Biology subjects

Ebert, D.

Publications and source records attributed to Ebert, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Genomic evidence for within-species thermal adaptation in collagen genes

Collagen is the most abundant protein in animals. Its thermal stability depends on its specific amino acid composition within the repeated Gly-Xaa-Yaa motifs forming the triple helix structure. Proline increases collagen rigidity, while serine enhances its elasticity--properties that contribute to collagen function and that vary with temperature. Although variation in collagen composition has been linked to temperature adaptation across evolutionary distinct taxa, its role within a species remains unclear. Here, we tested whether collagen genes across populations of the freshwater crustacean, Daphnia magna, show a signature of local adaptation to the ambient temperature. Analysing 39 collagen genes from 215 D. magna populations across three phylogeographic lineages spawning four continents, we found that animals from populations in warmer climates have higher proline and lower serine content in collagen--consistent with enhanced protein stability at higher temperatures. This variation was also associated with experimentally measured upper temperature tolerance. Parallel directional patterns of amino acid change appeared across genetically distinct lineages. Collagen genes also showed strong signatures of positive selection, comparable to that of immune-related genes, supporting a scenario of polygenic molecular role in adaptive responses. Our findings provide evidence of intraspecific molecular evolution in collagen amino acid composition driven by environmental temperature. Additionally, our study bridges macroevolutionary patterns with microevolutionary processes, posing the first intraspecific evidence that collagen genes can contribute to responses to environmental gradients at the molecular level, and thus, advancing our understanding of molecular adaptation of constrained structural proteins in an environmental context.

evolutionary biology↗

bioRxiv2026

Chromosome-scale Daphnia magna genome assembly resolves scaffolding discrepancies

Daphnia magna is a widely used model organism in ecological genomics, ecotoxicology, and evolutionary biology. While a few genome assemblies of this species of freshwater crustacean are available, disagreements in their chromosomal arrangements point toward scaffolding problems. We present the most contiguous chromosome-level genome assembly of D. magna, the first based on PacBio HiFi sequencing technology. The assembly spans 184.38 Mb and has a scaffold N50 of 12.4 Mb. Eight of ten chromosomal scaffolds consist of mainly two contigs, representing one chromosome arm each. Eleven of 20 telomeric regions are fully resolved. Using a genomic map and comparative genomics, we were able to not only resolve the problems of previous assemblies, but also to demonstrate that some of the scaffolding errors followed a systematic pattern, most likely resulting from mis-joins during Hi-C scaffolding. Additionally, we provide expression profiles for annotated genes derived from different D. magna RNA-seq datasets, enabling rapid assessment of predicted gene expression and identification of potential pseudogenes. The new genomic and transcriptomic resource enables comparative genomic studies on genome architecture, structural variation, and gene family evolution in this important model organism.

genomics↗

bioRxiv2026

Assessing planktivorous fish as vectors of a plankton parasite

Predators are often considered regulators of disease in prey populations, a concept central to the "healthy herd hypothesis". This hypothesis suggests that by preferentially removing infected individuals, predators can reduce parasite prevalence. However, predators may also act as disease vectors, facilitating the spread of parasites. We investigated whether stickleback fish (Gasterosteus aculeatus) can act as vectors for the transmission of the obligate bacterial parasite Pasteuria ramosa to its Daphnia host, a widespread freshwater zooplanktor. We fed infected D. magna to sticklebacks, and subsequently analysed faecal samples for the presence, viability, and infectivity of parasite transmission stages (= spores). We recovered approximately 60% of the consumed spores from fish faeces and these spores did not suffer from reduced infectivity to D. magna. Additionally, spores associated with sloppy feeding did not reduce infection rates. Thus, consumption of infected hosts by fish does not eliminate the parasite, but in contrary, may contribute to the spread and persistence of P. ramosa in natural populations, potentially influencing parasite dynamics in natural freshwater ecosystems.

ecology↗

bioRxiv2026

Near-future warming amplifies natural heatwave impacts and reorganizes freshwater communities

