Supplemental Material for Gamez et al., 2020

Figure 1 Global dynamics of gene expression.Figure 2 Soft clustering and principal component analysis on <i>Ae. albopictus</i> genes. Figure 3 Orthology analysis of <i>Ae. aegypti</i> and <i>Ae. albopictus</i> samples across corresponding developmental time points.Figure S1 Read mapping statistics and read count data across all developmental stages.Figure S2 Expression dynamics of protein genes involved in miRNA, siRNA and piRNA pathways.Figure S3 E-value score distribution for best reciprocal BLAST hits for <i>Ae. aegypt</i>i and <i>Ae. albopictus </i>orthologs.Figure S4 Sample correlations of each developmental time point between <i>Ae. aegypti</i> and <i>Ae. albopictus.</i>Figure S5 MA plots depicting expression of orthologous genes in sex specific tissues.Figure S6 MA plots depicting expression of orthologous genes in blood-fed female ovaries and carcasses at different 12-hr time points.Figure S7 MA plots depicting expression of orthologous genes during embryogenesis of <i>Ae. albopictus</i> compared to <i>Ae. aegypti</i>. Figure S8 MA plots depicting expression of orthologous genes in the larval instars and diapause samples of <i>Ae. albopictus</i> compared to <i>Ae. aegypti</i>. Table S1 Summary of sequenced datasets. Table S2 Gene descriptions of <i>Ae. albopictus</i> loci. Table S3 Read mapping analysis of <i>Ae. albopictus</i> transcripts. Table S4 Detected counts, TPM, and FPKM of each developmental stage. Table S5 Complete developmental transcriptome transcripts of <i>Ae. albopictus</i>. Table S6 Pearson correlation matrix. Table S7 Gene ontology enrichment analysis of <i>Ae. albopictus</i> clusters 1 through 20. Table S8 AALF genes mFuzz cluster membership and descriptions. Table S9 Female-biased genes. Table S10 Male-biased genes. Table S11 Genes involved in small RNA production. Table S12 Best reciprocal hits orthology between <i>Ae. albopictus</i> and <i>Ae. aegypti</i>. Table S13 Count summary of <i>Ae. albopictus</i> reads mapping to orthologs. Table S14 Pearson correlation values of <i>Ae. aegypti </i>and <i>Ae. albopictus </i>at each developmental stage. Table S15 Upregulated genes in <i>Ae. aegypti</i> and <i>Ae. albopictus </i>expressed orthologs. Table S16 <i>Ae. aegypti-Ae. albopictus</i> male testes and carcass raw DESeq2 results. Table S17 <i>Ae. aegypti-Ae. albopictus</i> pupae raw DESeq2 results. Table S18 <i>Ae. aegypti-Ae. albopictus</i> female NBF and PBM ovary DESeq2 results. Table S19 <i>Ae. aegypti-Ae. albopictus</i> female NBF and PBM carcass DESeq2 results. Table S20 <i>Ae. aegypti-Ae. albopictus</i> embryogenesis DESeq2 results. Table S21 <i>Ae. aegypti-Ae. albopictus</i> larval stages and diapause raw DESeq2 results.File S1 Script for processing count data produced by featureCountsFile S2 Script used for parsing out BLAST outputFile S3 Script used to identify best reciprocal match

