Investigating the evolution and ecology of obscure bacterial symbioses found in invertebrates, ciliates and algae.

Bacterial symbioses form a fundamental part of the biology of most eukaryotic lifeforms, influencing their evolution, ecology, and behaviour. Their importance has been increasingly recognised in the last few decades, aided by advances in genomic and bioinformatic methods and analyses. As with most emerging fields, most of our knowledge comes from selected ‘model’ case studies, leaving the breadth of possible symbioses poorly explored. In this thesis I utilise a combination of bioinformatics, genomics, fieldwork, and microscopy to explore obscure symbioses across invertebrates, algae, and ciliates. First, I broaden the scope of available genomic and metabolic data available for rarer symbionts in invertebrates, a group that are often studied for their heritable symbionts. I argue that the group previously called Torix Rickettsia is distinct and diverse and should be regarded as a genus with at least three species, which I name ‘Candidatus Tisiphia’. I also report the first genome for the genus ‘Candidatus Megaira’, a widely recorded but poorly understood symbiont of microeukaryotes. I then explored the distribution of various symbiotic bacteria found in ciliates and algae, two host groups that are known to have strong links to symbiotic bacteria and the origins of symbioses but are rarely examined. I show the genus ‘Ca. Megaira’ appears as a deeply diverse, multi-species group of symbionts that is deserving of family status. I find ‘Ca. Megaira’ in both algae and ciliate species and infer that they have the potential to form protective symbioses. Likewise, I find diverse Parachlamydiales in algae and ciliates and propose three new species groups to aid taxonomic clarification of these bacteria. I provide potential microeukaryotic hosts for a group that are often divorced from host species when described and propose the possibility of nutritional and protective symbioses. Lastly, I develop a potential host-symbiont study system for future functional studies. Here, I demonstrate the existence of a likely heritable Ca. Tisiphia symbiont in the mosquito Anopheles plumbeus. It represents a potentially important system for onward application in manipulation of anopheline vector populations, which are currently restricted to a single symbiont. Finally, I synthesize these findings and argue future research should focus on the phenotypes of real-world symbioses discovered within this research

Classification of porcine reproductive and respiratory syndrome clinical impact in Ontario sow herds using machine learning approaches

Since the early 1990s, porcine reproductive and respiratory syndrome (PRRS) virus outbreaks have been reported across various parts of North America, Europe, and Asia. The incursion of PRRS virus (PRRSV) in swine herds could result in various clinical manifestations, resulting in a substantial impact on the incidence of respiratory morbidity, reproductive loss, and mortality. Veterinary experts, among others, regularly analyze the PRRSV open reading frame-5 (ORF-5) for prognostic purposes to assess the risk of severe clinical outcomes. In this study, we explored if predictive modeling techniques could be used to identify the severity of typical clinical signs observed during PRRS outbreaks in sow herds. Our study aimed to evaluate four baseline machine learning (ML) algorithms: logistic regression (LR) with ridge and lasso regularization techniques, random forest (RF), k-nearest neighbor (KNN), and support vector machine (SVM), for the clinical impact classification of ORF-5 sequences and demographic data into high impact and low impact categories. First, baseline classifiers were evaluated using different input representations of ORF-5 nucleotides, amino acid sequences, and demographic data using a 10-fold cross-validation technique. Then, we designed a consensus voting ensemble approach to aggregate the different types of input representations for genetic and demographic data for classifying clinical impact. In this study, we observed that: (a) for abortion and pre-weaning mortality (PWM), different classifiers gained improvement over baseline accuracy, which showed the plausible presence of both genotypic-phenotypic and demographic-phenotypic relationships, (b) for sow mortality (SM), no baseline classifier successfully established such linkages using either genetic or demographic input data, (c) baseline classifiers showed good performance with a moderate variance of the performance metrics, due to high-class overlap and the small dataset size used for training, and (d) the use of consensus voting ensemble techniques helped to make the predictions more robust and stabilized the performance evaluation metrics, but overall accuracy did not substantially improve the diagnostic metrics over baseline classifiers

RNA Interference

RNA interference (RNAi), a hallmark of all biological sciences of twenty-first century, is an evolutionarily conserved and double-stranded RNA-dependent eukaryotic cell defense process. Opportunity to utilize an organisms own gene and to systematically induce and trigger RNAi for any desired sequence made RNAi an efficient approach for functional genomics, providing a solution for conventional longstanding obstacles in life sciences. RNAi research and application have significantly advanced during past two decades. This book RNA interference provides an updated knowledge and progress on RNAi in various organisms, explaining basic principles, types, and property of inducers, structural modifications, delivery systems/methodologies, and various successful bench-to-field or clinic applications and disease therapies with some aspects of limitations, alternative tools, safety, and risk assessment

