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Characterization of transcriptional activation and inserted-into-gene preference of various transposable elements in the Brassica species

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Abstract

Transposable elements (TEs) have attracted increasing attention because of their tremendous contributions to genome reorganization and gene variation through dramatic proliferation and excision via transposition. However, less known are the transcriptional activation of various TEs and the characteristics of TE insertion into genomes at the genome-wide level. In the present study, we focused on TE genes for transposition and gene disruption by insertion of TEs in expression sequences of Brassica, to investigate the transcriptional activation of TEs, the biased insertion of TEs into genes, and their salient characteristics. Long terminal repeat (LTR-retrotransposon) accounted for the majority of these active TE genes (70.8%), suggesting that transposition activation varied with TE type. 6.1% genes were interrupted by LTR-retrotransposons, which indicated their preference for insertion into genes. TEs were preferentially inserted into cellular component-specific genes acted as “binding” elements and involved in metabolic processes. TEs have a biased insertion into some host genes that were involved with important molecular functions and TE genes exhibited spatiotemporal expression. These results suggested that various types of transposons differentially contributed to gene variation and affected gene function.

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Acknowledgments

This work was supported financially by grants from the Fundamental Research Funds for the Central Universities, National Natural Science Foundation of China (code: 31071450) and National Science and Technology Ministry (code: 2009BADA8B01). We would like to thank Lu Junxing, Li Xiaoxia and Fu Chun for technical assistance. We would like to thank Doctor Katrin Link for her constructive comments on this review and editing the manuscript.

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Authors and Affiliations

  1. Chongqing Engineering Research Center for Rapeseed, Center of South Upland Agriculture of Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China

    Caihua Gao, Meili Xiao, Jiana Li, Jiaming Yin, Xiaodong Ren, Wei Qian, Ortegón Oscar, Donghui Fu & Zhanglin Tang

  2. College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China

    Lingyan Jiang

  3. Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China

    Donghui Fu

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  1. Caihua Gao
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Correspondence to Donghui Fu or Zhanglin Tang.

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Caihua Gao and Meili Xiao contributed equally to this work.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Online Resource 1. Phylogenetic analysis of TE genes for transposition and TEs that inserted in genes. (XLS 28 kb)

11033_2012_1585_MOESM2_ESM.xls

Online Resource 2. Genes disrupted by TE that homologous to the genes known to control traits in Arabidopsis thaliana. (XLS 32 kb)

11033_2012_1585_MOESM3_ESM.xls

Online Resource 3. List of cellular components, biological process and molecular function of the genes that inserted by LTR-retrotranspons, and SINE-retransposons. (XLS 546 kb)

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Gao, C., Xiao, M., Jiang, L. et al. Characterization of transcriptional activation and inserted-into-gene preference of various transposable elements in the Brassica species. Mol Biol Rep 39, 7513–7523 (2012). https://doi.org/10.1007/s11033-012-1585-0

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