Future climate change may reshape ecological communities not only by increasing mean temperature, but also by altering the consequences of increasingly frequent heatwaves. Predicting these effects requires understanding how background warming interacts with short heatwaves in natural communities, where responses can arise through direct thermal stress and species interactions. We tested this using 32 outdoor freshwater mesocosms exposed to sustained near-future warming while capturing a documented natural heatwave. Warming raised temperature maxima that exceeded the thermal threshold of the pond snail, a main grazer in the community. Warmed communities showed lower grazer abundance, increased macrophyte and insect herbivore abundance, reduced phytoplankton biomass, and lower zooplankton density. Complementary assays showed that heatwave-level temperatures promoted macrophyte growth and reduced grazer survival, whereas reduced zooplankton performance mainly reflected indirect warming effects via food-web cascades. Thus, near-future warming can amplify natural heatwave impacts by exceeding consumer thermal thresholds and propagating through species interactions.

ecology↗

bioRxiv2026

From SNPs to Pathways: A genome-wide benchmark of annotation discrepancies and their impact on protein- and pathway-level inference

BackgroundAccurate single-nucleotide polymorphism (SNP) annotation is central to genomic research yet widely used tools and gene models often yield divergent results. Prior studies have shown such discrepancies in small datasets, but the extent of genome-wide variation and its impact on downstream pathway analysis remain unclear. ResultsWe conducted a comprehensive comparison of three commonly used SNP annotation tools, ANNOVAR, SnpEff, and VEP, using both Ensembl and RefSeq gene models to evaluate more than 40 million SNPs from the Haplotype Reference Consortium. At the protein level, annotation output differed significantly across tools and gene models (p-adj < 0.001), with discrepancies present in both genic and intergenic regions. RefSeq produced broader annotation coverage, particularly for intergenic SNPs, while Ensembl showed greater internal consistency. SnpEff provided the most complete coverage overall, whereas no single tool or model configuration achieved full annotation recovery of the union reference. Integration across tools and models maximized coverage and reduced annotation loss. In a case study of 204 colorectal cancer-associated SNPs from the FIGI GWAS, pathway enrichment results varied depending on annotation strategy. The fully integrated approach identified all four significant pathways, whereas several single-tool or single-model strategies missed one or more. ConclusionSNP annotation outcomes are influenced by both the tool and gene model used, and relying on a single approach may result in incomplete coverage. A multi-tool, multi-model strategy provides the most comprehensive annotation and preserves enriched pathways, supporting more robust and reproducible genomic interpretation.

bioinformatics↗

bioRxiv2026

Weak dispersal and landscape size inevitably promote local biodiversity in heterogeneous metacommunities of competing species

We provide a general theoretical explanation for a longstanding result in spatial ecology: weak dispersal among habitat patches promotes local biodiversity. Using analytical approximations of spatial Lotka-Volterra competition models, we show that species persistence in heterogeneous landscapes can be expressed as a function of regional abundance and local invasion growth rates. We further demonstrate that local multispecies coexistence is governed by the feasibility domain, linking spatial coexistence to a structural property of nonspatial competitive systems. Together, these results explain why weak dispersal increases local species richness and why this effect strengthens with landscape size. We test these predictions using numerical simulations and find that the theory breaks down only when both dispersal and competitive interactions are very strong, in which case dispersal has a unimodal effect on coexistence. In contrast, landscape size retains a positive effect on coexistence whenever an effect is detectable. We then apply the theory to long-term data from a natural Daphnia metacommunity. We detect strong preemptive competition among species and find no detectable effect of dispersal rate on local coexistence, whereas species co-occurrence increases with local landscape size, as predicted by theory. Together, our results identify how dispersal, interaction strength, and landscape size jointly regulate biodiversity in competitive systems.

ecology↗

bioRxiv2025

Matching-Allele-Models explain host specificity and high diversity of Collagen-Like Proteins in a virulent pathogen

