Biology subjects

Haudry, A.

Publications and source records attributed to Haudry, A..

4 recordsLinked to original sources

bioRxiv2025

Manual versus automatic annotation of transposable elements: case studies in Drosophila melanogaster and Aedes albopictus, balancing accuracy and biological relevance

Transposable elements (TEs) play a pivotal role in genome evolution, yet their detection and annotation remain challenging due to the limitations of current methods. Manual curation is considered the gold standard for generating TE libraries, particularly for TE focused studies, although it requires extensive training and time. With the rapid increase in genome assembly publications and the growing need for large-scale comparative analyses, automated software for TE annotation has become indispensable. This study compares manual and automated approaches to TE detection and annotation, focusing on two species: Drosophila melanogaster and Aedes albopictus. In D. melanogaster, a species with a well-annotated TE repertoire and a smaller genome, the differences between manual curation (MCTE) and automated annotation (ATTE) are relatively minor. However, significant differences arise when analysing Ae. albopictus, a species with a larger genome and higher TE diversity. While automated methods identified a greater number of TEs, including many smaller and fragmented elements, manual curation provided more detailed classifications and on average larger consensi. Automated pipelines offer a viable alternative for genome-wide analyses such as TE content estimate, particularly when time and resources are limited. However, caution is advised when interpreting results, as finer details of TE dynamics may be overlooked. This study highlights that the choice of annotation method depends on the intended analysis. Manual curation is more suitable for TE population genomics and studies focusing on recent transposable element activity, while automated methods are appropriate for larger comparative analyses or genome assembly projects. Ultimately, both methods have their strengths and limitations, and understanding the specific features of the genome and repeatome under study is essential for selecting the appropriate approach.

genomics↗

bioRxiv2024

Effective population size does not explain long-term variation in genome size and transposable element content in animals

Animal genomes exhibit a remarkable variation in size, but the evolutionary forces responsible for such variation are still debated. As the effective population size (Ne) reflects the intensity of genetic drift, it is expected to be a key determinant of the fixation rate of nearly-neutral mutations. Accordingly, the Mutational Hazard Hypothesis postulates lineages with low Ne to have bigger genome sizes due to the accumulation of slightly deleterious transposable elements (TEs), and those with high Ne to maintain streamlined genomes as a consequence of a more effective selection against TEs. However, the existence of both empirical confirmation and refutation using different methods and different scales precludes ts general validation. Using high-quality public data, we estimated genome size, TE content and rate of non-synonymous to synonymous substitutions (dN/dS) as Ne proxy for 807 species including vertebrates, molluscs and insects. After collecting available life-history traits, we tested the associations among population size proxies, TE content and genome size, while accounting for phylogenetic non-independence. Our results confirm TEs as major drivers of genome size variation, and endorse life-history traits and dN/dS as reliable proxies for Ne. However, we do not find any evidence for increased drift to result in an accumulation of TEs across animals. Within more closely related clades, only a few isolated and weak associations emerge in fishes and birds. Our results outline a scenario where TE dynamics vary according to lineage-specific patterns, lending no support for genetic drift as the predominant force driving long-term genome size evolution in animals.

evolutionary biology↗

bioRxiv2019

Evidence for purifying selection on conserved noncoding elements in the genome of Drosophila melanogaster

Identification of regulatory regions within genomes is a key challenge for understanding the influence of functional traits on species evolution. Development of whole-genome sequencing programs in the early 2000s has been associated with the rise of comparative genomics as a powerful tool for predicting functional regions in genomes, using structural characteristics of DNA sequences. Conserved Noncoding Elements (CNEs, i.e. untranslated sequences highly similar across divergent species) were early identified as candidate regulatory regions in metazoans, plants, and fungi. CNEs have been repeatedly discriminated from mutational cold-spots, but only few studies have assessed their functional relevance at a genome-wide scale. In the present study, we used a whole-genome alignment of 27 insect species to build a coherent mapping of CNEs in the genome of Drosophila melanogaster. We then exploited polymorphism data from 48 European populations of D. melanogaster to estimate levels of nucleotide diversity and adaptive evolution in CNEs. We show here that about 35% of D. melanogaster autosomes fall into conserved noncoding regions that exhibit reduced genetic diversity and undergo purifying selection. In addition, we report six insertions of Transposable Elements (TEs) in the genome of D. melanogaster showing high levels of conservation across Drosophila species. Half of these insertions are located in untranslated transcribed regions (UTRs) of genes involved in developmental pathways and thus represent potential relics of ancient TE domestication events.

evolutionary biology↗

bioRxiv2018

Genomic analysis of European Drosophila melanogaster populations on a dense spatial scale reveals longitudinal population structure and continent-wide selection

Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatio-temporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. Here, we address these issues using a collaborative approach, sequencing 48 pooled population samples from 32 locations, and perform the first continent-wide genomic analysis of genetic variation in European Drosophila melanogaster. Our analyses uncover longitudinal population structure, provide evidence for continent-wide selective sweeps, identify candidate genes for local climate adaptation, and document clines in chromosomal inversion and transposable element frequencies. We also characterise variation among populations in the composition of the fly microbiome, and identify five new DNA viruses in our samples.

evolutionary biology↗