Biology subjects

Poulin, R.

Publications and source records attributed to Poulin, R..

9 recordsLinked to original sources

bioRxiv2025

Revealing the genetic mechanisms underpinning the parasite-induced water-seeking behaviour of insects through RNA-seq

The water-seeking behaviour in arthropods infected by mermithid nematodes or nematomorphs is a classic example of host manipulation, yet how these parasites induce the behavioural change is poorly known. We investigated the molecular mechanisms at the basis of this aberrant behaviour in European earwigs (Forficula auricularia) infected with the nematode Mermis nigrescens. We performed comparative RNA-seq analysis at different stages of infection and behaviour manipulation in both the host and the parasite. We detected a total of 12,876 and 9,722 expressed genes in the earwig and nematode, respectively. Differential gene expression (DGE) analysis showed 673 genes upregulated and 593 downregulated in earwigs, and 2,672 genes upregulated and 2,293 downregulated in nematodes across all comparisons between stages of infection and parasite sizes. Clustering analysis produced six and four clusters of differentially expressed genes in earwigs and nematodes, respectively, based on temporal patterns of expression across stages of infection. With overrepresented analysis using gene ontology terms, we found that the earwig shows increased signalling and sensory pathways, while the nematode ramps up transport and secretory genes during manipulation. We found shared GATA transcription factor motif enriched in the differentially over expressed genes during manipulation in both host and the parasite. Our study provides valuable insights into candidate pathways and genes in the host and the parasite, improving our understanding of the molecular regulation of water-seeking behaviour.

ecology↗

bioRxiv2024

Comparative genomics of parasitoid lifestyle as exemplified by Mermithidae and Nematomorpha

Mermithidae and Nematomorpha are parasitoids united by the commonalities in their lifestyle - immature stages infect arthropod hosts, species from both phyla can manipulate their host to induce a similar water-seeking behaviour, and both have a final free-living non-feeding adult reproductive stage, often killing their host upon emergence. Some of these species are of great economic importance, being evaluated as biological control agents against mosquito vectors responsible for diseases like malaria, and other insect pests, but with scarce genomic resources currently available. Nematomorpha, despite being closely related to Nematoda, received insufficient attention in genomic research, leading to gaps in our understanding of their diverse genetic makeup. This study aimed to investigate the genetic features encoded in the genomes of both parasitoid taxa to identify similarities and parallels linked to their ecological lifestyles. We performed a comparative analysis of 12 genomes, comprising parasitoid, parasitic and free-living worms. The investigation revealed genomic signatures unique to parasitoid species, including expanded gene families enriched in neural transmission modulation, likely linked to the known host manipulation that both mermithids and nematomorphs exert on their hosts. The analysis also uncovered a diverse array of conserved transposable element superfamilies across both lineages. The findings from this study provide valuable insights into the potential genomic adaptations associated with parasitoidism in nematode and nematomorph worms. The identification of expanded gene families and conserved transposable element superfamilies sheds light on the molecular underpinnings of their unique biological traits. Additionally, the core set of orthologs specific to parasitoid worms offers new avenues for understanding the evolution of parasitism within these groups of organisms.

genomics↗

bioRxiv2023

What can New Zealand bats tell us about Coronaviruses?

The current Covid-19 pandemic emphasizes the dramatic consequences of emerging zoonotic pathogens and stimulates the need for an assessment of the evolution and natural cycle of such microbes in a One Health framework. A number of recent studies have revealed an astonishing diversity of bat-borne Coronaviruses, including in insular environments, which can be considered as simplified biological systems suited for the exploration of the transmission cycles of these viruses in nature. In this work, we present two new lineages of alpha Coronaviruses detected by screening the only two extant New Zealand bat species: the lesser short-tailed bat (Mystacina tuberculata) and the long-tailed bat (Chalinolobus tuberculatus). Infection prevalence reaching 60% in long-tailed bats makes this host-pathogen model relevant for the investigation of maintenance mechanisms in a bat reservoir with peculiar physiological adaptations to temperate climates. A phylogenetic analysis shows that these viral lineages do cluster with Coronaviruses hosted by bat sister species from Australia, supporting co-diversification processes and confirming that the evolution of these viruses is tightly linked to that of their hosts. These patterns provide an interesting framework for further research aiming at elucidating the natural history and biological cycles of these economically-devastating zoonotic viruses.

