Enhanced Araport11 annotation

The official *Arabidopsis thaliana* genome annotation (Araport11) provides comprehensive information on genes, noncoding RNAs, and transposable elements (TEs). However, the distributed GFF3 file merges all genomic features, like protein-coding genes, noncoding RNAs, and transposable elements, into a single annotation file without explicit TE classification. Moreover, this lack of classification metadata makes it difficult to extract and analyze specific TE families or subclasses. Consequently, the original format is not optimal for downstream applications such as RNA-seq read alignment, TE expression analysis, or TE–gene association studies.

To address this limitation, TE classification information was incorporated into the Araport11 annotation based on the TAIR Transposon Family Database. The revised annotation includes a standardized RepeatMasker and EDTA style classification (classification=subclass/family/clade) tag for each TE entry. The full annotation was also separated into multiple feature-specific files (e.g., protein-coding genes, TE genes, and TEs), providing more flexibility for different genomic analyses such as gene expression quantification or TE characterization.

All the scripts used in this process are provided, and the resulting files are available via Figshare.

Please feel free to reach out if there are any questions.