Biology subjects

Pombert, J.-F.

Publications and source records attributed to Pombert, J.-F..

4 recordsLinked to original sources

bioRxiv2026

SecretTarget: A pipeline for identifying host-interacting effector candidates through secondary localization features

Intracellular parasites cause over 226 million disability-adjusted life years (DALY) globally each year. Current treatment methods fall short of desirable impact due to adverse effects and growing resistance, shifting focus to parasitic effectors for future therapeutic development. Unfortunately, the divergent nature of parasitic proteins has impeded in silico discovery of - and functional inference for - parasitic effectors. Here, we present SecretTarget, a pipeline designed to identify host-interacting effector candidates through secondary localization features. By truncating signal peptides from predicted extracellular proteins ({Delta}SP), we unmask potential underlying localization features that dictate subcellular trafficking within the host. Applying our pipeline to a set of Toxoplasma gondii secreted effectors with known localizations and interactions, we propose a novel host ER-parasite interaction critical for parasite survival, recapitulate published localizations, and provide meaningful biological insights aligning with recent host-parasite interaction discoveries.

bioinformatics↗

bioRxiv2024

SYNY: a pipeline to investigate and visualize collinearity between genomes

Investigating collinearity between chromosomes is often used in comparative genomics to help identify gene orthologs, pinpoint genes that might have been overlooked as part of annotation processes and/or perform various evolutionary inferences. Collinear segments, also known as syntenic blocks, can be inferred from sequence alignments and/or from the identification of genes arrayed in the same order and relative orientations between investigated genomes. To help perform these analyses and assess their outcomes, we built a simple pipeline called SYNY (for synteny) that implements the two distinct approaches and produces different visualizations. The SYNY pipeline was built with ease of use in mind and runs on modest hardware. The pipeline is written in Perl and Python and is available on GitHub (https://github.com/PombertLab/SYNY) under the permissive MIT license.

bioinformatics↗

bioRxiv2023

Near chromosome-level genome assembly of the microsporidium Hamiltosporidium tvaerminnensis

Microsporidia are intracellular parasitic fungi whose genomes rank among the smallest of all known eukaryotes. A number of outstanding questions remain concerning the evolution of their large-scale variation in genome architecture, responsible for genome size variation of more than an order of magnitude. This genome report presents a first near-chromosomal assembly of a large-genome microsporidium, Hamiltosporidium tvaerminnensis. Combined Oxford Nanopore, Pacific Biosciences, and Illumina sequencing led to a genome assembly of 17 contigs, 11 of which represent complete chromosomes. Our assembly is 21.64 Mb in length, has an N50 of 1.44 Mb, and consists of 39.56 % interspersed repeats. We introduce a novel approach in microsporidia, PacBio Iso-Seq, as part of a larger annotation pipeline for obtaining high-quality annotations of 3,573 protein-coding genes. Based on direct evidence from the full-length Iso-Seq transcripts, we present evidence for alternative polyadenylation and variation in splicing efficiency, which are potential regulation mechanisms for gene expression in microsporidia. The generated high-quality genome assembly is a necessary resource for comparative genomics that will help elucidate the evolution of genome architecture in response to intracellular parasitism. SignificanceMicrosporidia are a model for genome evolution in response to intracellular parasitism, but we lack high-quality resources from species with large genomes. We present a near complete assembly of a large-genome microsporidium, Hamiltosporidium tvaerminnensis, and obtain high-quality gene annotations through full-length transcripts using Iso-Seq, a novel approach in microsporidia. Our study provides insights into gene regulation and paves the way for comparative genomic analyses aiming to understand the evolution of genome reduction and expansion in these intracellular parasites.

genomics↗

bioRxiv2020

Longitudinal survey reveals delayed effects of forager gene expression on stingless bee colony health

Bee populations are declining globally due to different environmental stressors, such as pathogens, malnutrition, and agrochemicals. Brazil is the home of hundreds of stingless bee species, some of them now considered endangered, though very little is known about the impact of disease on native bees. In Southern Brazil the endangered stingless bee Melipona quadrifasciata is affected by an annual syndrome that causes sudden death of workers, eventually leading colonies to collapse. Although novel viruses were found in foragers from diseased colonies, none has been consistently implicated in the outbreak. Here we used transcriptomics in combination with an integrative longitudinal survey on managed colonies to identify predictors for preventing M. quadrifasciata colony failures. We found that key genes related to xenobiotic metabolization, nutrition and immune responses are downregulated in foragers from colonies that became diseased three months later. The period that preceded the outbreak was marked by pronounced forager weight loss as well as behavioural changes. Our findings support the proposition that worldwide bee mortality is influenced by a combination of diverse sublethal factors, and increase awareness of the long-term effects of genetic diversity erosion in stingless bee species, which enhances their vulnerability to environmental stressors.

pathology↗