Biology subjects

Dallaire, A.

Publications and source records attributed to Dallaire, A..

6 recordsLinked to original sources

bioRxiv2025

Reductive evolution of the DNA replication machinery in endosymbiotic fungi

The molecular machinery for replicating and repairing DNA accurately is critically important for life and highly conserved across the Tree of Life. Here we show that two major lineages of fungi, Glomeromycotina and Microsporidia, lost DNA polymerase complexes involved in replication and translesion synthesis. Catalytic and non-catalytic subunits of DNA polymerases are co-eliminated, consistent with their physical and functional interactions described in other eukaryotes. We detect lineage-specific variation in genome-wide mutation rates, showing that DNA polymerase gene losses correlate with increased genetic variation. We find that the Glomeraceae family of arbuscular mycorrhizal (AM) fungi has lived for [~]360 My without a leading strand replisome, raising the question of how these fungi can replicate DNA. We provide evidence that the cell cycle of Rhizophagus irregularis is active when in symbiosis with a host, but not without. This indicates a higher level of integration between AM fungi and plants than previously appreciated, and suggests the existence of a regulatory or functional contribution provided by a host to the fungal cell cycle. We propose that alternative modes of DNA replication and cell cycle provide mutational opportunities for fungal adaptation, and play roles in the evolution of endosymbioses.

evolutionary biology↗

bioRxiv2024

Transposable elements drive regulatory and functional innovation of F-box genes

Protein domains of transposable elements (TEs) and viruses increase the protein diversity of host genomes by recombining with other protein domains. By screening 10 million eukaryotic proteins, we identified several domains that define multi-copy gene families and frequently co-occur with TE/viral domains. Among these, a Tc1/Mariner transposase helix-turn-helix (HTH) domain was captured by F-box genes in the Caenorhabditis genus, creating a new class of F-box genes. For specific members of this class, like fbxa-215, we found that the HTH domain is required for diverse processes including germ granule localisation, fertility, and thermotolerance. Furthermore, we provide evidence that HSF-1 mediates the transcriptional integration of fbxa-215 into the heat-shock response by binding to Helitron TEs directly upstream of the fbxa-215 locus. The interactome of HTH-bearing F-box factors suggests roles in post-translational regulation and proteostasis, consistent with established functions of F-box proteins. Based on AlphaFold2 multimer proteome-wide screens, we propose that the HTH domain may diversify the repertoire of protein substrates that F-box factors regulate post-translationally. We further demonstrate that F-box genes repeatedly and independently captured TE domains throughout eukaryotic evolution, and describe an additional instance in zebrafish. In conclusion, we identify recurrent TE domain captures by F-box genes in eukaryotes and provide insights into how these novel proteins are integrated within host gene regulatory networks.

evolutionary biology↗

bioRxiv2024

Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes

East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable elements (TEs) have been associated with phenotypic variation in cichlids, little is known about their transcriptional activity and epigenetic silencing. Here, we describe dynamic patterns of TE expression in African cichlid gonads and during early development. Orthology inference revealed an expansion of piwil1 genes in Lake Malawi cichlids, likely driven by PiggyBac TEs. The expanded piwil1 copies have signatures of positive selection and retain amino acid residues essential for catalytic activity. Furthermore, the gonads of African cichlids express a Piwi-interacting RNA (piRNA) pathway that target TEs. We define the genomic sites of piRNA production in African cichlids and find divergence in closely related species, in line with fast evolution of piRNA-producing loci. Our findings suggest dynamic co-evolution of TEs and host silencing pathways in the African cichlid radiations. We propose that this co-evolution has contributed to cichlid genomic diversity.

evolutionary biology↗

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

Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis

Arbuscular mycorrhizal (AM) fungi form mutualistic relationships with most land plant species and have long been considered as ancient asexuals. Long-term clonal evolution would be remarkable for a eukaryotic lineage and suggests the importance of alternative mechanisms to promote genetic variability facilitating adaptation. Here, we assessed the potential of transposable elements (TEs) for generating genomic diversity. The dynamic expression of TEs during Rhizophagus irregularis spore development suggests ongoing TE activity. We find Mutator-like elements located near genes belonging to highly expanded gene families. Characterising the epigenomic status of R. irregularis provides evidence of DNA methylation and small RNA production occurring at TE loci. Our results support a potential role for TEs in shaping the genome, and roles for DNA methylation and small RNA-mediated silencing in regulating TEs. A well-controlled balance between TE activity and repression may therefore contribute to genome evolution in AM fungi.

genomics↗

bioRxiv2019

C. elegans transgenerationally adapts to bacterial infection by increasing the expression of cysteine synthases in progeny

Parental exposure to pathogens can prime offspring immunity in diverse organisms. The mechanisms by which this heritable priming occurs are largely unknown. Here we report that the soil bacteria Pseudomonas vranovensis is a natural pathogen of the nematode Caenorhabditis elegans and that parental exposure of animals to P. vranovensis promotes offspring resistance to infection. Furthermore, we demonstrate a transgenerational enhancement of progeny survival when three consecutive generations of animals are exposed to P. vranovensis. By investigating the mechanisms by which animals heritably adapt to P. vranovensis infection, we found that parental infection by P. vranovensis results in increased expression of the cysteine synthases CYSL-1 and CYSL-2 and the regulator of hypoxia inducible factor RHY-1 in progeny and that these three genes are required for adaptation to P. vranovensis. To our knowledge, these observations represent the largest heritable increase in offspring survival in response to a pathogen infection reported in any organism to date and establish a new CYSL-1, CYSL-2, and RHY-1 dependent mechanism by which animals adapt to infection.

genetics↗