Genome-enabled insights into the biology of thrips as crop pests

Background The western flower thrips, Frankliniella occidentalis (Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber, and ornamental crops. The underlying genetic mechanisms of the processes governing thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance are largely unknown. To address this gap, we present the F. occidentalis draft genome assembly and official gene set. Results We report on the first genome sequence for any member of the insect order Thysanoptera. Benchmarking Universal Single-Copy Ortholog (BUSCO) assessments of the genome assembly (size = 415.8 Mb, scaffold N50 = 948.9 kb) revealed a relatively complete and well-annotated assembly in comparison to other insect genomes. The genome is unusually GC-rich (50%) compared to other insect genomes to date. The official gene set (OGS v1.0) contains 16,859 genes, of which ~ 10% were manually verified and corrected by our consortium. We focused on manual annotation, phylogenetic, and expression evidence analyses for gene sets centered on primary themes in the life histories and activities of plant-colonizing insects. Highlights include the following: (1) divergent clades and large expansions in genes associated with environmental sensing (chemosensory receptors) and detoxification (CYP4, CYP6, and CCE enzymes) of substances encountered in agricultural environments; (2) a comprehensive set of salivary gland genes supported by enriched expression; (3) apparent absence of members of the IMD innate immune defense pathway; and (4) developmental- and sex-specific expression analyses of genes associated with progression from larvae to adulthood through neometaboly, a distinct form of maturation differing from either incomplete or complete metamorphosis in the Insecta. Conclusions Analysis of the F. occidentalis genome offers insights into the polyphagous behavior of this insect pest that finds, colonizes, and survives on a widely diverse array of plants. The genomic resources presented here enable a more complete analysis of insect evolution and biology, providing a missing taxon for contemporary insect genomics-based analyses. Our study also offers a genomic benchmark for molecular and evolutionary investigations of other Thysanoptera species

Genome-enabled insights into the biology of thrips as crop pests

Background The western flower thrips,Frankliniella occidentalis(Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber, and ornamental crops. The underlying genetic mechanisms of the processes governing thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance are largely unknown. To address this gap, we present theF. occidentalisdraft genome assembly and official gene set.Results We report on the first genome sequence for any member of the insect order Thysanoptera. Benchmarking Universal Single-Copy Ortholog (BUSCO) assessments of the genome assembly (size = 415.8 Mb, scaffold N50 = 948.9 kb) revealed a relatively complete and well-annotated assembly in comparison to other insect genomes. The genome is unusually GC-rich (50%) compared to other insect genomes to date. The official gene set (OGS v1.0) contains 16,859 genes, of which similar to 10% were manually verified and corrected by our consortium. We focused on manual annotation, phylogenetic, and expression evidence analyses for gene sets centered on primary themes in the life histories and activities of plant-colonizing insects. Highlights include the following: (1) divergent clades and large expansions in genes associated with environmental sensing (chemosensory receptors) and detoxification (CYP4, CYP6, and CCE enzymes) of substances encountered in agricultural environments; (2) a comprehensive set of salivary gland genes supported by enriched expression; (3) apparent absence of members of the IMD innate immune defense pathway; and (4) developmental- and sex-specific expression analyses of genes associated with progression from larvae to adulthood through neometaboly, a distinct form of maturation differing from either incomplete or complete metamorphosis in the Insecta.Conclusions Analysis of theF. occidentalisgenome offers insights into the polyphagous behavior of this insect pest that finds, colonizes, and survives on a widely diverse array of plants. The genomic resources presented here enable a more complete analysis of insect evolution and biology, providing a missing taxon for contemporary insect genomics-based analyses. Our study also offers a genomic benchmark for molecular and evolutionary investigations of other Thysanoptera species.Animal science

Etude de peptides de venin de fourmis : diversité moléculaire et lien avec la fonction immunitaire

Les venins d’animaux sont des bibliothèques naturelles de composés bioactifs optimisés au cours de l’évolution, appelés toxines. Les venins de nombreux animaux restent néanmoins inexploités, notamment ceux des insectes. Plusieurs études portant sur les venins de fourmis ont révélé que ces venins étaient riches en peptides. La caractérisation du peptidome du venin de Tetramorium bicarinatum a également permis de constater que, malgré la diversité de peptides matures, ces derniers se classent en 3 grandes familles de précurseurs dont certaines ont déjà été décrites chez d’autres hyménoptères. Il est de plus apparu que des gènes codant certains d’entre eux s’expriment en dehors du système vulnérant. Ces résultats posent les questions des mécanismes impliqués dans la diversification des toxines peptidiques de venins de fourmis, ainsi que leur rôle en dehors de la fonction venimeuse. Pour répondre à ces problématiques, la première partie de ce travail de thèse a consisté en la caractérisation via des approches protéotranscriptomiques, des venins de 7 espèces de fourmis appartenant aux différentes tribus phylogénétiques de la sousfamille des Myrmicinae, et du venin d’une espèce appartenant à une sous-famille proche, les Pseudomyrmecinae. Cent toxines peptidiques aux structures variées ont ainsi été identifiées et classées en 8 superfamilles de précurseurs. La seconde partie a consisté en l’exploration du lien entre les toxines peptidiques du venin de T. bicarinatum et son immunité innée via des méthodes de biologie moléculaire et cellulaire. La présence de transcrits codant certains peptides a été vérifiée dans des organes impliqués dans l’immunité innée (i.e. corps gras, tubes digestifs). L’expression des gènes les codant a également été évaluée suite à une infection bactérienne. Il a ainsi été montré que les transcrits codant les peptides de venin sélectionnés sont présents dans les organes testés, et que certains sont produits dans les corps gras en réponse à une infection bactérienne. Ces résultats confirment l’existence d’un lien entre les peptides de venin et l’immunité innée de la fourmi T. bicarinatum, bien que des études complémentaires soient nécessaire