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

Background: The lower dipteran fungus gnat, Bradysia (Sciara) coprophila, has unusual chromosome biology. Chromosome imprinting was first discovered in this system. All paternal chromosomes are eliminated during spermatogenesis whereas both maternal X sister chromatids are retained. Embryos start out with three copies of the X chromosome, but 1-2 copies are eliminated from all somatic cells as a part of sex determination, and one is eliminated in the germline to restore diploidy. These developmentally normal features present opportunities to study unusual chromosome movements that may occur as rare/abnormal events in other systems. To help with such studies, we previously generated a highly contiguous optical-map-scaffolded long-read assembly (Bcop\_v1) of the male somatic genome that contains four chromosomes. 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. Findings: Male pupae chromatin conformation capture (Hi-C) data was collected and used to first produce a corrected Bcop\_v1 assembly by breaking contigs at mis-joined regions, and then used to order and orient the corrected contigs into chromosome-scale scaffolds. The resulting assembly (Bcop\_v2) had four chromosome-scale scaffolds as expected. Previously known chromosomal locations of locus-specific sequences were used to (i) identify the corresponding chromosome for each scaffold, and (ii) orient the chromosome scaffolds in the same order as published polytene chromosome maps. Finally, the gene annotations produced for Bcop\_v1 were lifted over to Bcop\_v2 to allow a seamless transition in adopting the updated chromosome-scale assembly. Conclusions: Studies 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. ### Competing Interest Statement The authors have declared no competing interest.