ecology↗

bioRxiv2022

Genome assembly and annotation of the mermithid nematode Mermis nigrescens

Genetic studies of nematodes have been dominated by Caenorhabditis elegans as a model species. Lack of genomic resources has been a limiting factor for expansion of genetic research to other groups of nematodes. Here, we report a draft genome assembly of a mermithid nematode, Mermis nigrescens. Mermithidae are insect parasitic nematodes with hosts including a wide range of terrestrial arthropods. We sequenced, assembled, and annotated the whole genome of M. nigrescens using nanopore long-reads and 10X chromium link-reads. The assembly is 524 Mb in size consisting of 867 scaffolds. The N50 value is 2.42 Mb, and half of the assembly is in the 30 longest scaffolds. The assembly BUSCO score from the eukaryotic database (eukaryota_odb10) indicates that the genome is 86.7% complete and 5.1% partial. The genome has a high level of heterozygosity (6.6%) with a repeat content of 78.7%. mRNA-seq reads from different sized nematodes ([≤]2 cm, 3.5-7 cm, and >7 cm body length) representing different developmental stages were also generated and used for the genome annotation. Using ab initio and evidence-based gene model predictions, 12,313 protein-coding genes and 24,186 mRNAs were annotated. These genomic resources will help researchers investigate the various aspects of the biology and host-parasite interactions of mermithid nematodes.

genomics↗

bioRxiv2022

Historical dispersal and host-switching formed the evolutionary history of a globally distributed multi-host parasite - the Ligula intestinalis species complex

Studies on parasite biogeography and host spectrum provide insights into the processes driving parasite diversification. Global geographical distribution and a multi-host spectrum make the tapeworm Ligula intestinalis a promising model for studying both the vicariant and ecological modes of speciation in parasites. To understand the relative importance of host association and biogeography in the evolutionary history of this tapeworm, we analysed mtDNA and reduced-represented genomic SNP data for a total of 139 specimens collected from 18 fish-host genera across a distribution range representing 21 countries. Our results strongly supported the existence of at least 10 evolutionary lineages and estimated the deepest divergence at approximately 4.99-5.05 Mya, which is much younger than the diversification of the fish host genera and orders. Historical biogeography analyses revealed that the ancestor of the parasite diversified following multiple vicariance events and was widespread throughout the Palearctic, Afrotropical, and Nearctic between the late Miocene and early Pliocene. Cyprinoids were inferred as the ancestral hosts for the parasite. Later, from the late Pliocene to Pleistocene, new lineages emerged following a series of biogeographic dispersal and host-switching events. Although only a few of the current Ligula lineages show narrow host-specificity (to a single host genus), almost no host genera, even those that live in sympatry, overlapped between different Ligula lineages. Our analyses uncovered the impact of historical distribution shifts on host switching and the evolution of host specificity without parallel host-parasite co-speciation. Historical biogeography reconstructions also found that the parasite colonized several areas (Afrotropical and Australasian) much earlier than was suggested by only recent faunistic data.

evolutionary biology↗

bioRxiv2022

A high-quality genome assembly and annotation of the European earwig Forficula auricularia.

The European earwig Forficula auricularia is an important model for studies of maternal care, sexual selection, sociality and host-parasite interactions. However, detailed genetic investigations of this species are hindered by a lack of genomic resources. Here we present a high-quality hybrid genome assembly for F. auricularia. The genome was assembled using nanopore long-reads and 10x chromium link-reads. The final assembly is 1.06Gb in length with 31.03% GC content. It consists of 919 scaffolds with an N50 of 12.55Mb. Half of the genome is present in only 20 scaffolds. Benchmarking Universal Single-Copy Orthologs scores are ~90% from three sets of single-copy orthologs (eukaryotic, insect, and arthropod). The total repeat elements in the genome are 64.62%. The MAKER2 pipeline annotated 12,876 protein-coding genes and 21,031 mRNAs. A phylogenetic analysis revealed the isolate used in our genomic analysis belongs to Subspecies B, one of the two known genetic subspecies of F. auricularia. The genome assembly, annotation, and associated resources will be of high value to a large and diverse group of researchers working on Dermapterans.

