Approche plurielle à l'étude de la structure tertiaire de l'ARN chez les virus

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal

Correlation of LNCR rasiRNAs Expression with Heterochromatin Formation during Development of the Holocentric Insect Spodoptera frugiperda

Repeat-associated small interfering RNAs (rasiRNAs) are derived from various genomic repetitive elements and ensure genomic stability by silencing endogenous transposable elements. Here we describe a novel subset of 46 rasiRNAs named LNCR rasiRNAs due to their homology with one long non-coding RNA (LNCR) of Spodoptera frugiperda. LNCR operates as the intermediate of an unclassified transposable element (TE-LNCR). TE-LNCR is a very invasive transposable element, present in high copy numbers in the S. frugiperda genome. LNCR rasiRNAs are single-stranded RNAs without a prominent nucleotide motif, which are organized in two distinct, strand-specific clusters. The expression of LNCR and LNCR rasiRNAs is developmentally regulated. Formation of heterochromatin in the genomic region where three copies of the TE-LNCR are embedded was followed by chromatin immunoprecipitation (ChIP) and we observed this chromatin undergo dynamic changes during development. In summary, increased LNCR expression in certain developmental stages is followed by the appearance of a variety of LNCR rasiRNAs which appears to correlate with subsequent accumulation of a heterochromatic histone mark and silencing of the genomic region with TE-LNCR. These results support the notion that a repeat-associated small interfering RNA pathway is linked to heterochromatin formation and/or maintenance during development to establish repression of the TE-LNCR transposable element. This study provides insights into the rasiRNA silencing pathway and its role in the formation of fluctuating heterochromatin during the development of one holocentric organism

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Approche plurielle à l'étude de la structure tertiaire de l'ARN chez les virus

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal

Transposable Element Annotation in Completely Sequenced Eukaryote Genomes

Chapter 2With the development of new sequencing techniques, the number of sequenced plant genomes is increasing. However, accurate annotation of these sequences remains a major challenge, in particular with regard to transposable elements (TEs). The aim of this chapter is to provide a roadmap for researchers involved in genome projects to address this issue. We list several widely used tools for each step of the TE annotation process, from the identification of TE families to the annotation of TE copies. We assess the complementarities of these tools and suggest that combined approaches, using both de novo and knowledge-based TE detection methods, are likely to produce reasonably comprehensive and sensitive results. Nevertheless, existing approaches still need to be supplemented by expert manual curation. Hence, we describe good practice required for manual curation of TE consensus sequences

Roadmap for Annotating Transposable Elements in Eukaryote Genomes

Chapter 3Current high-throughput techniques have made it feasible to sequence even the genomes of non-model organisms. However, the annotation process now represents a bottleneck to genome analysis, especially when dealing with transposable elements (TE). Combined approaches, using both de novo and knowledge-based methods to detect TEs, are likely to produce reasonably comprehensive and sensitive results. This chapter provides a roadmap for researchers involved in genome projects to address this issue. At each step of the TE annotation process, from the identification of TE families to the annotation of TE copies, we outline the tools and good practices to be use

Transcript profiling reveals the role of PDB1, a subunit of the pyruvate dehydrogenase complex, in Candida albicans biofilm formation

International audienceCandida albicans, the most prevalent fungal pathogen in the human microbiota can form biofilms on implanted medical devices. These biofilms are tolerant to conventional antifungal drugs and the host immune system as compared to the free-floating planktonic cells. Several in vitro models of biofilm formation have been used to determine the C. albicans biofilm-forming process, regulatory networks, and their properties. Here, we performed a genome-wide transcript profiling with C. albicans cells grown in YPD medium both in planktonic and biofilm condition. Transcript profiling of YPD-grown biofilms was further compared with published Spider medium-grown biofilm transcriptome data. This comparative analysis highlighted the differentially expressed genes and the pathways altered during biofilm formation. In addition, we demonstrated that overexpression of the PDB1 gene encoding a subunit of the pyruvate dehydrogenase resulted in defective biofilm formation. Altogether, this comparative analysis of transcript profiles from two different studies provides a robust reading on biofilm-altered genes and pathways during C. albicans biofilm development

Lepido-DB, a new bioinformatic resource for the annotation and cross-comparisons of lepidopteran genomes.

International audienceLepido-DB is a centralized bioinformatic resource that was first developed to facilitate the comparative genomics of two major lepidopteran pests, the noctuid moths Helicoverpa armigera and Spodoptera frugiperda, by the analyzis of syntenic relationships and genome rearrangements of 15 pairs of BACs sequences and their corresponding colinear regions extracted from 10 Bombyx mori chromosomes. In this context, Lepido-DB Information System was designed to store, organize, display and distribute various genomic data and annotations of the three species. For instance, we supplied Lepido-DB with the KAIKOGAAS automatic annotations, the comparisons to insects proteomes and UniProt, the alignments of transcript sequences (retrieved from the Spodoptera SpodoBase, from CSIRO Helicoverpa ESTs or from NCBI Bombyx ESTs), the REPET pipeline's transposable elements predictions, or results of different cross-comparisons process to emphasize conserved regions and orthologous genes. The system was constructed using open source software tools from the Generic Model Organism Database (GMOD, http://www.gmod.org) including - a Chado database, - Gbrowse, a simple but rapid genome browser, - CMAP a graphical tool which facilitates the navigation within multiple maps or genome sequences, - Apollo, an application for the manual curation. Finally, beside a blast search and a full text search facilities, we released a gene report system offering gene information at a glance, such as transcripts and peptides sequences, functional annotations, or expression level based on its EST coverage. Lepido-DB can be accessed at http://www.inra.fr/lepidodb. In a larger scope, ensuing the AphidBase experience, this system may definitely support complete genomes sequencing and annotation projects, or any other project based on deep sequencing strategies (expression profiling by RNA-Seq, variability studies, ChIP- Seq, ...) for various Lep species

Dynamique, déterminants de la colonisation et évolution génomique de Candida albicans en situation de commensalisme : une étude dans une population amérindienne vivant isolée en Guyane française

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