencing of the partial 45S rRNA gene, we show that four strains of R. irregularis produce spores of two distinct morphotypes, one corresponding to the morphotype described in the R. irregularis protologue and the other having the phenotype of R. fasciculatus. The two spore morphs are easily distinguished by spore colour, thickness of the subtending hypha, thickness of the second wall layer, lamination of the innermost layer, and the dextrinoid reaction of the two outer spore wall layers to Melzer's reagent. The glomalin gene of the two spore morphs is identical and that of the PacBio sequences of the partial SSU-ITS-LSU region (2780 bp) obtained from single spores of the R. cf fasciculatus morphotype has a median pairwise similarity of 99.8% (SD = 0.005%) to the rDNA ribotypes of R. irregularis DAOM 197198. Based on these results, we conclude that the model AMF species R. irregularis is dimorphic, which has caused taxonomic confusion in culture collections and possibly in AMF research.
RESUMEN
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 is a close to T2T genome assembly of the model AM fungus Rhizophagus irregularis DAOM197198, achieved through Nanopore long-read DNA sequencing and Hi-C data. This haploid genome assembly of R. irregularis, alongside short- and long-read RNA-Sequencing data, was used to produce a comprehensive annotation catalog 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 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.
Asunto(s)
Glomeromycota , Micorrizas , Simbiosis/genética , Micorrizas/genética , Genómica , Glomeromycota/genética , ARNRESUMEN
The arbuscular mycorrhizal fungi (AMFs) are obligate root symbionts in the subphylum Glomeromycotina that can benefit land plants by increasing their soil nutrient uptake in exchange for photosynthetically fixed carbon sources. To date, annotated genome data from representatives of the AMF orders Glomerales, Diversisporales and Archaeosporales have shown that these organisms have large and highly repeated genomes, and no genes to produce sugars and fatty acids. This led to the hypothesis that the most recent common ancestor (MRCA) of Glomeromycotina was fully dependent on plants for nutrition. Here, we aimed to further test this hypothesis by obtaining annotated genome data from a member of the early diverging order Paraglomerales (Paraglomus occultum). Genome analyses showed this species carries a 39.6 Mb genome and considerably fewer genes and repeats compared to most AMF relatives with annotated genomes. Consistent with phylogenies based on ribosomal genes, our phylogenetic analyses suggest P. occultum as the earliest diverged branch within Glomeromycotina. Overall, our analyses support the view that the MRCA of Glomeromycotina carried hallmarks of obligate plant biotrophy. The small genome size and content of P. occultum could either reflect adaptive reductive processes affecting some early AMF lineages, or indicate that the high gene and repeat family diversity thought to drive AMF adaptability to host and environmental change was not an ancestral feature of these prominent plant symbionts.
Asunto(s)
Glomeromycota , Micorrizas , Hongos , Glomeromycota/genética , Micorrizas/genética , Filogenia , Plantas , Microbiología del SueloRESUMEN
Arbuscular mycorrhizal fungi (AMF) are widespread obligate root symbionts that assist plants in obtaining nutrients and protection against environmental stresses. In the model species Rhizophagus irregularis, heterokaryotic strains (AMF dikaryons) carry thousands of nuclei originating from two parental strains whose frequency varies depending on strains and host identity. Here, using digital droplet PCR, we demonstrate that surrounding abiotic factors (temperature, phosphorus, and pH) also change the nuclear dynamics of such strains in root organ cultures. Furthermore, when spatially separated portions of the AMF mycelium grow under different abiotic conditions, all the produced spores carry highly similar nuclear ratios. Overall, these findings demonstrate that abiotic stressors impact the nuclear organization of a widespread group of multinucleate plant symbionts, and reveal remarkable mechanisms of nuclear ratio harmonization across the mycelium in these prominent symbionts.
