Additional file 1 of Integrative transcriptome and proteome analyses provide new insights into different stages of Akebia trifoliata fruit cracking during ripening

Additional file 1: Fig. S1. The size distribution of the assembled transcript and unigene sequences of A. trifoliate. Fig. S2. Volcano plot depicting the transcriptome and proteome data of A. trifoliate. a, c Volcano plot depicting the transcriptome and proteome data in PM_PS. b, d Volcano plot depicting the transcriptome and proteome data in PL_PM. Absolute log10 and log2 fold changes are plotted on the y-axis and x-axis, respectively. Horizontal dotted line presents p values of 0.05 cut-off position while the vertical dotted lines discriminate between genes and proteins having absolute log2 fold change of 1. Red dots represent significantly different upregulated genes. Green dots represent significantly different downregulated genes. Pink dots represent a log2 fold change &gt;1 with p &lt; 0.05 in protein expression. Black dots indicate no difference in gene and protein expression. Fig. S3. Molecular weight and peptide count distribution were identified from TMT proteomics by searching against the database. a Distribution of the proteins that were identified among different molecular weights. b Distribution of peptide count of the proteins were identified from TMT data. Fig. S4. GO and KEGG pathway functional enrichment analysis of co-regulated genes and proteins in A. trifoliate. a, b GO enrichment analysis of co-regulated genes and proteins in PM_PS and PL_PM, respectively. c, d KEGG pathways enrichment analysis of co-regulated genes and proteins in PM_PS and PL_PM, respectively. Table S1. Sequencing statistics for A. trifoliate. Table S2. Statistical data of unigenes annotation. Table S3. The summary of the total number of transcripts and proteins identified from different stages and replicates. Table S4. The summary of the DEGs and DAPs identified from different stages and replicates. Table S5. Sequences of specific primers used for qPCR experiment.附加文件1：图S1 三叶木通（A. trifoliate）组装转录本与单基因（unigene）序列的长度分布。 图S2 展示三叶木通转录组与蛋白质组数据的火山图：其中a、c为PM_PS组中转录组与蛋白质组数据的火山图，b、d为PL_PM组中转录组与蛋白质组数据的火山图。纵轴与横轴分别对应以10为底的对数转换后的p值（-log₁₀ p值）与以2为底的基因/蛋白质表达倍数变化（log₂ fold change）。水平虚线代表p值阈值0.05的位置，垂直虚线则用于区分绝对log₂表达倍数变化绝对值为1的基因与蛋白质。红色圆点代表显著上调的差异基因/蛋白质，绿色圆点代表显著下调的差异基因/蛋白质；粉色圆点代表蛋白质表达中log₂倍数变化>1且p<0.05的条目；黑色圆点代表基因与蛋白质表达无显著差异的条目。 图S3 通过数据库检索TMT（串联质量标签）蛋白质组学数据所鉴定得到的蛋白质分子量与肽段数量分布：其中a为不同分子量区间的鉴定蛋白质分布情况，b为TMT数据中鉴定得到的蛋白质肽段数量分布情况。 图S4 三叶木通共调控基因与蛋白质的GO（基因本体）与KEGG（京都基因与基因组百科全书）通路功能富集分析：其中a、b分别为PM_PS组与PL_PM组中共调控基因与蛋白质的GO富集分析结果；c、d分别为PM_PS组与PL_PM组中共调控基因与蛋白质的KEGG通路富集分析结果。 表S1 三叶木通测序数据统计信息 表S2 单基因（unigene）注释统计数据 表S3 不同样本阶段与生物学重复中鉴定得到的转录本与蛋白质总数量汇总 表S4 不同样本阶段与生物学重复中鉴定得到的DEGs（差异表达基因）与DAPs（差异丰度蛋白质）汇总信息 表S5 qPCR（实时定量聚合酶链反应）实验所用特异性引物序列