Biology subjects

Boudry, A.

Publications and source records attributed to Boudry, A..

2 recordsLinked to original sources

bioRxiv2025

Rapid temporal adaptation structures tolerance to toxic cyanobacteria in a natural population of the water flea Daphnia.

Cyanobacteria blooms pose a substantial threat to freshwater systems globally. While zooplankton grazers such as Daphnia can have an important role in suppressing cyanobacteria blooms, cyanobacteria can adversely impact Daphnia fitness and even kill them. Earlier work has shown an evolutionary increase in tolerance to cyanobacteria across years and strong genotype x genotype interactions determining the interaction between Daphnia and the cyanobacterium Microcystis. Here, we test the hypothesis that D. magna can adapt during one growing season to changes in dominant strains of Microcystis. Over two consecutive years, we collected D. magna clonal lineages and Microcystis strains from a single pond early and late in the growing season and we assessed whether Daphnia survival differed when exposed to Microcystis strains from either the same or a different time point within the growth season. Our findings reveal important Daphnia genotype x Microcystis genotype interactions, with Daphnia survival being higher when exposed to Microcystis from the same time point than when exposed to Microcystis of a different time point. Our results extend earlier findings to variation within one single natural system and growth season, and suggest an important impact of rapid (co)evolutionary dynamics shaping the tolerance of zooplankton grazers to cyanobacteria.

evolutionary biology↗

bioRxiv2022

Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r

BackgroundInternal tandem duplications in the FLT3 gene, termed FLT3-ITDs, are useful molecular markers in acute myeloid leukemia (AML) for patient risk stratification and follow-up. FLT3-ITDs are increasingly screened through high-throughput sequencing (HTS) raising the need for robust and efficient algorithms. We developed a new algorithm, which performs no alignment and uses little resources, to identify and quantify FLT3-ITDs in HTS data. ResultsOur algorithm (FiLT3r) focuses on the k-mers from reads covering FLT3 exons 14 and 15. We show that those k-mers bring enough information to accurately detect, determine the length and quantify FLT3-ITD duplications. We compare the performances of FiLT3r to state-of-the-art alternatives and to fragment analysis, the gold standard method, on a cohort of 185 AML patients sequenced with capture-based HTS. On this dataset FiLT3r is more precise (no false positive nor false negative) than the other software evaluated. We also assess the software on public RNA-Seq data, which confirms the previous results and shows that FiLT3r requires little resources compared to other software. ConclusionFiLT3r is a free software available at https://gitlab.univ-lille.fr/filt3r/filt3r. The repository also contains a Snakefile to reproduce our experiments. We show that FiLT3r detects FLT3-ITDs better than other software while using less memory and time.

bioinformatics↗