Biology subjects

Baril, T. J.

Publications and source records attributed to Baril, T. J..

6 recordsLinked to original sources

bioRxiv2026

Earl Grey ParTEA: scalable, consistent transposable element annotation from pangenomes to deep phylogenetic scopes

Transposable elements (TEs) are major drivers of genomic diversity, yet understanding their mobility and functional impact requires their accurate description in genomes. TE annotation is still typically performed genome-by-genome. TEs are often shared between some members of the same or closely related species. Hence, TE annotation with a library from a single reference misses families absent from that assembly, whereas building independent per-genome libraries fails to consistently surface shared TEs, hindering comparison. Here, we present Earl Grey ParTEA, a fully automated Snakemake pipeline extending the functionality of Earl Grey for comparative TE annotation across genome panels. ParTEA builds a single non-redundant TE library from all input genomes, resolves chimeric consensus sequences, and uses this shared library to annotate every genome, enabling direct comparison of TE family diversity, abundance, shared and private content, and activity landscapes. Optional modules provide TE library saturation analysis, BUSCO-based assembly quality control, and phylogenetic ordering of outputs. We applied ParTEA to sets of genomes spanning evolutionary scales: ten Arabidopsis thaliana accessions, ten Drosophila species, and ten species spanning the fungal kingdom. The Drosophila TE library expanded from 343 to 1,852 curated families including a previously missed rolling circle element with over 6,000 copies in D. miranda. The proportion of TE families shared across all genomes was highest within A. thaliana (97.3%), 37.7% across Drosophila species and only 0.5% across the set of fungi. ParTEA is available through Bioconda and represents a computationally efficient reproducible framework for comparative TE analysis in the era of large-scale genome analyses.

bioinformatics↗

bioRxiv2025

MycoMobilome: A community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom

Transposable elements (TEs) are found in nearly all eukaryotic genomes. Despite significant advances in the sequencing of genomes, TE resources remain sparse, leading to a lack of traceability, reproducibility, and duplication of effort when annotating TEs. Here, we focus on the fungal kingdom and present MycoMobilome, a non-redundant database of TE consensus sequences systematically curated using a set of 4,309 genomes covering all major clades. The initial database contains 276,641 consensus sequences after filtering to remove putative host genes and low-quality consensus sequences. We provide a consistent naming convention to surface information on the confidence in the classification including potential conflicting ORF functions, along with metadata to enable evaluation of TEs of interest and to determine whether further curation work is required on a case-by-case basis. Finally, we provide guidelines for community contributions, and encourage researchers to deposit new or curated sequences, which will be incorporated into future MycoMobilome releases.

genomics↗

bioRxiv2025

Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen

Transposable elements (TEs) can drive the evolution of host-pathogen interactions and gains in antimicrobial resistance. However, how adaptive TEs arise in populations and historical contingencies affect TE dynamics remains unknown. Fungal pathogens in agriculture provide unique frameworks to address such questions due to the availability of spatially explicit sampling and well- characterized niche conditions. We characterised TE evolutionary dynamics using an extensive intraspecies sampling of 1,953 genomes across the global distribution range of the major fungal wheat pathogen Zymoseptoria tritici. Employing a pangenomic approach, we characterise genomic diversity and benchmark methods to robustly infer TE insertion polymorphism, before systematically assessing TEs as a source of adaptive variation. We annotated [~]3.2 million TE loci among genomes, finding substantial variation in TE content within and among populations. TE activity surged during the pathogens expansion from its centre of origin in the Middle East, with unique TE activity profiles arising in derived populations. TE-mediated adaptation emerged from distinct waves of TE mobilization. The highest rates of TE activity were observed over timescales as short as 25 years. 45 TE loci showing local adaptation signatures within 1kb of 49 host genes were identified, with adaptive TE insertions likely related to adaptation to antifungals and the plant host environment. This work highlights the power of vast genomic datasets to unravel intraspecies TE invasion histories and pinpoint factors likely driving recent adaptation. This argues for a shift in focus to incorporate deep population-level TE activity surveys in our pursuit to uncover the molecular drivers of adaptive evolution.

genomics↗

bioRxiv2023

Patterns of transposable element accumulation at resistance loci: a comparative genomic analysis in aphids