Host specificity is a defining feature of many parasitic interactions, yet the genetic mechanisms behind this specificity remain unclear. Pasteuria ramosa, a bacterial pathogen of Daphnia magna, provides a model for studying genotype-specific infectivity. We investigate the role of collagen-like proteins (PCLs) in mediating host attachment using genome-wide association studies (GWAS) and presence/absence variation (PAV) analyses. Our results reveal high diversity and lineage-specific patterns within the PCL gene family. For three PCL triplets, we find strong associations with parasites attachment phenotypes. Nearly perfect genotype-phenotype matches for certain PCL alleles support the matching allele model (MAM), considered to be an important model of host-parasite coevolution and balancing selection. This is the first molecular evidence of MAM in a pathogen. This study highlights the role of PCL genes in infection specificity, advancing our understanding of host-pathogen coevolution and supporting the Red Queen hypothesis as a driver of genetic diversity.

evolutionary biology↗

bioRxiv2025

Variation in genome architecture and epigenetic modification across the microsporidia phylogeny

Microsporidia are a model clade for studying intracellular parasitism, being well-known for their streamlined genomes and their extreme life history. Although microsporidia are highly diverse and ecologically important to a broad range of hosts, previous research on genome architecture has focused primarily on the mammal-infecting genus Encephalitozoon. Here, we expand that work, testing the universality of the patterns observed in Encephalitozoon by investigating and comparing variation in genetic and epigenetic architectures in the high-quality genome assemblies of several major microsporidia clades. Our comparison of nine genomes, including the first genome assemblies of Binucleata daphniae, Gurleya vavrai, and Conglomerata obtusa, and revised, improved assemblies of Glugoides intestinalis and Ordospora colligata, found limited conservation of genetic and epigenetic architecture across all microsporidia, although many genomic characteristics, such as nucleotide composition and repeat content, were shared between genomes of the same or related clades. For example, rRNA genes were hypermethylated in all species, but their position close to chromosome ends was only found in the Encephalitozoon and its sister clade. GC-content varied widely, linked to genome size, phylogenetic position and activity of repeat elements. These findings enhance our insight into genome evolution and, consistent with findings from other systems, suggest epigenetic modification as a regulatory mechanism of gene expression and repeat element activity in microsporidia. Our comparative genome analysis reveals higher variation among microsporidia than previously supposed.

evolutionary biology↗

bioRxiv2024

Terrestrial herbivory drives adaptive evolution in an aquatic community via indirect effects

Indirect ecological effects, which occur when the impact of one species on another is mediated by a third species or the shared environment, are ubiquitous in nature. Given the complexity of natural systems, indirect ecological effects were thought to be important in driving eco-evolutionary processes across community boundaries. However, we know remarkably little about such effects. Here we show that indirect effects of terrestrial insect (aphids) herbivory on macrophytes (duckweed) drives adaptive evolution of water fleas (Daphnia) in large outdoor aquatic mesocosms. Aphid herbivory reduced macrophyte growth and increased the abundance of phytoplankton, which in turn increased the abundance of Daphnia. Whole genome pool sequencing and phenotypic assays revealed an impact on the genetic compositions of the Daphnia populations and transplant experiments indicated that these evolutionary changes were adaptive. Furthermore, these changes in the aquatic community altered the interactions of the aphids and the macrophytes. These results demonstrate that indirect ecological effects can shape eco-evolutionary interactions between different communities.

evolutionary biology↗

bioRxiv2024

Genetic basis of resistance in hosts facing alternative infection strategies by a virulent bacterial pathogen

