Comprehensive stage- and tissue-specific transcriptome of the global ecosystem service insect, marmalade hoverfly Episyrphus balteatus

Hoverflies (Diptera: Syrphidae) are globally beneficial insects that provide key ecological services, such as pollination and biological pest control. Importantly, extensive research has revealed that numerous species within this group engage in long-distance migrations, thereby enabling these services to operate across broad spatial scales. Hence, the conservation and sustainable use of this functionally important group is crucial for maintaining ecosystem balance and stability, especially in the face of ongoing losses of ecosystem functioning. However, limited genomic and transcriptomic resources hinder the advancement of research on this significant group. To address this gap, we generated a comprehensive developmental- and tissue-resolved transcriptome for Episyrphus balteatus, the dominant and most extensively researched migratory hoverfly species. We sequenced 30 RNA-seq libraries across three life stages (egg, larva, and pupa) and seven adult tissues (antenna, proboscis, head, thorax, body, leg, and wing), yielding 133.87 Gb of clean reads. The subsequent de novo assembly yielded 85,676 unigenes (N50 = 1,028 bp) exhibiting high completeness (97.9% BUSCO), and 45,479 unigenes (53.08%) were functionally annotated. Notably, differential expression analysis identified key gene sets and enriched pathways linked to development, sensory perception, and environmental responsiveness, which are molecular characteristics that may facilitate long-distance migration and ecosystem service delivery. Together, this dataset serves as a valuable community resource for ecological, evolutionary, and comparative research on hoverflies and other beneficial insects.