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Miniature inverted-repeat transposable elements (MITEs) are ubiquitous, non-autonomous class II transposable elements. Here, we conducted genome-wide comparative analysis of 20 MITE families in  B. rapa ,  B. oleracea , and  Arabidopsis thaliana . A total of 5894 and 6026 MITE members belonging to the 20 families were found in the whole genome pseudo-chromosome sequences of  B. rapa  and  B. oleracea , respectively. Meanwhile, only four of the 20 families, comprising 573 members, were identified in the  Arabidopsis  genome, indicating that most of the families were activated in the  Brassica  genus after divergence from  Arabidopsis . Copy numbers varied from 4 to 1459 for each MITE family, and there was up to 6-fold variation between  B. rapa  and  B. oleracea . In particular, analysis of intact members showed that whereas eleven families were present in similar copy numbers in  B. rapa  and  B. oleracea , nine families showed copy number variation ranging from 2- to 16-fold. Four of those families (BraSto-3, BraTo-3, 4, 5) were more abundant in  B. rapa , and the other five (BraSto-1, BraSto-4, BraTo-1, 7 and BraHAT-1) were more abundant in  B. oleracea . Overall, 54% and 51% of the MITEs resided in or within 2 kb of a gene in the  B. rapa  and  B. oleracea  genomes, respectively. Notably, 92 MITEs were found within the CDS of annotated genes, suggesting that MITEs might play roles in diversification of genes in the recently triplicated  Brassica  genome. MITE insertion polymorphism (MIP) analysis of 289 MITE members showed that 52% and 23% were polymorphic at the inter- and intra-species levels, respectively, indicating that there has been recent MITE activity in the  Brassica  genome. These recently activated MITE families with abundant MIP will provide useful resources for molecular breeding and identification of novel functional genes arising from MITE insertion.

Genome-Wide Comparative Analysis of 20 Miniature Inverted-Repeat Transposable Element Families in Brassica rapa and B. oleracea