图1 基因表达全局动态特征（Global dynamics of gene expression）. 图2 白纹伊蚊（Aedes albopictus, Ae. albopictus）基因的软聚类与主成分分析（Soft clustering and principal component analysis on Ae. albopictus genes）. 图3 对应发育时间点下埃及伊蚊（Aedes aegypti, Ae. aegypti）与白纹伊蚊样本的直系同源分析（Orthology analysis of Ae. aegypti and Ae. albopictus samples across corresponding developmental time points）. 补充图S1 所有发育阶段的读段比对统计与读段计数数据（Read mapping statistics and read count data across all developmental stages）. 补充图S2 参与miRNA（microRNA）、siRNA（small interfering RNA）及piRNA（Piwi-interacting RNA）通路的蛋白编码基因的表达动态（Expression dynamics of protein genes involved in miRNA, siRNA and piRNA pathways）. 补充图S3 埃及伊蚊与白纹伊蚊直系同源基因的最佳双向BLAST（Basic Local Alignment Search Tool）比对命中的E值得分分布（E-value score distribution for best reciprocal BLAST hits for Ae. aegypti and Ae. albopictus orthologs）. 补充图S4 埃及伊蚊与白纹伊蚊各发育时间点的样本相关性（Sample correlations of each developmental time point between Ae. aegypti and Ae. albopictus）. 补充图S5 展示性别特异性组织中直系同源基因表达的MA图（Mean-Average plot）. 补充图S6 展示不同12小时时间点下吸血雌蚊卵巢及躯体中直系同源基因表达的MA图（Mean-Average plot）. 补充图S7 对比埃及伊蚊与白纹伊蚊胚胎发生过程中直系同源基因表达的MA图（Mean-Average plot）. 补充图S8 对比埃及伊蚊与白纹伊蚊幼虫龄期及滞育样本中直系同源基因表达的MA图（Mean-Average plot）. 补充表S1 测序数据集汇总（Summary of sequenced datasets）. 补充表S2 白纹伊蚊基因座的基因注释信息（Gene descriptions of Ae. albopictus loci）. 补充表S3 白纹伊蚊转录本的读段比对分析（Read mapping analysis of Ae. albopictus transcripts）. 补充表S4 各发育阶段的检出计数、每百万转录本片段数（Transcripts Per Million, TPM）及每千碱基每百万比对片段数（Fragments Per Kilobase per Million mapped reads, FPKM）（Detected counts, TPM, and FPKM of each developmental stage）. 补充表S5 白纹伊蚊完整发育转录组转录本（Complete developmental transcriptome transcripts of Ae. albopictus）. 补充表S6 皮尔逊相关矩阵（Pearson correlation matrix）. 补充表S7 白纹伊蚊1至20号聚类的基因本体（Gene Ontology, GO）富集分析结果（Gene ontology enrichment analysis of Ae. albopictus clusters 1 through 20）. 补充表S8 AALF基因的mFuzz聚类归属及注释信息（AALF genes mFuzz cluster membership and descriptions）. 补充表S9 雌性偏好表达基因（Female-biased genes）. 补充表S10 雄性偏好表达基因（Male-biased genes）. 补充表S11 参与小RNA生成的基因（Genes involved in small RNA production）. 补充表S12 白纹伊蚊与埃及伊蚊的最佳双向比对直系同源关系（Best reciprocal hits orthology between Ae. albopictus and Ae. aegypti）. 补充表S13 比对至直系同源基因的白纹伊蚊读段计数汇总（Count summary of Ae. albopictus reads mapping to orthologs）. 补充表S14 各发育阶段埃及伊蚊与白纹伊蚊的皮尔逊相关系数值（Pearson correlation values of Ae. aegypti and Ae. albopictus at each developmental stage）. 补充表S15 埃及伊蚊与白纹伊蚊中表达的直系同源基因的上调基因（Upregulated genes in Ae. aegypti and Ae. albopictus expressed orthologs）. 补充表S16 埃及伊蚊-白纹伊蚊雄性精巢及躯体的DESeq2原始分析结果（Ae. aegypti-Ae. albopictus male testes and carcass raw DESeq2 results）. 补充表S17 埃及伊蚊-白纹伊蚊蛹的DESeq2原始分析结果（Ae. aegypti-Ae. albopictus pupae raw DESeq2 results）. 补充表S18 埃及伊蚊-白纹伊蚊未吸血（Non-blood-fed, NBF）雌蚊与吸血后（Post-blood meal, PBM）雌蚊卵巢的DESeq2分析结果（Ae. aegypti-Ae. albopictus female NBF and PBM ovary DESeq2 results）. 补充表S19 埃及伊蚊-白纹伊蚊未吸血（Non-blood-fed, NBF）雌蚊与吸血后（Post-blood meal, PBM）雌蚊躯体的DESeq2分析结果（Ae. aegypti-Ae. albopictus female NBF and PBM carcass DESeq2 results）. 补充表S20 埃及伊蚊-白纹伊蚊胚胎发生的DESeq2分析结果（Ae. aegypti-Ae. albopictus embryogenesis DESeq2 results）. 补充表S21 埃及伊蚊-白纹伊蚊幼虫阶段及滞育样本的DESeq2原始分析结果（Ae. aegypti-Ae. albopictus larval stages and diapause raw DESeq2 results）. 补充文件S1 处理featureCounts生成的计数数据的脚本（Script for processing count data produced by featureCounts）. 补充文件S2 用于解析BLAST输出结果的脚本（Script used for parsing out BLAST output）. 补充文件S3 用于识别最佳双向匹配的脚本（Script used to identify best reciprocal match）