<p>The annotation of genomes progresses slower than their sequencing and assembly. Also, species that were previously annotated can benefit from reannotation using more recent RNA-Seq and protein data, as well as from state-of-the-art annotation methods whose accuracy has improved. Heterogeneous annotations performed with different tools and protein databases can introduce artifactual differences when comparing gene sets or gene structures between species. Recently, the BRAKER3 annotation pipeline was introduced that integrates evidence from RNA-Seq and a protein database. Here, we introduce an automated genome annotation workflow based on BRAKER3 that allows one to annotate a list of species with minimal manual intervention. We selected a diverse set of 200 insect species from different families, including 85 species previously lacking annotations in GenBank. Using currently available RNA-Seq and protein sequence data, we applied our automated workflow to annotate these genomes and conducted downstream analyses typically performed in comparative genomics studies. We present the resulting gene structures, protein sequences, gene ontology terms, orthologous gene groups and a species tree.</p>