Additional file 2 of Comprehensive repeatome annotation reveals strong potential impact of repetitive elements on tomato ripening

Table S1. Genome coverage of the different repeat families. For each repeat family, a coverage calculation has been performed and the percentage of coverage of each family was calculated.by relating the cover of every family with respect to the overall repeat coverage of the genome. Table S2. Compartmentalization of the tomato genome in three major regions. Coordinates in gff3 format of the three regions of the genome based on the repeats and genes coverage calculation into 500Â kb windows with overlap of 50Â kb.Table S3. Names of identified TE-genes. List of ID and name of each gene identified as a TE-gene. Table S4. Statistical results of the analysis of transposable elements consensus by the method of Makarevitch and al. Table S5. Functional annotation of differentially expressed genes candidate as RIN targets. (XLSX 89 kb)

表S1 不同重复序列家族的基因组覆盖度。针对每个重复序列家族均开展了覆盖度计算，并通过将各家族的覆盖度与基因组整体重复序列覆盖度进行关联，计算得到各家族的覆盖度占比。
表S2 番茄基因组的三大区域划分。基于重复序列与基因覆盖度分析，将基因组划分为重叠50 kb的500 kb窗口，并以GFF3格式给出三大基因组区域的坐标信息。
表S3 已鉴定的转座因子关联基因（TE-gene）名称列表。该表收录了所有被鉴定为转座因子关联基因的基因ID与基因名称。
表S4 采用Makarevitch等人的方法对转座因子一致性序列开展分析所得的统计结果。
表S5 被候选为RIN靶标的差异表达基因的功能注释。(XLSX 89 kb)