Additional file 1 of Dynamic roles of small RNAs and DNA methylation associated with heterosis in allotetraploid cotton (Gossypium hirsutum L.)

Additional file 1: Table S1. Mean of mid and better parent heterosis observed for yield traits in two location and two-year field experimentation. Table S2. Statistics of RNA sequencing data production. Table S3. Overlapping differentially expressed genes among the in MH, SM, and 1DPA in hybrid. Table S4. Statistics of small RNA sequencing data production. Table S5.  Number of the non-additively expressed genes had siRNA clusters in coding regions or 2kb flanking regions in MH, SM, and 1DPA. Table S6a. List of known differentially expressed miRNA in F1 and its Parents. S6b. List of target prediction of known miRNAs. S6c. List of target prediction of novel miRNAs. Table S7. Alignment summary statistics of whole-genome bisulfite sequencing (WGBS). Table S8. List of common DMRs among parental lines and hybrids. Table S9. Association of DMRs and sRNA among hybrid and its parental lines. Table S10. REVIGO combines the biological process GO with hybrid MPV DEGs. The unified terms of REVIGO GO are organized by major groups. To make understanding the data even easier, clusters are grouped into "main clusters" with broad categories. Table S11. Details of the primers used to validate RNA-seq and bisulfite sequencing data.

附加文件1：表S1：两个地点、两年田间试验中产量性状的中亲优势与超亲优势均值。表S2：RNA测序数据产出统计。表S3：杂交种内MH、SM与1DPA样本间的重叠差异表达基因。表S4：小RNA测序数据产出统计。表S5：杂交种内MH、SM与1DPA样本中，编码区或其2kb侧翼区域存在小干扰RNA（small interfering RNA, siRNA）簇的非加性表达基因数量。表S6a：F1及其亲本中已知差异表达微小RNA（microRNA, miRNA）列表。表S6b：已知微小RNA的靶基因预测列表。表S6c：新型微小RNA的靶基因预测列表。表S7：全基因组亚硫酸氢盐测序（whole-genome bisulfite sequencing, WGBS）比对汇总统计。表S8：亲本与杂交种间的共有差异甲基化区域（differentially methylated regions, DMRs）列表。表S9：杂交种与其亲本间差异甲基化区域与小RNA的关联分析结果。表S10：REVIGO将杂交种中亲值（mid parent value, MPV）差异表达基因与生物学过程基因本体论（Gene Ontology, GO）注释进行整合；该工具将GO统一术语按主要类别进行组织，为便于理解数据，将聚类结果归入具备宽泛类别的"主聚类"中。表S11：用于验证RNA测序与亚硫酸氢盐测序数据的引物详情。