Supplemental Material for Sless, Searle, and Danforth, 2022

"1 Assembly.zip" contains the contig-level genome assembly of the brood parasitic bee Holcopasites calliopsidis. Also included are computed statistics from QUAST and the results of a BUSCO analysis to assess the completeness of the assembly."2 Repetitive Elements.zip" contains results files from RepeatMasker and RepeatModeler runs used to identify repetitive DNA sequences within the genome. The first of the two RepeatMasker runs used a public library of canonical repetitive sequences (Dfam). The output of this run was then fed into the second run using a custom species-specific repeat library generated by RepeatModeler."3 Annotation.zip" contains data from annotation pipelines run on the genome assembly. BRAKER2 was first used to identify putative genes using both Augustus and GeneMark. Proteins and transcripts of annotated genes were extracted using EvidenceModeler and gffread. These loci were then functionally annotated with parallel runs of two software pipelines InterProScan and Blast2GO."4 Orthology.zip" contains the results from orthology detection analyses of the putative coding regions from the H. calliopsidis genome. OrthoFinder was used to identify orthogroups based on this species and thirteen additional hymenopteran taxa, with Drosophila melanogaster as an outgroup. The program CAFE was then used to identify rapidly evolving gene families among these orthogroups. Since the species tree produced by OrthoFinder was not in agreement with taxonomic consensus, a custom tree was created as input for CAFE using dates from Peters et al. 2017.

1 'Assembly.zip' 文件包含了蜜蜂 Holcopasites calliopsidis 的基因组连续组装信息。此外，还包括了由 QUAST 计算得出的统计数据以及 BUSCO 分析结果，以评估组装的完整性。2 'Repetitive Elements.zip' 文件包含了 RepeatMasker 和 RepeatModeler 运行的结果文件，用于识别基因组内的重复DNA序列。其中，两个 RepeatMasker 运行的第一个使用了一个公开的典型重复序列库（Dfam），其输出结果随后被用于第二次运行，该次运行使用的是 RepeatModeler 生成的特定物种的重复库。3 'Annotation.zip' 文件包含了在基因组组装上运行的注释管道数据。首先使用 BRAKER2 结合 Augustus 和 GeneMark 来识别潜在的基因。利用 EvidenceModeler 和 gffread 从注释基因中提取蛋白质和转录本。这些位点随后通过并行运行两个软件管道 InterProScan 和 Blast2GO 进行功能注释。4 'Orthology.zip' 文件包含了 H. calliopsidis 基因组潜在编码区域的同源性检测分析结果。使用 OrthoFinder 根据该物种及其十三种其他膜翅目物种，以黑腹果蝇 Drosophila melanogaster 作为外群，识别同源群。随后，程序 CAFE 用于识别这些同源群中的快速进化的基因家族。由于 OrthoFinder 生成的物种树与分类学共识不一致，因此使用 Peters 等人于 2017 年提供的数据创建了一个自定义树作为 CAFE 的输入。