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Genomics 1 12:00 - 13:00 Tuesday, 20Th July, 2021 Genomics Presentation Type Oral Genomics 1 12:00 - 13:00 Tuesday, 20th July, 2021 Genomics Presentation type Oral 12:00 - 12:15 O-2035 Divergence in Small RNA pathways between parasitic and free-living flatworms Santiago Fontenla1, Mauricio Langleib1, Gabriel Rinaldi2, Jose Tort1 1Departamento de Génetica, Facultad de Medicina-UdelaR, Montevideo, Uruguay. 2Wellcome Sanger Institute, Wellcome Genome Campus, Cambridgeshire, United Kingdom Abstract Platyhelminthes (‘flatworms’) comprise one of the major phyla of invertebrate animals, inhabiting a wide range of ecosystems, and one of the most successful in adapting to parasitic life. Small non-coding RNAs have been implicated in regulating complex developmental transitions in model parasitic species. Here, we analyzed and compared the conservation of key proteins of the small RNA pathways among several free-living (‘turbellarians’) and parasitic species (Neodermatans) to disentangle possible adaptations during the transition to parasitism. Additionally, we studied the expression of these genes in available databases of Platyhelminthes. Our findings showed that whilst all turbellarians have conserved Piwi pathway proteins, these were lost in parasitic Neodermantans. We identified a novel Piwi class Argonaute exclusive of turbellarians, which we named ‘Fliwi’. Additionally, Vasa, a mediator of the Piwi pathway, was detected in all turbellarians. Both, Fliwi and Vasa were preferentially expressed in neoblast cells (somatic stem cells). On the other hand, a flatworm- specific class of Argonautes (‘FLAgo’) was expanded in Neodermatans but not in turbellarians. Notably, FLAgo showed differential expression between the two clades. While displaying ubiquitous expression in turbellarian cells, in Neodermatans FLAgos were preferentially expressed in neoblasts and germline progenitors. Similar patterns were observed for PL-10, a paralogue of Vasa. Interestingly, the differences in the expression of these genes were not limited to the tissue level, showing important fluctuations across developmental stages in Neodermatans. Particular variants of Dicer genes without the amino terminal domains were found in trematodes and some species of turbellarians while an inverted tandem duplication in Food-borne trematodes may have led to a novel divert gene. In conclusion, the remarkable divergencies in the small RNA pathways between free-living and parasitic flatworms suggests that they may have been involved in the adaptation to parasitism of Neodermatans. Presenting author photograph Presenting author biography My name is Santiago Fontenla, I work at Department of Genetics, in the faculty of Medicine, in Montevideo, Uruguay. For the past 10 years I have been working in the genetics and genomics of helminthes, with special interest in the regulation by small RNAs and the small RNA pathways. 12:15 - 12:30 O-2036 Transcriptomic analysis of ivermectin resistance in Haemonchus contortus using a controlled genetic cross Roz Laing1, Stephen R Doyle2, Jennifer McIntyre1, Kirsty Maitland1, Ilona Flis1, Alison Morrison3, David Bartley3, Umer Chaudhry4, Neil Sargison5,6, Ray Kaplan7, Matthew Berriman2, Andy Tait1, James A Cotton2, Collette Britton1, Eileen Devaney1 1University of Glasgow, Glasgow, United Kingdom. 2Wellcome Sanger Institute, Cambridge, United Kingdom. 3Moredun Research Institute, Edinburgh, United Kingdom. 4University of Surrey, Surrey, United Kingdom. 5University of Edinburgh, Edinburgh, United Kingdom. 6Roslin Institute, Edinburgh, United Kingdom. 7University of Georgia, Athens, USA Abstract Infections with parasitic nematodes are ubiquitous in grazing livestock throughout the world and are a major threat to global food security. Related nematodes cause debilitating diseases in billions of humans in some of the poorest countries in the world. Control of parasitic infections in animals and humans currently relies on mass drug administration of a limited number of anthelmintics. However, this is not sustainable due to the emergence and spread of anthelmintic resistance. Haemonchus contortus is a highly pathogenic gastrointestinal nematode of small ruminants, which is becoming increasingly difficult to control due to multi-drug resistance. In the case of ivermectin, the mechanism(s) underlying resistance are poorly understood, with studies comparing resistant and sensitive parasites confounded by high levels of genetic diversity within and between populations. To overcome this, we crossed a well-characterised multi-drug resistant isolate of H. contortus (MHco18.UGA2004) with a drug susceptible isolate (MHco3.ISE) to study ivermectin resistance while controlling for background variation. F2 adults were treated with ivermectin in vivo and pools of their L3 progeny pre and