Identification of related empty sites by sequence comparison of MITE flanking regions with corresponding regions from <i>B. rapa</i> (A genome) or <i>B. oleracea</i> (C genome) homologs.

<p>The chromosome numbers and start positions of the sequences are indicated at the beginning of the sequence. TSD sequences are shown in bold.</p

MITE insertion polymorphism (MIP) analysis of 19 MITE families in the <i>Brassica</i> genome.

<p>The accessions used here: 1- <i>B. napus</i> (Tapidor), 2- <i>B. napus</i> (Ningyou 7), 3- <i>B. rapa</i> (Chiifu), 4- <i>B. rapa</i> (Kenshin), 5- <i>B. oleracea</i> (C1234), 6- <i>B. oleracea</i> (C1184), 7- <i>B. oleracea</i> (C1235), 8- <i>A. thaliana</i> (Columbia). M, molecular size marker. <i>Black</i> and <i>gray</i> arrowheads indicate the products with and without MITE insertion, respectively.</p

MITE insertion introduced a new exon into the Bra016667 gene of <i>B. rapa</i>.

<p>(A) Dot-plot comparison of genomic regions of BraTo-9-inserted gene Bra016667 with its paralogs Bra026774, Bra026150 and orthologs (At1g15270, <i>TRANSLATION MACHINERY ASSOCIATED7</i>) and Bol038124, Bol029240 and Bol031556 from <i>B. rapa</i>, <i>A. thaliana</i>, and <i>B. oleracea</i>, respectively. (B) Comparison of exon arrays of the genes shown in (A). The MITE based neo-exon is indicated as a green bar. The exon arrays were determined based on similarity to the ortholog At1g15270.</p

Differential distribution of MITE family members in <i>B. rapa</i> and <i>B. oleracea</i>.

<p>MITE families with intact members were used for <i>in silico</i> map construction on the 256 Mb <i>B. rapa</i> (A) and the 385 Mb <i>B. oleracea</i> (B) pseudo-chromosome sequences based on the physical positions. The physical position information for the MITE families of <i>B. rapa</i> and <i>B. oleracea</i> are listed in Table S3 and S4, respectively.</p

Comparison of 29 genes harboring BraTo-9 fragments with their homologous genes.

a<p>MITE position and alignment information can be found in Table S3.</p>b<p>Triplicated paralogs of <i>B. rapa</i> and orthologs from <i>A. thaliana</i> and <i>B. oleracea</i> were identified from BRAD annotation information. Bold indicates the gene with BraTo-9 insertion.</p