The evolution of resistance is a major challenge for the sustainable control of pests and pathogens. Thus, a deeper understanding of the evolutionary and genomic mechanisms underpinning resistance evolution is required to safeguard health and food production. Several studies have implicated transposable elements (TEs) in xenobiotic resistance evolution in insects. However, analyses are generally restricted to one insect species and/or one or a few xenobiotic gene families (XGFs). We examine evidence for TE accumulation at XGFs by performing a comparative genomic analysis across 20 aphid genomes, considering major subsets of XGFs involved in metabolic resistance to insecticides: Cytochrome P450s, glutathione S-transferases, esterases, UDP-glucuronosyltransferases, and ABC transporters. We find that TEs are significantly enriched at XGFs compared to other genes. XGFs show similar levels of TE enrichment to housekeeping genes. But unlike housekeeping genes, XGFs are not constitutively expressed in germline cells, supporting the selective enrichment of TEs at XGFs, rather than enrichment due to chromatin availability. Hotspots of extreme TE enrichment occur around certain XGFs. In aphids of agricultural importance, we find particular enrichment of TEs around cytochrome P450 genes with known functions in the detoxification of synthetic insecticides. Our results provide evidence supporting a general role for TEs as a source of genomic variation at host XGFs, and highlight the existence of considerable variability in TE content across XGFs and host species. These findings demonstrate the need for detailed functional verification analyses to clarify the significance of individual TE insertions and elucidate underlying mechanisms at TE-XGF hotspots.

genomics↗

bioRxiv2022

Earl Grey: a fully automated user-friendly transposable element annotation and analysis pipeline

Transposable elements (TEs) are major components of eukaryotic genomes and are implicated in a range of evolutionary processes. Yet, TE annotation and characterisation remains challenging, particularly for non-specialists, since existing pipelines are typically complicated to install, run, and extract data from. Current methods of automated TE annotation are also subject to issues that reduce overall quality, particularly: (i) fragmented and overlapping TE annotations, leading to erroneous estimates of TE count and coverage; (ii) repeat models represented by short sections of total TE length, with poor capture of 5 and 3 ends. To address these issues, we present Earl Grey, a fully automated TE annotation pipeline designed for user-friendly curation and annotation of TEs in eukaryotic genome assemblies. Using nine simulated genomes and an annotation of Drosophila melanogaster, we show that Earl Grey outperforms current widely-used TE annotation methodologies in ameliorating the issues mentioned above, whilst scoring highly in benchmarking for TE annotation and classification, and being robust across genomic contexts. Earl Grey provides a comprehensive and fully automated TE annotation toolkit that provides researchers with paper-ready summary figures and outputs in standard formats compatible with other bioinformatics tools. Earl Grey has a modular format, with great scope for the inclusion of additional modules focussed on further quality control and tailored analyses in future releases.

bioinformatics↗

bioRxiv2021

Bursts of recent transposable element activity and signatures of element removal in the monarch genome, Danaus plexippus

BackgroundLepidoptera (butterflies and moths) are an important model system in ecology and evolution. A high-quality chromosomal genome assembly is available for the monarch butterfly (Danaus plexippus), but it lacks an in-depth transposable element (TE) annotation, presenting an opportunity to explore monarch TE dynamics and the impact of TEs on shaping the monarch genome. ResultsWe find 6.21% of the monarch genome is comprised of TEs, a reduction of 6.85% compared to the original TE annotation performed on the draft genome assembly. Monarch TE content is low compared to two closely related species with available genomes, Danaus chrysippus (33.97% TE) and Danaus melanippus (11.87% TE). The biggest TE contributions to genome size in the monarch are LINEs and Penelope-like elements, and three newly identified families, r2-hero_dPle (LINE), penelope-1_dPle (Penelope-like), and hase2-1_dPle (SINE), collectively contribute 34.92% of total TE content. We find evidence of recent TE activity, with two novel Tc1 families rapidly expanding over recent timescales (tc1-1_dPle, tc1- 2_dPle). LINE fragments show signatures of genomic deletions indicating a high rate of TE turnover. We investigate associations between TEs and wing colouration and immune genes and identify a three-fold increase in TE content around immune genes compared to other host genes. ConclusionsWe provide a detailed TE annotation and analysis for the monarch genome, revealing a considerably smaller TE contribution to genome content compared to two closely related Danaus species with available genome assemblies. We identify highly successful novel DNA TE families rapidly expanding over recent timescales, and ongoing signatures of both TE expansion and removal highlight the dynamic nature of repeat content in the monarch genome. Our findings also suggest that insect immune genes are promising candidates for future interrogation of TE-mediated host adaptation.

genomics↗