post treatment were sequenced. Bulk segregant analyses of these populations identified a major locus on chromosome V under ivermectin selection. This locus contains none of the previously studied ‘candidate’ resistance genes from the literature and no putative target genes, implicating a novel driver of resistance. Functional characterisation is ongoing in H. contortus and transgenic Caenorhabditis elegans to identify which genes in the locus confer ivermectin resistance. Transcriptomic analysis of the parental isolates and F2 adults with and without ivermectin treatment identified differential expression of a small number of genes associated with neuronal development or plasticity, including a single gene within the chromosome V locus (HCON_00155390: cky-1) that is highly upregulated in geographically separated resistant populations. This gene has been the focus of our investigations so far. Presenting author photograph Presenting author biography I am a Wellcome Clinical Research Career Development Fellow at the University of Glasgow. My research interests include genomic and transcriptomic analyses of anthelmintic resistance in parasitic nematodes and improving diagnostics for veterinary parasites. 12:30 - 12:45 O-2037 Genomic landscape of anthelmintic selection in the gastrointestinal pathogen Haemonchus contortus Stephen Doyle Wellcome Sanger Institute, Cambridge, United Kingdom Abstract Introduction Drug resistance in parasitic helminths is widespread in a number of domesticated animal systems and represents a genuine threat to the sustainable control of species that parasitise humans. Unfortunately, the genetic basis of resistance to most anthelmintics remains poorly resolved. Materials and Methods As a key aim of the BUG Consortium, we have used a forward genetics approach together with whole-genome sequencing to unravel the genetic mediators of multidrug resistance in the gastrointestinal parasite, Haemonchus contortus. We performed a genetic cross between susceptible MHco3(ISE) and triple resistant (benzimidazole, levamisole & ivermectin) MHco18(UGA) parasites, after which we sampled the F3 population both pre- and post-treatment of the F2 population in vivo for each of the three drug classes. Results For each of the drug classes, we identify discrete, non-overlapping regions of the genome linked to resistance, including known and novel putatively causal variants with strong association benzimidazole and levamisole resistance. For ivermectin, a more complex signature of selection was apparent, indicative of multiple genes contributing to resistance. However, together with sampling of phenotyped field isolates, we have refined a major QTL leading to the identification of a novel candidate gene. Discussion These data provide an important genome-wide overview of the genetic response to anthelmintic treatment and an insight into the evolution and spread of resistance. Presenting author photograph Presenting author biography Stephen is a molecular and computational biologist at the Wellcome Sanger Institute near Cambridge, UK. His work is focused on characterising the genetic diversity of human and veterinary helminths to understand their evolutionary history and how they will adapt to change in the future. He primarily uses genomic approaches to reconstruct parasite genomes to generate genetic "blueprints" of a parasite, and then uses high-throughput approaches to analyse genetic variation in many individuals and population to uncover how they adapt to different environments, and in particular, the genetic changes to become resistant to the drugs we use to control them. 12:45 - 13:00 O-2038 Comparison of gene expression in different developmental stages of Cystoisospora suis Teresa Cruz-Bustos, Emmanouil Lyrakis, Anna Sophia Feix, Marlies Dolezal, Bärbel Ruttkowski, Anja Joachim Vetmeduni Vienna, Vienna, Austria Abstract Cystoisospora suis is an apicomplexan parasite and an entero-pathogen of suckling piglets. As with all coccidian parasites, the lifecycle is characterized by asexual multiplication followed by sexual development with two morphologically distinct cell types which presumably fuse to form a zygote from which the oocyst arises. The aim of this project was to perform RNAseq of C. suis harvested at different developmental stages in vitro to better understand the transcriptional changes underlying the developmental processes in this parasite and possibly closely related species. Epithelial cells were infected with C. suis and supernatants were harvested at three time points (T) at 6 to 14 days of cultivation to obtain merozoites as well as gamonts and oocysts. We produced poly-A enriched 75bp single end, stranded RNA-seq data for differential gene expression analysis. Data was mapped against a hybrid genome of C. suis (strain Wien I) and
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