File S1 - Genome-Wide Comparative Analysis of 20 Miniature Inverted-Repeat Transposable Element Families in <i>Brassica rapa</i> and <i>B. oleracea</i>

Figure S1. Representation of predicted secondary structure and expected loop formation of 20 MITE families used in this study. Figure S2. Distribution of nearly intact MITE members in B. rapa, B. oleracea and A. thaliana. The physical position information for the 20 MITE families in (A) B. rapa and (B) B. oleracea pseudo-chromosome sequences are listed in Table S3 and S4. (C) The distribution of members of four homologous MITE families in the A. thaliana genome. Figure S3. Comparisons of the amino acid sequences encoded by the MITE-inserted gene Bra016667 and its paralogs Bra026774, Bra026150 and orthologs (At1g15270, TRANSLATION MACHINERY ASSOCIATED7) and Bol038124, Bol029240 and Bol031556. The sequence added by the BraTo-9 insertion is indicated and highlighted. Table S1. Primers and polymorphism profile from MITE insertion polymorphism analysis of 19 MITE families. Table S2. Characteristics of 20 MITE families and their copy numbers in B. rapa, B. oleracea and A. thaliana. Table S3. Physical positions and characterization of the members of 20 MITE families in the B. rapa genome. Table S4. Physical positions and characterization of the members of 20 MITE families in the B. oleracea genome. Table S5. miRNAs associated with MITE families. Table S6. Analysis of MITE distribution in various genomic locations based on gene annotation in the B. rapa and B. oleracea genomes. Table S7. MITE insertion polymorphism analysis with primers based on B. rapa MITE members. Table S8. MITE insertion polymorphism analysis with primers based on B. oleracea MITE members. (ZIP)补充图S1：本研究所用20个MITE（Miniature Inverted-repeat Transposable Elements，微型反向重复转座元件）家族的预测二级结构与预期环结构形成示意图。 补充图S2：白菜型油菜（Brassica rapa）、甘蓝（Brassica oleracea）及拟南芥（Arabidopsis thaliana）中近乎完整MITE成员的分布情况。其中（A）白菜型油菜和（B）甘蓝假染色体序列中20个MITE家族的物理位置信息详见补充表S3和S4；（C）拟南芥基因组中4个同源MITE家族成员的分布情况。 补充图S3：携带MITE插入的基因Bra016667及其旁系同源基因Bra026774、Bra026150，以及直系同源基因（At1g15270，TRANSLATION MACHINERY ASSOCIATED7）、Bol038124、Bol029240和Bol031556所编码氨基酸序列的比对。BraTo-9插入所引入的序列已标注并高亮显示。 补充表S1：19个MITE家族的MITE插入多态性分析所用引物及多态性概况。 补充表S2：20个MITE家族的特征及其在白菜型油菜、甘蓝及拟南芥中的拷贝数。 补充表S3：白菜型油菜基因组中20个MITE家族成员的物理位置及特征信息。 补充表S4：甘蓝基因组中20个MITE家族成员的物理位置及特征信息。 补充表S5：与MITE家族相关的微小RNA（miRNAs）。 补充表S6：基于白菜型油菜和甘蓝基因组基因注释的不同基因组区域MITE分布分析结果。 补充表S7：基于白菜型油菜MITE成员设计引物的MITE插入多态性分析。 补充表S8：基于甘蓝MITE成员设计引物的MITE插入多态性分析。 （压缩包）