Fig. 1

The fungus gnat chromosome cycle and chromosome-scale scaffolding flowchart. A The chromosome behaviors across the somatic cell lineage of males and females starting from the initial zygotic genome. In early embryogenesis, L chromosomes are eliminated first from all nuclei destined for the somatic cell lineage. Then either one or two paternal X chromosomes (Xp) are eliminated. Male-producing females produce offspring that eliminate two Xp and become males. Female-producing females contain a variant of the X chromosome, X’ (X prime), and produce offspring that eliminate one Xp and become male-producing and female-producing females depending on whether they inherit the maternal X or X’. The two types of females can be distinguished by whether they have wavy or straight wings. L* represents the presence of two L chromosomes, L1 and L2 [6]. The subscripts “M” and “P” indicate maternal and paternal origin, respectively. The reference genome, Bcop_v1, was made from male embryos, and represents the male somatic genome (highlighted in yellow) box. B The chromosome dynamics across the germline lineage for males and females. Male meiosis is non-Mendelian, and results in a single product through paternal genome elimination and maternal X-non-disjunction. Female meiosis is Mendelian. Purple chromosomes represent that their origin can be from any parent at random. C A flowchart and summary of updating the reference genome, Bcop_v1, with Hi-C. Bcop_v1 is a long read assembly, incorporating both PacBio and Nanopore data, that was scaffolded with optical maps from BioNano Genomics [9]. Bcop_v2 is the result of correcting and scaffolding Bcop_v1 with Hi-C data. The numbers in parentheses denotes how many contigs and scaffolds are in the given component of the assembly