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

Earl Grey ParTEA expands comparative transposable element annotation by building a shared library across genome panels, increasing Drosophila TE families from 343 to 1,852.

• Why it matters: Genome-by-genome TE annotation and reference-only libraries miss families and reduce consistency, limiting comparisons of shared versus private TE content and activity across evolutionary scales.
• What they did: The fully automated Snakemake pipeline constructs one non-redundant TE library from all input genomes, resolves chimeric consensuses, and annotates each genome with optional saturation, BUSCO QC, and phylogenetic ordering.
• The result: Shared TE-family proportions are highest in Arabidopsis thaliana (97.3%), moderate across Drosophila species (37.7%), and very low across fungal species (0.5%), enabling direct cross-genome diversity comparisons.

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