Additional file 2 of Cytological, transcriptome and miRNome temporal landscapes decode enhancement of rice grain size

Additional file 2: Table S1. Summary of reads obtained from total RNA sequencing of 36 cDNA libraries from the five seed developmental stages (S1-S5) and flag leaf (L) of SN and LGR. Table S2. Pearson’s correlation between biological replicates of the five seed developmental stages (S1-S5) and flag leaf (L) of SN and LGR. Table S3. FPKM values of all rice genes (transposable elements removed) in flag leaf and five seed development tissues of SN and LGR. The higlighted ones indicate significant DEGs in at least one seed stage. Table S4. Log2fold change values in seed development stages, of significant DEGs (Log2FC≥1, q value≤0.05, p value ≤0.05, FPKM≥1). Non-significant differential expression is indicated by ‘-’. Table S5. Stage-specific DEGs common between SN and LGR. Log2 fold change values of DEGs which are specific (log2FC≥1 in that stage and <1 in rest) to the same stage of SN and LGR. Table S6. FPKM values of cell cycle related genes specifically up regulated in seeds of SN and LGR. Table S7. List of DEGs preferential to S3 stage of LGR by comparison with SN S3/LGR S2 and SN S2/LGR S2. Genes which are LGR S3 preferential in both analyses have been highlighted. Table S8. List of TF encoding genes (with their log2fold changes), significantly differentially expressed at log2fc≥1 in at least one seed developmental stage of SN and/or LGR. “-” indicates non-significant values. Table S9. FPKM values of phytohormone encoding genes, which were present in different expression clusters (variation in expression pattern) and had higher expression values (difference in log2FPKM≥0.5; variation in expression level) in a stage in either SN or LGR. Table S10. Summary of grain size QTLs identified using a mapping population (Sonasal x LGR) in rice. Table S11. Log2 fold change values of genes which are significantly differentially expressed amongst SN and LGR seed development stages and are located within QTLs associated with a seed size-related trait. Table S12a. Summary of reads obtained from small RNA sequencing of each library from the five seed developmental stages (S1-S5) and flag leaf (L) of SN. In all samples, _1, _2, _3 represent biological replicates. Table S12b. Summary of reads obtained from small RNA sequencing of each library from the five seed developmental stages (S1-S5) and flag leaf (L) of LGR. In all samples, _1, _2, _3 represent biological replicates. Table S13. Pearson's correlation between biological replicates of the five seed developmental stages (S1-S5) and flag leaf (L) of SN and LGR obtained from small RNA sequencing. Table S14. Expression of all miRs in seed and flag leaf of SN and LGR. The TPM values of 604 miRs detected in at least one of the tissues used has been mentioned. The TPM values ≥50 have been highlighted in gray. Table S15. Comparison of DEMs between SN and LGR. The orange colored cells indicate the log2 fold changes of 467 DEMs for each stage of seed development. The yellow color indicates comparison between similar stages (by developmental event) of SN and LGR. The grey color indicates comparison between same stage (by DAP) of SN and LGR. U implies 'up regulation' while D implies 'down regulation' in the respective stage mentioned. - indicates non-significant differential expression. The up regulated genes have been marked in green while down regulated ones are in red. Table S16. List of miRNA-target modules for miRNAs up and down-regulated in all five seed developmental stages of either SN or LGR. Table S17. List of primers for validation. Table S18. Details of replicate data.

附加文件2：表S1. SN和LGR的5个种子发育阶段（S1-S5）及旗叶（L）的36个cDNA文库总RNA测序获得的reads汇总。表S2. SN和LGR的5个种子发育阶段（S1-S5）及旗叶（L）生物学重复之间的Pearson相关性。表S3. SN和LGR的旗叶及5个种子发育组织中所有水稻基因（已去除转座元件）的FPKM值。高亮部分表示至少在一个种子阶段中显著的差异表达基因（DEGs）。表S4. 显著差异表达基因（DEGs）在种子发育阶段的Log2倍变化值（Log2FC≥1、q值≤0.05、p值≤0.05、FPKM≥1）。非显著差异表达用“-”表示。表S5. SN和LGR共有的阶段特异性差异表达基因（DEGs）。SN和LGR同一阶段特异性（该阶段log2FC≥1且其余阶段<1）DEGs的Log2倍变化值。表S6. SN和LGR种子中特异性上调的细胞周期相关基因的FPKM值。表S7. 通过SN S3/LGR S2和SN S2/LGR S2比较得到的优先在LGR S3阶段表达的差异表达基因（DEGs）列表。在两种分析中均优先在LGR S3阶段表达的基因已高亮显示。表S8. 在SN和/或LGR的至少一个种子发育阶段中log2fc≥1的显著差异表达转录因子（TF）编码基因列表（含其log2倍变化值）。“-”表示非显著值。表S9. 植物激素编码基因的FPKM值，这些基因存在于不同表达聚类（表达模式差异）中，且在SN或LGR的某个阶段具有更高的表达值（log2FPKM差异≥0.5；表达水平差异）。表S10. 利用水稻作图群体（Sonasal × LGR）鉴定到的粒型数量性状位点（QTLs）汇总。表S11. 在SN和LGR种子发育阶段间显著差异表达且位于粒型相关性状QTL区域内的基因的Log2倍变化值。表S12a. SN的5个种子发育阶段（S1-S5）及旗叶（L）各文库小RNA测序获得的reads汇总。所有样本中，_1、_2、_3代表生物学重复。表S12b. LGR的5个种子发育阶段（S1-S5）及旗叶（L）各文库小RNA测序获得的reads汇总。所有样本中，_1、_2、_3代表生物学重复。表S13. SN和LGR的5个种子发育阶段（S1-S5）及旗叶（L）小RNA测序生物学重复之间的Pearson相关性。表S14. SN和LGR种子及旗叶中所有微小RNA（miRs）的表达情况。提及了在至少一种所用组织中检测到的604个miRs的转录本每百万（TPM）值。TPM值≥50的已用灰色高亮显示。表S15. SN和LGR之间差异表达微小RNA（DEMs）的比较。橙色单元格表示467个DEMs在每个种子发育阶段的log2倍变化值。黄色表示SN和LGR相似阶段（按发育事件）的比较。灰色表示SN和LGR同一阶段（按DAP）的比较。U表示提及阶段中的上调，D表示下调。“-”表示非显著差异表达。上调基因用绿色标记，下调基因用红色标记。表S16. 在SN或LGR所有5个种子发育阶段中上调或下调的miRNA的miRNA-靶标模块列表。表S17. 验证用引物列表。表S18. 重复数据详情。