Chromosome-scale scaffolding of the fungus gnat genome (Diptera: Bradysia coprophila)

BackgroundThe fungus gnat, Bradysia (Sciara) coprophila, has compelling chromosome biology. Paternal chromosomes are eliminated during spermatogenesis whereas both maternal X sister chromatids are retained. Embryos start with three copies of the X chromosome, but 1-2 copies are eliminated from somatic cells as part of sex determination, and one is eliminated in the germline to restore diploidy. These developmentally normal events present opportunities to study chromosome movements that are unusual in other systems. To support such studies, we previously generated a highly contiguous optical-map-scaffolded long-read assembly (Bcop_v1) of the male somatic genome. However, the scaffolds were not chromosome-scale, the majority of the assembly lacked chromosome assignments, and the order and orientation of the contigs along chromosomes remained unknown. FindingsMale pupae Hi-C data was used to correct, order, and orient the contigs from Bcop_v1 into chromosome-scale scaffolds, producing the updated assembly, Bcop_v2. Several orthogonal analyses allowed us to (i) identify the corresponding chromosome for each scaffold, (ii) orient them with respect to polytene maps, and (iii) determine that they were highly concordant with the chromosomes they represent. Gene annotations produced for Bcop_v1 were lifted over to Bcop_v2. Chromosomal repeat distributions highlight a potential telomeric sequence. Finally, the Hi-C data shed new light on three "fold-back regions" seen to physically interact in images of polytene X chromosomes. ConclusionsStudies of the unusual chromosome movements in Bradysia coprophila will benefit from the updated assembly (Bcop_v2) where each somatic chromosome is represented by a single scaffold.