New insights into nested long terminal repeat retrotransposons in Brassica species

Wei, Lijuan, Xiao, Meili, An, Zeshan, Ma, Bi, Mason, Annaliese S., Qian, Wei, Li, Jiana and Fu, Donghui (2013) New insights into nested long terminal repeat retrotransposons in Brassica species. Molecular Plant, 6 2: 470-482. doi:10.1093/mp/sss081

Author Wei, Lijuan
Xiao, Meili
An, Zeshan
Ma, Bi
Mason, Annaliese S.
Qian, Wei
Li, Jiana
Fu, Donghui
Title New insights into nested long terminal repeat retrotransposons in Brassica species
Formatted title
New insights into nested long terminal repeat retrotransposons in Brassica species
Journal name Molecular Plant   Check publisher's open access policy
ISSN 1674-2052
Publication date 2013-03
Year available 2012
Sub-type Article (original research)
DOI 10.1093/mp/sss081
Volume 6
Issue 2
Start page 470
End page 482
Total pages 13
Place of publication Oxford, United Kingdom
Publisher Oxford University Press
Collection year 2013
Language eng
Formatted abstract
Long terminal repeat (LTR) retrotransposons, one of the foremost types of transposons, continually change or modify gene function and reorganize the genome through bursts of dramatic proliferation. Many LTR-TEs preferentially insert within other LTR-TEs, but the cause and evolutionary significance of these nested LTR-TEs are not well understood. In this study, a total of 1.52Gb of Brassica sequence containing 2020 bacterial artificial chromosomes (BACs) was scanned, and six bacterial artificial chromosome (BAC) clones with extremely nested LTR-TEs (LTR-TEs density: 7.24/kb) were selected for further analysis. The majority of the LTR-TEs in four of the six BACs were found to be derived from the rapid proliferation of retrotransposons originating within the BAC regions, with only a few LTR-TEs originating from the proliferation and insertion of retrotransposons from outside the BAC regions approximately 5–23Mya. LTR-TEs also preferably inserted into TA-rich repeat regions. Gene prediction by Genescan identified 207 genes in the 0.84Mb of total BAC sequences. Only a few genes (3/207) could be matched to the Brassica expressed sequence tag (EST) database, indicating that most genes were inactive after retrotransposon insertion. Five of the six BACs were putatively centromeric. Hence, nested LTR-TEs in centromere regions are rapidly duplicated, repeatedly inserted, and act to suppress activity of genes and to reshuffle the structure of the centromeric sequences. Our results suggest that LTR-TEs burst and proliferate on a local scale to create nested LTR-TE regions, and that these nested LTR-TEs play a role in the formation of centromeres.
Keyword LTR retrotransposons
Transposon burst
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ
Additional Notes First published online: 28 August 2012.

Document type: Journal Article
Sub-type: Article (original research)
Collections: Centre for Integrative Legume Research Publications
School of Agriculture and Food Sciences
Official 2013 Collection
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Citation counts: TR Web of Science Citation Count  Cited 5 times in Thomson Reuters Web of Science Article | Citations
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Created: Mon, 03 Sep 2012, 11:55:27 EST by Annaliese Mason on behalf of School of Agriculture and Food Sciences