Biology subjects

Bonfante, P.

Publications and source records attributed to Bonfante, P..

3 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↗

bioRxiv2020

Intragenic Complementation of Cellulose Synthase-Like D1 alleles in Root Hair Development

Root hair cells form the primary interface of plants with the soil environment, playing key roles in nutrient uptake and plant defense. In addition, they are typically the first cells infected by nitrogen-fixing soil bacteria during the root nodule symbiosis. Here we report a role for the Cellulose Synthase-Like D1 (CSLD1) gene in root hair development in Lotus japonicus. CSLD1 belongs to the cellulose synthase protein family that includes cellulose synthases, and cellulose synthase-like proteins, the latter thought to be involved in the biosynthesis of hemicellulose. We describe 11 csld1 mutant alleles that have either short (Ljcsld1-1) or variable length roots hairs (Ljcsld1-2 to 11). Examination of Ljcsld1-1 and one variable-length root hair mutant, Ljcsld1-6 showed increased root hair cell wall thickness, which in Ljcsld1-1 was more pronounced, suggesting a possible link with the defect in root nodule symbiosis. In addition, Ljcsld1-1 heterozygotes had intermediate root hair lengths, between those of wild type and the homozygotes. Intragenic complementation was observed between alleles with mutations in the N-terminal domain and other alleles, suggesting modularity of CSLD1 function and that it may operate as a homodimer or multimer. One sentence summaryThis research describes novel gain- and loss-of-function mutations at the Lotus japonicus CELLULOSE SYNTHASE-LIKE D1 locus and analyzes their impact on root hair development.

plant biology↗

bioRxiv2019

Symbiotic signalling is at the core of an endophytic Fusarium solani-legume association

Legumes interact with a wide range of microbes in their root system, ranging from beneficial symbionts to pathogens. Symbiotic rhizobia and arbuscular mycorrhizal glomeromycetes trigger a so-called common symbiotic signalling pathway (CSSP), including the induction of nuclear calcium spiking in the root epidermis. In our study, the recognition of an endophytic Fusarium solani strain K in Lotus japonicus induced the expression of LysM receptors for chitin-based molecules, CSSP members and CSSP-dependent genes in L. japonicus. In LysM and CSSP mutant/RNAi lines, root penetration and fungal intraradical progression was either stimulated or limited while FsK exudates are perceived in a CSSP-dependent manner, triggering nuclear calcium spiking in epidermal cells of Medicago truncatula Root Organ Cultures. Our results corroborate that the CSSP is a more common pathway than previously envisaged, involved in the perception of signals from other microbes beyond the restricted group of symbiotic interactions sensu stricto.

plant biology↗