Having alternative infection routes is thought to help parasites circumvent host resistance, provided that these routes are associated with different host resistance loci. This study examines whether alternate infection routes of the parasite Pasteuria ramosa are linked to distinct resistance loci in its crustacean host, Daphnia magna. We focus on the P. ramosa isolate P15, which can attach and penetrate the host through either the hindgut or the foregut. Using a global panel of 174 D. magna genotypes supplemented with breeding experiments, we analyzed resistance patterns for each of these infection routes. Our findings confirm our hypothesis: in D. magna, hindgut attachment is determined by the D locus, while foregut attachment is controlled by a newly identified G locus. We established a gene model for the G locus that indicated Mendelian segregation and epistatic interaction with at least one other resistance locus for P. ramosa, the C locus. Using genomic Pool-sequencing data, we localized the G locus within a known Pasteuria Resistance Complex on chromosome 4 of D. magna, whereas the D locus is on chromosome 7. Two candidate genes for the G locus, belonging to the Glycosyltransferase gene family, were identified. Our study sheds new light on host-parasite coevolution and enhances our understanding of how parasites evolve infection strategies. Author summaryParasites continuously evolve strategies to overcome host resistance, including the use of alternative infection routes. However, this strategy is advantageous only if host resistance loci are specific to each entry point; otherwise, a single host gene could provide resistance to all infection routes. In this study, we tested this hypothesis using the freshwater crustacean Daphnia magna and a strain of the parasite Pasteuria ramosa that can infect its host via the esophagus (foregut) or the hindgut. By conducting a phenotypic assay of P. ramosa attachment on a global panel of D. magna genotypes, we demonstrate that foregut and hindgut infections are associated with independent genetic host resistance loci. Through a breeding experiment on a subset of D. magna genotypes, we were able to propose a gene model for the newly discovered G locus linked to foregut attachment, while the previously identified D locus is linked to hindgut attachment. We also discovered that the foregut infection route is influenced by an epistatic interaction between the G locus and another P. ramosa resistance locus, the C locus. Using genomic data, we confirmed that the G and D loci are not overlapping, with the G locus being part of the Pasteuria Resistance Complex on chromosome 4, whereas the D locus is on chromosome 7. Two potential genes involved in glycosylation processes were identified as candidates for the G locus. Overall, our study confirms a key postulate in the understanding of host-parasite co-evolution, highlighting the importance of infection strategies in host resistance.

evolutionary biology↗

bioRxiv2024

The Evolution of Extreme Genetic Variability in a Parasite-Resistance Complex in a Planktonic Crustacean

Genomic regions that play a role in parasite defense are often found to be highly variable, with the MHC serving as an iconic example. Single nucleotide polymorphisms may represent only a small portion of this variability, with Indel polymorphisms and copy number variation further contributing. In extreme cases, haplotypes may no longer be recognized as homologs. Understanding the evolution of such highly divergent regions is challenging because the most extreme variation is not visible using reference-assisted genomic approaches. Here we analyze the case of the Pasteuria Resistance Complex (PRC) in the crustacean Daphnia magna, a defense complex in the host against the common and virulent bacterium Pasteuria ramosa. Two haplotypes of this region have been previously described, with parts of it being non-homologous, and the region has been shown to be under balancing selection. Using pan-genome analysis and tree reconciliation methods to explore the evolution of the PRC and its characteristics within and between species of Daphnia and other Cladoceran species, our analysis revealed a remarkable diversity in this region even among host species, with many non-homologous hyper-divergent-haplotypes. The PRC is characterized by extensive duplication and losses of Fucosyltransferase (FuT) and Galactosyltransferase (GalT) genes that are believed to play a role in parasite defense. The PRC region can be traced back to common ancestors over 250 million years. The unique combination of an ancient resistance complex and a dynamic, hyper-divergent genomic environment presents a fascinating opportunity to investigate the role of such regions in the evolution and long-term maintenance of resistance polymorphisms. Our findings offer valuable insights into the evolutionary forces shaping disease resistance and adaptation, not only in the genus Daphnia, but potentially across the entire Cladocera class. SignificanceUnderstanding how organisms adapt to their environment requires insights into the evolution of genetic defenses against their parasites. While the Major Histocompatibility Complex (MHC) is a well-known example of a highly variable immune-related gene region, much remains unknown about the evolution of other such regions. Our study investigates the Pasteuria Resistance Complex (PRC) in water fleas, a genomic region crucial for defense against a parasitic bacterium. We discovered that the PRC is exceptionally diverse, with a history spanning hundreds of millions of years. This research provides new insights into the mechanisms underlying the maintenance of genetic diversity in the face of persistent parasite pressure. Our findings contribute to a broader understanding of how organisms evolve robust defenses against infectious diseases.

