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Evolutionary genomics of miniature inverted-repeat transposable elements (MITEs) in Brassica

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Abstract

Miniature inverted-repeat transposable elements (MITEs) are truncated derivatives of autonomous DNA transposons, and are dispersed abundantly in most eukaryotic genomes. We aimed to characterize various MITEs families in Brassica in terms of their presence, sequence characteristics and evolutionary activity. Dot plot analyses involving comparison of homoeologous bacterial artificial chromosome (BAC) sequences allowed identification of 15 novel families of mobile MITEs. Of which, 5 were Stowaway-like with TA Target Site Duplications (TSDs), 4 Tourist-like with TAA/TTA TSDs, 5 Mutator-like with 9–10 bp TSDs and 1 novel MITE (BoXMITE1) flanked by 3 bp TSDs. Our data suggested that there are about 30,000 MITE-related sequences in Brassica rapa and B. oleracea genomes. In situ hybridization showed one abundant family was dispersed in the A-genome, while another was located near 45S rDNA sites. PCR analysis using primers flanking sequences of MITE elements detected MITE insertion polymorphisms between and within the three Brassica (AA, BB, CC) genomes, with many insertions being specific to single genomes and others showing evidence of more recent evolutionary insertions. Our BAC sequence comparison strategy enables identification of evolutionarily active MITEs with no prior knowledge of MITE sequences. The details of MITE families reported in Brassica enable their identification, characterization and annotation. Insertion polymorphisms of MITEs and their transposition activity indicated important mechanism of genome evolution and diversification. MITE families derived from known Mariner, Harbinger and Mutator DNA transposons were discovered, as well as some novel structures. The identification of Brassica MITEs will have broad applications in Brassica genomics, breeding, hybridization and phylogeny through their use as DNA markers.

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Acknowledgments

This work was supported by Post-quake Development Plan, Hazara University Mansehra, Pakistan. We are grateful to Hazara University and Higher Education Commission of Pakistan for funding and support of this work. We thank Dr. Graham Teakle and Dr. Guy Barker from Warwick University, UK and Dr. Xian Hong Ge from University of Wuhan, China for supplying seeds or DNA from the Brassica accessions studied.

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  1. Faisal Nouroz

    Present address: Department of Botany, Hazara University Mansehra, Mansehra, 21300, Pakistan

Authors and Affiliations

  1. Molecular Cytogenetics Laboratory, Department of Biology, University of Leicester, Leicester, LE1 7RH, UK

    Faisal Nouroz & J. S. Heslop-Harrison

  2. Behavioural Genetics Laboratory, Department of Genetics, University of Leicester, Leicester, LE1 7RH, UK

    Shumaila Noreen

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  1. Faisal Nouroz
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Correspondence to Faisal Nouroz.

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Communicated by M.-A. Grandbastien.

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438_2015_1076_MOESM1_ESM.tif

Supplementary Fig. Dot plot of B. rapa BAC sequence (AC189298.1) against B. oleracea (EU642504.1) to identify MITE insertions. The diagonal line running from one corner to other shows the homology of the two sequence and gaps in the line show insertions in one or other species. Three MITEs (BrTOUR3-1, BoSTOW3-1, BoXMITE1-1) listed in Table 2a are shown in blue colour. The scale indicates the nucleotide numbers. (TIFF 1217 kb)

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Nouroz, F., Noreen, S. & Heslop-Harrison, J.S. Evolutionary genomics of miniature inverted-repeat transposable elements (MITEs) in Brassica . Mol Genet Genomics 290, 2297–2312 (2015). https://doi.org/10.1007/s00438-015-1076-9

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