File S1 contains methods and configuration files for assembling and reconciling genomes and our calculation for estimating Y-linked gene conversion rate.

Figure S1 shows our assembly pipeline with command lines and pointers to code and configuration files in the supplement and/or github.

Figure S2 has the MUMMER plots showing whole genome alignments between the R6 assembly and our new assembly for autosomes and X chromosome.

Figure S3 has the MUMMER plots showing the alignment between R6 Y chromosome assembly and our new Y chromosome assembly.

Figure S4 shows the median female-to-male coverage ratio of Illumina reads across different chromosomes based on the R6 annotation

Figure S5 shows the coverage of Pacbio reads for each Y-linked 10-kb window in our assembly and R6.

Figure S6 shows the coverage of Pacbio reads in first 700 kb of Y_scaffold4, which contains pp1-y1 and Ary.

Figure S7 shows repeat composition in heterochromatic regions.

Table S1 details the order that we reconciled genomes.

Table S2 lists the accession numbers for sequence data that we used in the study.

Table S3 contains the sequences and PCR condition for our primers.

Table S4 has the raw data from Figure S1, showing the median PacBio read coverage for every region of genome in 10 kb windows.

Table S5 shows the gaps we closed in the Drosophila melanogaster R6 assembly.

Table S6 lists the intron sizes of Y-linked genes in our assembly.

Table S7 lists the duplicated exons of Y-linked genes and their coordinates in our assembly.

Table S8 lists the expression level and annotation of every gene based on whole male and testes RNA-seq data.

Table S9 lists transposon and complex repeat composition for every contig/scaffold in our assembly.

Table S10 lists simple repeat composition for every contig/scaffold in the assembly.