evolutionary biology↗

bioRxiv2024

Trehalose mediates salinity-stress tolerance in a crustacean

Salinization poses an increasing problem worldwide, threatening freshwater organisms and raising questions about ability to adapt. We explore the mechanisms enabling a planktonic crustacean to tolerate elevated salinity. By gradually raising water salinity in clonal cultures from 185 Daphnia magna populations, we showed that salt tolerance strongly correlates with native habitat salinity, indicating local adaptation. A GWAS revealed a major effect of the Alpha,alpha-trehalose-phosphate synthase (TPS) gene, suggesting that trehalose production facilitates salinity tolerance. We found a positive correlation between water salinity and trehalose concentrations in tolerant animals, while intolerant animals failed to produce trehalose. Using CRISPR/Cas9, a silenced TPS gene supported the role of trehalose under salt stress. Our study highlights how a keystone freshwater animal adapts to salinity stress using an evolutionarily conserved mechanism known in plants and bacteria, but not in metabolic-active animals. HighlightsO_LISalinity tolerance is a locally adapted trait in Daphnia magna C_LIO_LIThe trehalose TPS gene shows a strong association with salinity tolerance C_LIO_LITrehalose content increases with water salinity allowing survival of tolerant genotypes C_LIO_LINon-functional TPS genes reduce salinity tolerance by preventing trehalose production C_LI

evolutionary biology↗

bioRxiv2024

The genome of Pasteuria ramosa reveals a high turnover rate of collagen-like genes

Collagen-like proteins (CLP) are commonly found in many pathogenic bacteria where they serve as adhesins to attach to host tissue. The repetition of the amino-acid pattern (Gly-Xaa-Yaa)n is the major feature of collagen and is essential to the formation of its stable triple helical structure. In the Daphnia magna-Pasteuria ramosa system, a model system for studying antagonistic coevolution, a specific CLP in the virulent parasite P. ramosa plays a pivotal role in host attachment, regulated by matching allele model. Recognizing the crucial role of CLPs in the infection process, we aimed to enhance our understanding of P. ramosa-CLPs by sequencing high-quality genomes of two isolates, using long-read technology. An analysis of a CLP gene tree of representative Bacillota species revealed a clear radiation of these genes in P. ramosa, which was not found in the closely related Pasteuria penetrans. A comparison of the isolates reveals a high synteny, with the exception of a few duplications and inversions, mainly involving CLPs or transposases. Across isolates, we observed a recent burst of transposases as well as duplications of CLP genes. On average, CLP genes are well conserved between isolates, but the presence/absence of individual CLP genes is not fully shared, with 39 and 43 genes in the two isolates. Our findings suggest a rapid radiation of CLP genes combined with a birth and death process of the large P. ramosa-CLP gene family, possibly driven by transposition and coevolution. ImportanceAlthough the host-pathogen Daphnia magna-Pasteuria ramosa system has served as a model for coevolution, we have, to date, lacked high-quality genomic resources for the parasite, as is the case for many such systems. By presenting a complete assembly of two distinct P. ramosa isolates, our study addresses this lack and provides deeper insights into the P. ramosa Collagen Like Protein (CLP) family, essential proteins involved in attachment to the host. We discover that the rapid radiation of CLP genes in P. ramosa appears to be driven by transposition and coevolution, enabling the parasite to adapt to host resistance mechanisms. These insights improve our understanding of host-parasite interactions and pave the way for comparative genomic analyses to better understand the evolution of these genes. They also have broader implications for disease control and therapeutic development targeting pathogenic bacteria adhesion mechanisms.