Asunto(s)
Micorrizas , Hongos , Micelio/genética , Micorrizas/genética , Fósforo , Raíces de PlantasRESUMEN
Chromosome folding links genome structure with gene function by generating distinct nuclear compartments and topologically associating domains. 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 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 upregulated 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 model plant symbionts, and opens avenues to study the epigenetic mechanisms that modify chromosome folding during host-microbe interactions.
Asunto(s)
Glomeromycota , Micorrizas , Hongos , Genoma Fúngico , Glomeromycota/genética , Glomeromycota/metabolismo , Micorrizas/fisiología , Plantas/genéticaRESUMEN
Arbuscular mycorrhizal fungi (AMF) are obligate plant symbionts that have the potential to improve crop yield. These multinucleate organisms are either "homokaryotic" or "dikaryotic". In AMF dikaryons, thousands of nuclei originating from two parental strains coexist in the same cytoplasm. In other fungi, homokaryotic and dikaryotic strains show distinct life history traits (LHTs), such as variation in growth rates and fitness. However, how such traits compare between dikaryons and homokaryons of AMF is unknown. To address this, we measured 20 LHT of four dikaryons and five homokaryons of the model fungus Rhizophagus irregularis across root organ cultures of three host plants (carrot, chicory, and tobacco). Our analyses show that dikaryons have clearly distinct life history strategies (LHSs) compared to homokaryons. In particular, spores of homokaryons germinate faster and to a higher proportion than dikaryons, whereas dikaryons grow significantly faster and create a more complex hyphal network irrespective of host plant species. Our study links AMF nuclear status with key LHT with possible implications for mycorrhizal symbiotic functioning.
RESUMEN
A recent study published by Mateus et al. [1] claimed that 18 "mating-related" genes are differentially expressed in the model arbuscular mycorrhizal fungus (AMF) Rhizophagus irregularis when genetically distinct fungal strains co-colonize a host plant. To clarify the level of evidence for this interesting conclusion, we first aimed to validate the functional annotation of these 18 R. irregularis genes using orthology predictions. These analyses revealed that, although sequence relationship exists, only 2 of the claimed 18 R. irregularis mating genes are potential orthologues to validated fungal mating genes. We also investigated the RNA-seq data from Mateus et al. [1] using classical RNA-seq methods and statistics. This analysis found that the over-expression during strain co-existence was not significant at the typical cut-off of the R. irregularis strains DAOM197198 and B1 in plants. Overall, we do not find convincing evidence that the genes involved have functions in mating, or that they are reproducibly up or down regulated during co-existence in plants.
Asunto(s)
Glomeromycota , Micorrizas , Hongos , Genes Fúngicos , Glomeromycota/genética , Micorrizas/genética , SimbiosisRESUMEN
Arbuscular mycorrhizal fungi (AMF) (subphylum Glomeromycotina)1 are among the most prominent symbionts and form the Arbuscular Mycorrhizal symbiosis (AMS) with over 70% of known land plants.2,3 AMS allows plants to efficiently acquire poorly soluble soil nutrients4 and AMF to receive photosynthetically fixed carbohydrates. This plant-fungus symbiosis dates back more than 400 million years5 and is thought to be one of the key innovations that allowed the colonization of lands by plants.6 Genomic and genetic analyses of diverse plant species started to reveal the molecular mechanisms that allowed the evolution of this symbiosis on the host side, but how and when AMS abilities emerged in AMF remain elusive. Comparative phylogenomics could be used to understand the evolution of AMS.7,8 However, the availability of genome data covering basal AMF phylogenetic nodes (Archaeosporales, Paraglomerales) is presently based on fragmentary protein coding datasets.9Geosiphon pyriformis (Archaeosporales) is the only fungus known to produce endosymbiosis with nitrogen-fixing cyanobacteria (Nostoc punctiforme) presumably representing the ancestral AMF state.10-12 Unlike other AMF, it forms long fungal cells ("bladders") that enclose cyanobacteria. Once in the bladder, the cyanobacteria are photosynthetically active and fix nitrogen, receiving inorganic nutrients and water from the fungus. Arguably, G. pyriformis represents an ideal candidate to investigate the origin of AMS and the emergence of a unique endosymbiosis. Here, we aimed to advance knowledge in these questions by sequencing the genome of G. pyriformis, using a re-discovered isolate.
