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

Tae Jin Yang; Soo Jin Kwon; Beom Soon Choi; Jung Sun Kim; Mina Jin; Ki Byung Lim; Jee Young Park; Jin A. Kim; Myung Ho Lim; Ho Il Kim; Hyo Jin Lee; Yong Pyo Lim; Andrew H. Paterson; Beom Seok Park

doi:10.1007/s00122-006-0463-3

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

Tae Jin Yang, Soo Jin Kwon, Beom Soon Choi, Jung Sun Kim, Mina Jin, Ki Byung Lim, Jee Young Park, Jin A. Kim, Myung Ho Lim, Ho Il Kim, Hyo Jin Lee, Yong Pyo Lim, Andrew H. Paterson, Beom Seok Park

Department of Horticultural Science

Research output: Contribution to journal › Article › peer-review

25 Scopus citations

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.

Original language	English
Pages (from-to)	627-636
Number of pages	10
Journal	Theoretical And Applied Genetics
Volume	114
Issue number	4
DOIs	https://doi.org/10.1007/s00122-006-0463-3
State	Published - Feb 2007

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Yang, T. J., Kwon, S. J., Choi, B. S., Kim, J. S., Jin, M., Lim, K. B., Park, J. Y., Kim, J. A., Lim, M. H., Kim, H. I., Lee, H. J., Lim, Y. P., Paterson, A. H., & Park, B. S. (2007). Characterization of terminal-repeat retrotransposon in miniature (TRIM) in Brassica relatives. Theoretical And Applied Genetics, 114(4), 627-636. https://doi.org/10.1007/s00122-006-0463-3

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title = "Characterization of terminal-repeat retrotransposon in miniature (TRIM) in Brassica relatives",

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.",

author = "Yang, {Tae Jin} and Kwon, {Soo Jin} and Choi, {Beom Soon} and Kim, {Jung Sun} and Mina Jin and Lim, {Ki Byung} and Park, {Jee Young} and Kim, {Jin A.} and Lim, {Myung Ho} and Kim, {Ho Il} and Lee, {Hyo Jin} and Lim, {Yong Pyo} and Paterson, {Andrew H.} and Park, {Beom Seok}",

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doi = "10.1007/s00122-006-0463-3",

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AU - Yang, Tae Jin

AU - Kwon, Soo Jin

AU - Choi, Beom Soon

AU - Kim, Jung Sun

AU - Jin, Mina

AU - Lim, Ki Byung

AU - Park, Jee Young

AU - Kim, Jin A.

AU - Lim, Myung Ho

AU - Kim, Ho Il

AU - Lee, Hyo Jin

AU - Lim, Yong Pyo

AU - Paterson, Andrew H.

AU - Park, Beom Seok

PY - 2007/2

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N2 - 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.

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

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