Supplemental Material for Chang and Larracuente, 2018

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 <i>pp1-</i><i>y1</i> and <i>Ary</i>.

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 <i>Drosophila melanogaster</i> 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.