genomics↗

bioRxiv2021

Haemosporidian taxonomic composition, network centrality and partner fidelity between resident and migratory avian hosts

Migration can modify interaction dynamics between parasites and their hosts with migrant hosts able to disperse parasites and impact local community transmission. Thus, studying the relationships among migratory hosts and their parasites is fundamental to elucidate how migration shapes host-parasite interactions. Avian haemosporidian parasites are some of the most prevalent, diverse, and important wildlife parasites, and are also widely used as models in ecological and evolutionary research. Here, we contrast parasite taxonomic composition, network centrality and partner fidelity among resident and non-resident hosts using avian haemosporidians as study model. In order to evaluate parasite taxonomic composition, we performed permutational multivariate analyses of variance to quantify dissimilarity in haemosporidian lineages infecting different host migratory categories. Additionally, we ran multilevel Bayesian models to assess the role of migration in determining centrality and partner fidelity in host-parasite networks of avian hosts and their respective haemosporidian parasites. We observed similar parasite taxonomic composition and partner fidelity among resident and migratory hosts. Conversely, we demonstrate that migratory hosts play a more central role in host-parasite networks than residents. However, when evaluating partially and fully migratory hosts separately, we observed that only partially migratory species presented higher network centrality when compared to resident birds. Therefore, migration does not lead to differences in both parasite taxonomic composition and partner fidelity. However, migratory behavior is positively associated with network centrality, indicating migratory hosts play more important roles in shaping host-parasite interactions and influence local transmission.

ecology↗

bioRxiv2020

Torix group Rickettsia are widespread in New Zealand freshwater amphipods: using blocking primers to rescue host COI sequences

Endosymbionts and intracellular parasites are common in arthropods and other invertebrate hosts. As a consequence, (co)amplification of untargeted bacterial sequences has been occasionally reported as a common problem in DNA barcoding. The bacterial genus Rickettsia belongs to the order Rickettsiales and consists of two lineages: one including diverse pathogens infecting arthropod hosts, the other consisting of non-pathogenic species with a broader host taxonomic range. While discriminating among amphipod species with universal primers for the COI region, we unexpectedly detected rickettsial endosymbionts belonging to the Torix group. To map the distribution and diversity of Rickettsia among amphipods hosts, we conducted a nationwide molecular screening of seven families of freshwater amphipods collected throughout New Zealand. In addition to uncovering a diversity of Torix group Rickettsia across multiple amphipod populations from three different families, our research indicates that 1) detecting Torix Rickettsia with universal primers is not uncommon, 2) obtaining Rickettsia COI sequences from many host individuals is highly likely when a population is infected, and 3) obtaining host COI may not be possible with a conventional PCR if an individual is infected. Because Rickettsia COI is highly conserved across diverse host taxa, we were able to design blocking primers that can be used in a wide range of host species infected with Torix Rickettsia. We propose the use of blocking primers to circumvent problems caused by unwanted amplification of Rickettsia and to obtain targeted host COI sequences for DNA barcoding, population genetics, and phylogeographic studies.

evolutionary biology↗

bioRxiv2017

The compound topology of a continent-wide host-parasite network explained by an integrative hypothesis of specialization.

Is there a prevalent pattern among interaction networks: nestedness or modularity? Must consumers always trade-off generalism for average performance in resource exploitation? These two questions have been addressed in various systems, with contradictory results. A recent integrative hypothesis combines both questions within a common theoretical framework, proposing that ecological specialization is structured by different prevailing processes in smaller and larger network units. This should produce both a compound interaction network, formed by internally nested modules, and a scale-dependence on the relationship between consumer performance and generalism. Here, we confirm both predictions in a large dataset on host-parasite interactions. We show that modules indeed constrain nestedness at the whole network level, and that the relationship between parasite generalism and performance on their hosts changed from negative at large to positive at small scales. Our results shed light on both debates, and provide some clues to their integration and solution.

ecology↗