Abstract
BackgroundMiniature inverted-repeat transposable elements (MITEs) are expected to play important roles in evolution of genes and genome in plants, especially in the highly duplicated plant genomes. Various MITE families and their roles in plants have been characterized. However, there have been fewer studies of MITE families and their potential roles in evolution of the recently triplicated Brassica genome.ResultsWe identified a new MITE family, BRAMI-1, belonging to the Stowaway super-family in the Brassica genome. In silico mapping revealed that 697 members are dispersed throughout the euchromatic regions of the B. rapa pseudo-chromosomes. Among them, 548 members (78.6%) are located in gene-rich regions, less than 3 kb from genes. In addition, we identified 516 and 15 members in the 470 Mb and 15 Mb genomic shotgun sequences currently available for B. oleracea and B. napus, respectively. The resulting estimated copy numbers for the entire genomes were 1440, 1464 and 2490 in B. rapa, B. oleracea and B. napus, respectively. Concurrently, only 70 members of the related Arabidopsis ATTIRTA-1 MITE family were identified in the Arabidopsis genome. Phylogenetic analysis revealed that BRAMI-1 elements proliferated in the Brassica genus after divergence from the Arabidopsis lineage. MITE insertion polymorphism (MIP) was inspected for 50 BRAMI-1 members, revealing high levels of insertion polymorphism between and within species of Brassica that clarify BRAMI-1 activation periods up to the present. Comparative analysis of the 71 genes harbouring the BRAMI-1 elements with their non-insertion paralogs (NIPs) showed that the BRAMI-1 insertions mainly reside in non-coding sequences and that the expression levels of genes with the elements differ from those of their NIPs.ConclusionA Stowaway family MITE, named as BRAMI-1, was gradually amplified and remained present in over than 1400 copies in each of three Brassica species. Overall, 78% of the members were identified in gene-rich regions, and it is assumed that they may contribute to the evolution of duplicated genes in the highly duplicated Brassica genome. The resulting MIPs can serve as a good source of DNA markers for Brassica crops because the insertions are highly dispersed in the gene-rich euchromatin region and are polymorphic between or within species.
Highlights
Miniature inverted-repeat transposable elements (MITEs) are expected to play important roles in evolution of genes and genome in plants, especially in the highly duplicated plant genomes
We discovered high amounts of insertion polymorphism inter- and intra-species, which can serve a good source of genetic markers in the Brassica species
Characterization of Brassica rapa MITE (BRAMI)-1 in Brassica We identified a 260 bp MITE in the Brassica rapa BAC clone, KBrB059A03 using MUST, a de novo program for MITE identification, and additional manual inspection
Summary
Miniature inverted-repeat transposable elements (MITEs) are expected to play important roles in evolution of genes and genome in plants, especially in the highly duplicated plant genomes. Miniature inverted-repeat transposable elements (MITEs) are Class II DNA transposons that are nonautonomous, with defective or absent of coding genes. MITEs were identified in the maize genome [11] and later found in Arabidopsis, rice, grape, mosquito, fish, bacteria and human as well as in several other genomes [1,12,13,14,15]. Recent studies have found that MITEs are a source of small interfering RNA (siRNA) evolution and may play an important role in gene regulation and epigenetic mechanisms [16,20,21,22]. MITE transposition into a new region of the genome causes insertion polymorphisms among accessions of same species that can be useful tools for development of various markers [23,24]
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