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Open Access Research article

A Gaijin-like miniature inverted repeat transposable element is mobilized in rice during cell differentiation

Hai-Tao Dong1, Lu Zhang1, Kang-Le Zheng2, Hai-Gen Yao3, Jack Chen4, Feng-Chi Yu3, Xiao-Xing Yu1, Bi-Zeng Mao1, Dong Zhao1, Jian Yao3 and De-Bao Li1*

Author Affiliations

1 Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310029, China

2 National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China

3 Jiaxing Academy of Agricultural Science, Jiaxing 314016, China

4 The Unit of Biocomputation, NICHD/NIH, Bethesda, MD 20892, USA

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BMC Genomics 2012, 13:135  doi:10.1186/1471-2164-13-135

Published: 13 April 2012

Abstract

Background

Miniature inverted repeat transposable element (MITE) is one type of transposable element (TE), which is largely found in eukaryotic genomes and involved in a wide variety of biological events. However, only few MITEs were proved to be currently active and their physiological function remains largely unknown.

Results

We found that the amplicon discrepancy of a gene locus LOC_Os01g0420 in different rice cultivar genomes was resulted from the existence of a member of Gaijin-like MITEs (mGing). This result indicated that mGing transposition was occurred at this gene locus. By using a modified transposon display (TD) analysis, the active transpositions of mGing were detected in rice Jiahua No. 1 genome under three conditions: in seedlings germinated from the seeds received a high dose γ-ray irradiation, in plantlets regenerated from anther-derived calli and from scutellum-derived calli, and were confirmed by PCR validation and sequencing. Sequence analysis revealed that single nucleotide polymorphisms (SNPs) or short additional DNA sequences at transposition sites post mGing transposition. It suggested that sequence modification was possibly taken place during mGing transposition. Furthermore, cell re-differentiation experiment showed that active transpositions of both mGing and mPing (another well studied MITE) were identified only in regenerated plantlets.

Conclusions

It is for the first time that mGing active transposition was demonstrated under γ-ray irradiation or in cell re-differentiation process in rice. This newly identified active MITE will provide a foundation for further analysis of the roles of MITEs in biological process.