Additional file 1 of Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest

Additional file 1:  Main Supplementary Information text file, including Tables S1-S17 and Figures S1-S18. Table S1. Sequencing, assembly, annotation statistics and accession numbers. Table S2. OrthoDB v10 comparison of five species for ortholog presence and copy-number in Hemiptera-level orthogroups. Table S3. Scaffolds present in the H. halys assembly (accession GCA_000696795.1) that may originate from contaminant sources. Table S4. Counts of repetitive DNA elements encountered in the H. halys genome assembly. Table S5. H. halys predicted protein products associated with the RNAi pathway. Table S6. Positional information for the annotated homeobox genes. Table S7. Nuclear receptors of H. halys. Table S8. Listing of candidate Y-linked genes. Table S9. Number of genes identified as putative cuticle proteins per family in the genome of H. halys. Table S10. Number of genes identified as putative cuticle proteins per species in the genomes of several insect orders. Table S11. Clusters of genes coding for cuticle proteins in the genome of H. halys. Table S12. Odorant-binding protein genes and pseudogenes (Ψ) annotated in the genome of H. halys. Table S13. Primer sequences used to validate the HhalOBP gene annotations. Table S14. Correspondences between H. halys predicted protein identifiers and cathepsin labels. Table S15. A total of 64 salivary effector proteins were identified in the H. halys genome. Table S16. A select subset of 15 H. halys salivary effector proteins having variable expression levels between nymphal and adult stages (up- or down-regulation). Table S17. Gene expression data for H. halys glutathione S-transferase genes. Figure S1. Phylogenetic organization of the Hemiptera. Figure S2. Ortholog distributions among hemipterans. Figure S3. Genome assembly quality control. Figure S4. Hox and Iro-C cluster gene loci. Figure S5. Halyomorpha mannosidase expansion. Figure S6. Maximum likelihood phylogenetic tree of selected mannosidase proteins from three bacterial outgroups and three hemipteran species. Figure S7. Phylogenetic tree of the OR family. Figure S8. Phylogenetic tree of the GR family. Figure S9. Phylogenetic tree of the IR family. Figure S10. Heteropteran global opsin gene tree. Figure S11. Array of β-esterase genes. Figure S12. Distribution of transcription factor families across insect genomes. Figure S13. Nanos amino acid sequence alignments from different species. Figure S14. Location of pair-rule gene orthologs in the H. halys genome. Figure S15. H. halys odd-family genes. Figure S16. Alignment of Wnt family domain proteins. Figure S17. Engrailed and Invected are shared among diverse insects. Figure S18. Phylogenetic analysis of hemipteran genes named “NR2E1” reveals that they are orthologous to NR2E6.

附加文件1：主要补充信息文本文件，包含表S1至S17以及图S1至S18。
表S1：测序、组装、注释统计信息及登录号。
表S2：直向同源数据库v10（OrthoDB v10）对半翅目（Hemiptera）级直系同源群中5个物种的直系同源基因存在情况与拷贝数的比较分析。
表S3：茶翅蝽（Halyomorpha halys，简称H. halys）基因组组装（登录号GCA_000696795.1）中可能源自污染来源的基因组支架（scaffold）。
表S4：茶翅蝽基因组组装中检测到的重复DNA元件数量统计。
表S5：与RNA干扰（RNAi）通路相关的茶翅蝽预测蛋白产物。
表S6：已注释同源框基因的位置信息。
表S7：茶翅蝽的核受体家族基因。
表S8：候选Y连锁基因列表。
表S9：茶翅蝽基因组中各家族推定表皮蛋白的编码基因数量。
表S10：多个昆虫目基因组中各物种推定表皮蛋白的编码基因数量。
表S11：茶翅蝽基因组中编码表皮蛋白的基因簇。
表S12：茶翅蝽基因组中注释得到的气味结合蛋白（odorant-binding protein）基因及假基因（Ψ）。
表S13：用于验证HhalOBP基因注释的引物序列。
表S14：茶翅蝽预测蛋白标识符与组织蛋白酶（cathepsin）标签的对应关系。
表S15：茶翅蝽基因组中共鉴定出64种唾液效应蛋白。
表S16：15个茶翅蝽唾液效应蛋白的精选子集，这些蛋白在若虫与成虫阶段的表达水平存在上调或下调差异。
表S17：茶翅蝽谷胱甘肽S-转移酶（glutathione S-transferase）基因的基因表达数据。
图S1：半翅目（Hemiptera）的系统发育组织结构。
图S2：半翅目昆虫间的直系同源基因分布特征。
图S3：基因组组装质量控制分析结果。
图S4：Hox基因簇与Iro-C基因簇的基因座位。
图S5：茶翅蝽的甘露糖苷酶家族扩增现象。
图S6：取自3个细菌外类群与3个半翅目物种的选定甘露糖苷酶蛋白的最大似然法系统发育树。
图S7：嗅觉受体（Odorant Receptor, OR）家族的系统发育树。
图S8：味觉受体（Gustatory Receptor, GR）家族的系统发育树。
图S9：离子型受体（Ionotropic Receptor, IR）家族的系统发育树。
图S10：异翅亚目全球视蛋白（opsin）基因系统发育树。
图S11：β-酯酶基因阵列。
图S12：昆虫基因组中转录因子（transcription factor）家族的分布模式。
图S13：不同物种nanos基因的氨基酸序列比对结果。
图S14：成对规则基因（pair-rule gene）直系同源物在茶翅蝽基因组中的定位。
图S15：茶翅蝽的odd家族基因。
图S16：Wnt家族结构域蛋白的序列比对结果。
图S17：engrailed基因与invected基因在多种昆虫中保守存在。
图S18：针对名为"NR2E1"的半翅目基因的系统发育分析表明，它们与NR2E6互为直系同源基因。