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Characterization of terminal-repeat retrotransposon in miniature (TRIM) in Brassica relatives

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Abstract

We have newly identified five Terminal-repeat retrotransposon in miniature (TRIM) families, four from Brassica and one from Arabidopsis. A total of 146 elements, including three Arabidopsis families reported before, are extracted from genomics data of Brassica and Arabidopsis, and these are grouped into eight distinct lineages, Br1 to Br4 derived from Brassica and At1 to At4 derived from Arabidopsis. Based on the occurrence of TRIM elements in 434 Mb of B. oleracea shotgun sequences and 96 Mb of B. rapa BAC end sequences, total number of TRIM members of Br1, Br2, Br3, and Br4 families are roughly estimated to be present in 660 and 530 copies in B. oleracea and B. rapa genomes, respectively. Studies on insertion site polymorphisms of four elements across taxa in the tribe Brassiceae infer the taxonomic lineage and dating of the insertion time. Active roles of the TRIM elements for evolution of the duplicated genes are inferred in the highly replicated Brassica genome.

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Acknowledgments

This work was supported by grants from the BioGreen 21 Program, RDA, and NIAB, Korea. The authors thank Macrogen (http://www.macrogen.com/english/index.html) for BAC end sequencing. We are grateful for Maryana Bhak and Chang-Bae Kim for valuable comments.

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Authors and Affiliations

  1. Department of Plant Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, South Korea

    Tae-Jin Yang

  2. Brassica Genomics Team, National Institute of Agricultural Biotechnology, Rural Development Administration, Suwon, 441-707, South Korea

    Soo-Jin Kwon, Beom-Soon Choi, Jung Sun Kim, Mina Jin, Jee Young Park, Jin-A Kim, Myung-Ho Lim, Ho-Il Kim, Hyo-Jin Lee & Beom-Seok Park

  3. School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 702-701, South Korea

    Ki-Byung Lim

  4. Department of Horticulture, Chungnam National University, Daejeon, 305-764, South Korea

    Yong Pyo Lim

  5. Plant Genome Mapping Lab, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA

    Andrew H. Paterson

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  1. Tae-Jin Yang
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  2. Soo-Jin Kwon
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  3. Beom-Soon Choi
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  14. Beom-Seok Park
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Corresponding author

Correspondence to Beom-Seok Park.

Additional information

Communicated by J. S. Heslop-Harrison.

Tae-Jin Yang and Soo-Jin Kwon have equally contributed to this work.

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Yang, TJ., Kwon, SJ., Choi, BS. et al. Characterization of terminal-repeat retrotransposon in miniature (TRIM) in Brassica relatives. Theor Appl Genet 114, 627–636 (2007). https://doi.org/10.1007/s00122-006-0463-3

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  • DOI: https://doi.org/10.1007/s00122-006-0463-3

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