genomics↗

bioRxiv2024

Genome-wide allele frequency changes reveal that dynamic metapopulations evolve differently

BackgroundTwo important characteristics of metapopulations are extinction- (re)colonization dynamics and gene flow between subpopulations. These processes can cause strong shifts in genome-wide allele frequencies that are generally not observed in "classical" (large, stable, panmictic) populations. Subpopulations founded by one or a few individuals, the so-called propagule model, are initially expected to show intermediate allele frequencies at polymorphic sites until natural selection and genetic drift drive allele frequencies toward a mutation-selection-drift equilibrium characterized by a negative exponential-like distribution of the site frequency spectrum (SFS). ResultsWe followed changes in SFS distribution in a natural metapopulation of the cyclically parthenogenetic pond-dwelling microcrustacean Daphnia magna using biannual pool-seq samples collected over a five-year period from 118 ponds occupied by subpopulations of known age. As expected under the propagule model, SFSs in newly founded subpopulations trended toward intermediate allele frequencies and shifted toward right skewed distributions as the populations aged. Immigration and subsequent hybrid vigor altered this dynamic. ConclusionsThe analysis of SFS dynamics is a powerful approach to understand evolution in metapopulations. It allowed us to disentangle evolutionary processes occurring in a natural metapopulation, where many subpopulations evolve in parallel. Thereby, stochastic processes like founder and immigration events lead to a pattern of subpopulation divergence, while genetic drift, leads to converging SFS distributions in the persisting subpopulations. The observed processes are well explained by the propagule model and highlight that metapopulations evolve differently from classical populations.

evolutionary biology↗

bioRxiv2023

Sperm competition favours intermediate sperm size in a hermaphrodite

Sperm competition is a potent mechanism of post-copulatory sexual selection that has been found to shape reproductive morphologies and behaviours in promiscuous animals. Especially sperm size has been argued to evolve in response to sperm competition through its effect on sperm longevity, sperm motility, the ability to displace competing sperm and ultimately fertilization success. Additionally, sperm size has been observed to co-evolve with female reproductive morphology. Theoretical work predicts that sperm competition may select for longer sperm but may also favour shorter sperm if sperm size trades off with number. In this study, we studied the relationship between sperm size and post-mating success in the free-living flatworm, Macrostomum lignano. Specifically, we used inbred isolines of M. lignano that varied in sperm size to investigate how sperm size translated into the ability of worms to transfer and deposit sperm in a mating partner. Our results revealed a hump-shaped relationship with individuals producing sperm of intermediate size having highest sperm competitiveness. This finding broadens our understanding of the evolution of sperm morphology by providing empirical support for stabilizing selection on sperm size under sperm competition.

evolutionary biology↗

bioRxiv2023

Ectopical expression of bacterial collagen-like protein supports its role as adhesin in host-parasite coevolution

