Gene-rich fungus gnat germline-restricted chromosomes are largely transcriptionally quiescent

Germline-restricted chromosomes (GRCs) constitute a unique class of chromosomes confined to germ cells. Arising in multiple evolutionarily distant lineages, GRCs have been identified in three insect families (non-biting midges, gall midges, and fungus gnats), each within the order Diptera. Genomic characterisation in fungus gnats has revealed GRCs to be large, gene-rich chromosomes, which, together with their persistence over millennia, implies they play important biological roles within this clade. However, transcription from these chromosomes has yet to be demonstrated, leaving key questions about their function and activity unresolved. Here, we present the first direct analysis of GRC transcription in Diptera, combining immunofluorescence staining with bulk RNA-seq data in the fungus gnat Bradysia coprophila (Sciaridae). We find that transcription from GRCs is highly limited during key developmental stages. In larval and adult gonads, elongating polymerase II appears to be active at all chromosomes except the GRCs in most cells. Furthermore, using stringent filtering criteria, we identify only 10 confidently expressed GRC-linked genes, mostly of unknown function. In addition, we report the surprising presence of a ∼290 kb region of bacterial-derived sequence on GRC2, likely acquired through horizontal transfer from germline-associated endosymbionts. Overall, these findings identify GRCs in fungus gnats as unique chromosomes, largely transcriptionally quiescent during key stages of B. coprophila development, yet capable of maintaining both endogenous and potentially horizontally acquired genes over evolutionary timescales. This raises fundamental questions about the mechanisms that maintain gene content in these chromosomes and their contribution, if any, to germline biology.