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 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.

补充材料文件S1收录了用于基因组组装与校正的方法及配置文件，同时包含我们估算Y连锁（Y-linked）基因转换率的计算过程。

补充材料图S1展示了我们的基因组组装流程，附带命令行代码，以及指向补充材料和/或GitHub中代码与配置文件的链接。

补充材料图S2展示了R6基因组组装版本与我们新组装的常染色体及X染色体基因组之间的全基因组比对结果，采用MUMMER比对图（MUMMER plots）形式呈现。

补充材料图S3展示了R6 Y染色体组装版本与我们新组装的Y染色体基因组之间的比对结果，同样采用MUMMER比对图形式。

补充材料图S4基于R6基因组注释信息，展示了不同染色体上Illumina测序读段（Illumina reads）的雌雄覆盖度中位数比值。

补充材料图S5展示了我们的组装版本与R6版本中，每个Y连锁10kb窗口的PacBio测序读段（PacBio reads）覆盖度。

补充材料图S6展示了Y_scaffold4前700kb区域的PacBio测序读段覆盖度，该区域包含pp1-y1与Ary基因。

补充材料图S7展示了异染色质区域的重复序列组成情况。

补充材料表S1详细列出了我们进行基因组校正的先后顺序。

补充材料表S2列出了本研究中使用的序列数据的登录号。

补充材料表S3收录了我们所用引物的序列及聚合酶链式反应（PCR）反应条件。

补充材料表S4包含补充材料图S1的原始数据，展示了以10kb窗口划分的基因组各区域的PacBio测序读段覆盖度中位数。

补充材料表S5展示了我们在黑腹果蝇（Drosophila melanogaster）R6组装版本中填补的序列缺口。

补充材料表S6列出了我们组装版本中Y连锁基因的内含子长度。

补充材料表S7列出了我们组装版本中Y连锁基因的重复外显子及其基因组坐标。

补充材料表S8基于全雄性个体及睾丸的RNA测序（RNA-seq）数据，列出了所有基因的表达水平及注释信息。

补充材料表S9列出了我们组装版本中每个重叠群/支架（contig/scaffold）的转座子（transposon）及复杂重复序列组成。

补充材料表S10列出了该组装版本中每个重叠群/支架的简单重复序列组成。