Supplemental Material for Clark et al., 2021

File S1 is a figure from FastQ Screen analysis. File S2 is a tarball containing the reference-guided assemblies for BA_411 and WI_6. Assembly files with "clean" appended to the name have been filtered for scaffolds without reference coverage. File S3 is a tarball containing Blobtools output. File S4 is a tarball containing BUSCO outputs. <br><b>Supplementary Figure 1: FastQC Screen Analysis Indicates the Expected Composition of Reads Based on Screened Genomes. </b>Read subsets from each <i>D. pulicaria </i>library were mapped against several common and selected sequencing contaminants using bowtie2. Plots indicate that majority of the reads are mapping uniquely to the bait genome PA42 (“<i>Daphnia</i>”), as expected. For other genomes in the search library, the reads did not map uniquely and likely represent low-complexity regions. There is a significant proportion of the read subset that does not map to any represented sequences represented with grey bars. <b></b> <b>Supplementary Figure 2: Sourmash Distance Estimates Indicate Higher Similarity Between <i>D. pulicaria</i> Strains (BA411 &amp; WI6), Relative to the <i>D. pulex</i> (PA42) Reference. </b>Dendrograms on the top and left recapitulate the relationship between samples in the distance analysis that is also visualized by the matrix. The color gradient indicates the sourmash distance estimate, where darker colors indicate high similarity between samples and lighter colors indicate more divergent samples. The <i>D. pulicaria</i> assemblies only vary by 0.1 when compared to each other.<b></b><br>

文件S1为FastQ Screen分析所得的图表。文件S2为压缩包，内含BA_411与WI_6的参考引导组装结果；文件名后缀带“clean”的组装文件已经过过滤，仅保留带有参考序列覆盖的scaffold（支架序列）。文件S3为Blobtools分析输出结果的压缩包。文件S4为BUSCO（Benchmarking Universal Single-Copy Orthologs，通用单拷贝同源基因评估工具）输出结果的压缩包。<br><b>补充图1：FastQ Screen分析结果显示，基于筛查基因组的测序读段预期组成</b>从每株<i>D. pulicaria</i>（水蚤属物种）的文库中获取的读段子集，使用Bowtie2（鲍氏序列比对工具2）比对至多种常见及选定的测序污染物基因组。结果显示，绝大多数reads（测序读段）可唯一比对至诱饵基因组PA42（即<i>Daphnia</i>，水蚤属），与预期一致。对于搜索文库中的其他基因组，读段无法实现唯一比对，大概率对应低复杂度区域。另有相当比例的读段子集无法比对至任何已收录序列，以灰色条带表示。<b></b> <b>补充图2：Sourmash距离估计结果显示，相较于<i>D. pulex</i>（PA42）参考基因组，<i>D. pulicaria</i>菌株BA411与WI6之间的相似度更高</b>顶部与左侧的聚类树重现了距离分析中样本间的亲缘关系，该关系同时通过距离矩阵热图进行可视化。颜色梯度代表Sourmash距离估计值：颜色越深表示样本间相似度越高，颜色越浅则表示样本间亲缘关系越远。<i>D. pulicaria</i>的组装结果两两比对间的差异仅为0.1。<b></b><br>