Mots-Clés

Naegleria Genome Assembly Annotation Comparative Genomics Virulence Linux Bioinformatics Pipeline

Description

TITLE: Comparative genomics of Naegleria species to improve knowledge on N. fowleri pathogenesis.

• Host institution : Institut Pasteur de la Guadeloupe (IPG)

• Director of the Institute: Antoine DES GRAVIERS

• Coordinator of the Training: Nina ALLOUCH (Research Engineer in Bioinformatics), Isabel MARCELINO (PhD, HDR)

Context and Research Problem :

Members of the Naegleria genus belong to the major eukaryotic lineage Heterolobosea. These free-living amoebae (unicellular eukaryotes) are ubiquitous in soils and freshwater habitats, being important predators of bacteria. Of the 47 Naegleria species described, N. fowleri is the only one being pathogenic to humans, causing a rare but fulminant primary amoebic meningoencephalitis, with 97% mortality. Despite the significant clinical implications of N. fowleri and ongoing research on its genome, the genomic mechanisms underlying its pathogenicity remain largely unknown. During this internship, the student will explore, for the first time, the genome of Naegleria australiensis (known to be pathogenic only to animals). For this, Illumina short reads and Nanopore long reads obtained from whole genome sequencing will be used, followed by reads assembly and structural and functional annotation of N. australiensis genome. The intern will then perform a comparative analysis between N. australiensis and N. fowleri genomes to identify key genetic differences that may drive pathogenicity and biology of these Naegleria species.

Objectives :

1. Genome Assembly and Annotation: Conduct the first complete genome assembly and annotation of Naegleria australiensis using established bioinformatics tools previously applied to Naegleria fowleri by our team. This process includes quality control, read filtration, assembly, repeat detection, and both structural and functional gene annotation.

2. Genomic and Comparative Analysis: Examine the genomic features of N. australiensis to identify potential virulence factors. Perform comparative genomics between N. australiensis and N. fowleri to investigate genetic variations (SNPs, structural rearrangements, differences in gene functions …) that may elucidate the distinct pathogenicity and biology of these species.

Expected Outcomes :

• A high-quality, annotated genome of Naegleria autraliensis.

• Identification of key genomic differences between N. australiensis and N. fowleri, improving our understanding of pathogenicity.

• An optimized bioinformatics pipeline for future Naegleria genome projects.

• Contribution to a peer-reviewed publication on the genomic characteristics of Naegleria australiensis and its comparison with N. fowleri.

Available Resources :

• Raw sequencing data from Naegleria australiensis isolates in Guadeloupe.

• Access to computational resources, including a cluster and servers at Université des Antilles.

• Guidance from a team of bioinformatician and biologist at the Institut Pasteur de la Guadeloupe.

Candidate Profile :

• Education: Master’s degree (M2) in Bioinformatics or a related field.

• Skills: Proficient in Linux and server environments, with familiarity in genome assembly and annotation tools as a plus.

• Biology: Strong foundation in biology and genomics.

• Collaboration: Excellent communication and writing skills, with ability to work effectively in a research team.

Internship Details :

Start Date: Between January-March 2025

Duration: 6 months

This internship offers the opportunity to work on an emerging pathogen using advanced genomic bioinformatics techniques. The candidate will gain hands-on experience in microbial genomics and contribute to the first genomic characterization of Naegleria australiensis.

Contact:  Send your CV and letter of motivation to nallouch@pasteur-guadeloupe.fr (Nina ALLOUCH)