Supplemental Material for Chang and Larracuente, 2018

<p>File S1 contains methods and configuration files for assembling and reconciling genomes and our calculation for estimating Y-linked gene conversion rate.</p> <p> </p> <p>Figure S1 shows our assembly pipeline with command lines and pointers to code and configuration files in the supplement and/or github. </p> <p> </p> <p>Figure S2 has the MUMMER plots showing whole genome alignments between the R6 assembly and our new assembly for autosomes and X chromosome. </p> <p> </p> <p>Figure S3 has the MUMMER plots showing the alignment between R6 Y chromosome assembly and our new Y chromosome assembly. </p> <p> </p> <p>Figure S4 shows the median female-to-male coverage ratio of Illumina reads across different chromosomes based on the R6 annotation</p> <p> </p> <p>Figure S5 shows the coverage of Pacbio reads for each Y-linked 10-kb window in our assembly and R6.</p> <p> </p> <p>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>.</p> <p> </p> <p>Figure S7 shows repeat composition in heterochromatic regions. </p> <p> </p> <p>Table S1 details the order that we reconciled genomes.</p> <p> </p> <p>Table S2 lists the accession numbers for sequence data that we used in the study.</p> <p> </p> <p>Table S3 contains the sequences and PCR condition for our primers.</p> <p> </p> <p>Table S4 has the raw data from Figure S1, showing the median PacBio read coverage for every region of genome in 10 kb windows.</p> <p> </p> <p>Table S5 shows the gaps we closed in the <i>Drosophila melanogaster</i> R6 assembly.</p> <p> </p> <p>Table S6 lists the intron sizes of Y-linked genes in our assembly.</p> <p> </p> <p>Table S7 lists the duplicated exons of Y-linked genes and their coordinates in our assembly.</p> <p> </p> <p>Table S8 lists the expression level and annotation of every gene based on whole male and testes RNA-seq data.</p> <p> </p> <p>Table S9 lists transposon and complex repeat composition for every contig/scaffold in our assembly.</p> <p> </p> <p>Table S10 lists simple repeat composition for every contig/scaffold in the assembly.</p>