Asunto(s)
Hongos/genética , Genoma Fúngico , Micorrizas , Plantas , Cianobacterias , Micorrizas/genética , Fijación del Nitrógeno , Filogenia , Plantas/microbiología , Simbiosis/genéticaRESUMEN
The arbuscular mycorrhizal fungi (AMF) are involved in one of the most ecologically important symbioses on the planet, occurring within the roots of most land plants.1 Knowledge of even basic elements of AM fungal biology is still poor, with the discovery that AMF may in fact have a sexual life cycle being only very recently reported.2-5 AMF produce asexual spores that contain up to several thousand individual haploid nuclei6 of either largely uniform genotypes (AMF homokaryons) or nuclei originating from two parental genotypes2-5 (AMF dikaryons or heterokaryons). In contrast to the sexual dikaryons in the phyla Ascomycota and Basidiomycota,7,8 in which pairs of nuclei coexist in single hyphal compartments, AMF dikaryons carry several thousand nuclei in a coenocytic mycelium. Here, we set out to better understand the dynamics of this unique multinucleate condition by combining molecular analyses with advanced microscopy and modeling. Herein, we report that select AMF dikaryotic strains carry the distinct nucleotypes in equal proportions to one another, whereas others show an unequal distribution of parental nucleotypes. In both cases, the relative proportions within a given strain are inherently stable. Simulation models suggest that AMF dikaryons may be maintained through nuclear cooperation dynamics. Remarkably, we report that these nuclear ratios shift dramatically in response to plant host identity, revealing a previously unknown layer of genetic complexity and dynamism within the intimate interactions that occur between the partners of a prominent terrestrial symbiosis.
Asunto(s)
Núcleo Celular , Micorrizas , Plantas/microbiología , Núcleo Celular/genética , Hongos , Micorrizas/genética , Raíces de Plantas/microbiología , SimbiosisRESUMEN
Arbuscular mycorrhizal fungi (AMF) live as obligate root symbionts on almost all land plants. They have long been regarded as ancient asexuals that have propagated clonally for millions of years. However, genomic studies in Rhizophagus irregularis and other AMF revealed many features indicative of sex. Surprisingly, comparative genomics of conspecific isolates of R. irregularis revealed an unexpected interstrain diversity, suggesting that AMF carry a high number of lineage-specific (LS) genes. Intriguingly, cryptic sex and LS genomic regions have previously been reported in a number of fungal pathogens of plants and humans. Here, we discuss these genomic similarities and highlight their potential relevance for AMF adaptation to the environment and for symbiotic functioning.
Asunto(s)
Glomeromycota , Micorrizas , Hongos , Genoma Fúngico , Micorrizas/genética , Simbiosis/genéticaRESUMEN
Oomycetes are notorious plant pathogens. It is known that genetically distinct oomycete strains can mate to increase their genetic diversity and virulence. A new paper finally reveals the genomic locus that may govern sexual compatibility in one oomycete species.
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Oomicetos , Genoma , Genómica , Oomicetos/genética , Plantas , VirulenciaRESUMEN
Evidence for the existence of dikaryote-like strains, low nuclear sequence diversity and inter-nuclear recombination in arbuscular mycorrhizal fungi has been recently reported based on single nucleus sequencing data. Here, we aimed to support evidence of inter-nuclear recombination using an approach that filters SNP calls more conservatively, keeping only positions that are exclusively single copy and homozygous, and with at least five reads supporting a given SNP. This methodology recovers hundreds of putative inter-nucleus recombination events across publicly available sequence data from individual nuclei. Challenges related to the acquisition and analysis of sequence data from individual nuclei are highlighted and discussed, and ways to address these issues in future studies are presented.