MOESM1 of Comparative transcriptomic and metabolic analysis of wild and domesticated wheat genotypes reveals differences in chemical and physical defense responses against aphids

Additional file 1: Table S1. Mapping sequence reads to the Chinese Spring reference genome. Table S2. Total RNA-seq values after rlog normalization. Annotations to the D subgenome or an unidentified subgenome (U) were eliminated. Table S3. Distribution of wheat genes into the eight clusters. Table S4. Gene annotation including the International Wheat Genome Sequencing Consortium database (IWGSC) and Phytozome gene ID. Table S5. Biological processes from the Singular Enrichment Analysis with agriGO v2 for significantly differentially expressed genes between each pair of genotypes. The data was divided into the eight k-means clusters. Only statistically significant GO terms are shown (FDR < 0.05). Queryitem: the number of genes containing the GO annotation; Querytotal: the total number of genes with GO annotations; bg item: the number of genes in wheat with this GO annotation; and bg total: the total number of genes in wheat with GO annotations. Table S6. Metabolites identified in leaves of 11-day-old wheat seedlings analyzed by GC-MS. The metabolites were normalized to the internal standard and presented as the relative abundance of the ion counts. Table S7. Weights of wheat leaf tissue used for water content calculation. The fresh, turgid and dry weights are measured in mg. Table S8. A full list of the Bx genes in bread wheat. The data include genes from Subgenome A, B, D, and U (not classified). Table S9. A full list of the trichome formation and regulation genes in bread wheat. The data include genes from Subgenome A, B, D, and U (not classified). Table S10. Benzoxazinoid annotation and fragment patterns detected and identified in wheat leaves by UPLC-QToF-MS analysis. Table S11. Levels of DIMBOA, DIM2BOA-Glc, and HDMBOA-Glc metabolites detected by HPLC-UV. Calibration curves were calculated by running authentic standards and crude extracts in different concentrations ranging from 0.5–50 μg/ml. The peak area of each compound was measured using Chromeleon software, and the final concentration was normalized to mg per gram fresh weight.附加文件1：表S1。将测序读段比对至中国春（Chinese Spring）参考基因组。表S2。经rlog标准化后的总RNA-seq数据，已剔除比对至D亚基因组或未分类亚基因组（U）的注释信息。表S3。小麦基因的8个k均值聚类簇分布情况。表S4。基因注释信息，包含国际小麦基因组测序联盟（International Wheat Genome Sequencing Consortium, IWGSC）数据库及Phytozome基因ID。表S5。针对各基因型对间的显著差异表达基因，采用agriGO v2工具开展单基因富集分析（Singular Enrichment Analysis, SEA）得到的生物学过程注释结果。数据已划分为8个k均值聚类簇，仅展示错误发现率（False Discovery Rate, FDR）<0.05的统计学显著性基因本体（Gene Ontology, GO）术语。字段说明如下：Queryitem：携带该GO注释的基因数量；Querytotal：所有携带GO注释的基因总数；bg item：小麦基因组中携带该GO注释的基因数量；bg total：小麦基因组中所有携带GO注释的基因总数。表S6。采用气相色谱-质谱联用（GC-MS）分析11日龄小麦幼苗叶片所鉴定得到的代谢物。代谢物经内标标准化后，以离子计数的相对丰度形式呈现。表S7。用于含水量计算的小麦叶片组织重量数据，记录鲜重、饱和重与干重，单位为毫克（mg）。表S8。普通小麦中Bx基因的完整列表，数据涵盖来自A、B、D亚基因组及未分类亚基因组（U）的基因。表S9。普通小麦中表皮毛形成与调控基因的完整列表，数据涵盖来自A、B、D亚基因组及未分类亚基因组（U）的基因。表S10。采用超高效液相色谱-四极杆飞行时间质谱联用（UPLC-QToF-MS）分析，在小麦叶片中检测并鉴定得到的苯并恶嗪类化合物注释信息及碎片模式。表S11。采用高效液相色谱-紫外检测（HPLC-UV）检测得到的DIMBOA、DIM2BOA-Glc及HDMBOA-Glc代谢物含量。校准曲线通过配制浓度范围为0.5–50 μg/ml的纯品标准品与粗提物进行绘制。采用Chromeleon软件测定各化合物的峰面积，最终浓度以每克鲜重毫克数进行标准化。