For a profound understanding of the mechanisms of antagonistic coevolution, it is necessary to identify the coevolving genes. The spore-forming bacterium Pasteuria ramosa and its host, the microcrustacean Daphnia, are a well-characterized paradigm for co-evolution, but the underlying genes remain largely unknown. A genome-wide association study identified a polymorphic carboxy-terminal globular domain of Pasteuria collagen-like protein 7 (Pcl7) as a candidate mediating parasite attachment and driving its coevolution with the host. Since P. ramosa cannot currently be genetically manipulated, we used Bacillus thuringiensis as a surrogate parasite to express a fusion protein of a Pcl7 carboxy-terminus from P. ramosa and the amino-terminal domain of a B. thuringiensis collagen-like protein. Mutant B. thuringiensis (Pcl7-Bt) spores but not wild-type B. thuringiensis (WT-Bt) spores, attached to the same site of susceptible hosts as P. ramosa. Furthermore, Pcl7-Bt spores attached readily to host genotypes that were susceptible to the P. ramosa clone that was the origin of the Pcl7 C-terminus, but only slightly to resistant host genotypes. These findings indicated that the fusion protein was properly expressed and folded and demonstrated that indeed the C-terminus of Pcl7 mediates attachment in a host genotype-specific manner. These results provide strong evidence for the involvement of a CLP in the coevolution of Daphnia and P. ramosa and opens new avenues for genetic epidemiological studies of host-parasite interactions. 150-word "Importance" paragraphDuring host-parasite coevolution, hosts evolve to evade the damaging effect of the parasite, while parasites evolve to maximize their benefits by exploiting the host. The genes underlying this coevolution remain largely unknown. For the prime model-system for coevolutionary research, the crustacean Daphnia and the parasite Pasteuria ramosa, collagen-like proteins (CLPs) in Pasteuria were suggested to play a crucial role for host-parasite interactions. Here we report that transferring part of a CLP coding gene from the unculturable P. ramosa to Bacillus thuringiensis (Bt), confirmed the function of this protein as a genotype-specific adhesin to the hosts cuticle. Our finding highlights the importance of a CLP in host-parasite interactions and will enable us to explore the population genetic dynamics of coevolution in this system.

evolutionary biology↗

bioRxiv2023

Near chromosome-level genome assembly of the microsporidium Hamiltosporidium tvaerminnensis

Microsporidia are intracellular parasitic fungi whose genomes rank among the smallest of all known eukaryotes. A number of outstanding questions remain concerning the evolution of their large-scale variation in genome architecture, responsible for genome size variation of more than an order of magnitude. This genome report presents a first near-chromosomal assembly of a large-genome microsporidium, Hamiltosporidium tvaerminnensis. Combined Oxford Nanopore, Pacific Biosciences, and Illumina sequencing led to a genome assembly of 17 contigs, 11 of which represent complete chromosomes. Our assembly is 21.64 Mb in length, has an N50 of 1.44 Mb, and consists of 39.56 % interspersed repeats. We introduce a novel approach in microsporidia, PacBio Iso-Seq, as part of a larger annotation pipeline for obtaining high-quality annotations of 3,573 protein-coding genes. Based on direct evidence from the full-length Iso-Seq transcripts, we present evidence for alternative polyadenylation and variation in splicing efficiency, which are potential regulation mechanisms for gene expression in microsporidia. The generated high-quality genome assembly is a necessary resource for comparative genomics that will help elucidate the evolution of genome architecture in response to intracellular parasitism. SignificanceMicrosporidia are a model for genome evolution in response to intracellular parasitism, but we lack high-quality resources from species with large genomes. We present a near complete assembly of a large-genome microsporidium, Hamiltosporidium tvaerminnensis, and obtain high-quality gene annotations through full-length transcripts using Iso-Seq, a novel approach in microsporidia. Our study provides insights into gene regulation and paves the way for comparative genomic analyses aiming to understand the evolution of genome reduction and expansion in these intracellular parasites.

genomics↗

bioRxiv2022

Uncovering the genomic basis of infection through co-genomic sequencing of hosts and parasites

Understanding the genomic basis of infectious disease is fundamental objective in coevolutionary theory with relevance to healthcare, agriculture, and epidemiology. Models of host-parasite coevolution often assume that infection requires specific combinations of host and parasite genotypes. Coevolving host and parasite loci are therefor expected to show associations that reflects an underlying infection/resistance allele matrix, yet little evidence for such genome-to-genome interactions has been observed among natural populations. We conducted a study to search for this genomic signature across 258 linked host (Daphnia magna) and parasite (Pasteuria ramosa) genomes. Our results show a clear signal of genomic association between multiple epistatically-interacting loci in the host genome, and a family of genes encoding for collagen-like protein in the parasite genome. These findings are supported by laboratory-based infection trials, which show strong correspondence between phenotype and genotype at the identified loci. Our study provides clear genomic evidence of antagonistic coevolution among wild populations.

genomics↗