Dynamic evolution of germ-line restricted chromosomes in three dark-winged fungus gnats (Sciaridae) revealed through chromosome level germline genomes

Germline restricted chromosomes (GRCs) have evolved in at least six different animal lineages, occur across large clades with thousands of species, and have persisted for tens of millions of years. Despite the fact that these chromosomes seem to be highly conserved in these clades, we know very little about their evolution. Part of the reason for this is that GRCs are difficult to study genomically, as they are restricted to a small subset of cells (i.e. the germline) early in development and so require germ tissue dissection in order to sequence. We have produced chromosome-scale genome assemblies including germline restricted chromosomes in three fly species (Sciaridae); Bradysia coprophila, B. impatiens , and Lycoriella ingenua . We compare the GRCs both between and within species and find that these chromosomes evolve in an extraordinarily dynamic fashion, with very little conservation of synteny or gene content. This is also true for the two species, B. coprophila and L. ingenua , that carry two of these chromosomes in their germline; the two GRCs within a species, which were thought to be homologous, are actually extremely divergent. We explore the implications of these findings for GRC evolution in flies, recombination between the GRCs, and exclusion of these chromosomes from somatic cells.