Dataset Information

Centromere-targeted de novo integrations of an LTR retrotransposon of Arabidopsis lyrata.

ABSTRACT: The plant genome evolves with rapid proliferation of LTR-type retrotransposons, which is associated with their clustered accumulation in gene-poor regions, such as centromeres. Despite their major role for plant genome evolution, no mobile LTR element with targeted integration into gene-poor regions has been identified in plants. Here, we report such targeted integrations de novo. We and others have previously shown that an ATCOPIA93 family retrotransposon in Arabidopsis thaliana is mobilized when the DNA methylation machinery is compromised. Although ATCOPIA93 family elements are low copy number in the wild-type A. thaliana genome, high-copy-number related elements are found in the wild-type Arabidopsis lyrata genome, and they show centromere-specific localization. To understand the mechanisms for the clustered accumulation of the A. lyrata elements directly, we introduced one of them, named Tal1 (Transposon of Arabidopsis lyrata 1), into A. thaliana by transformation. The introduced Tal1 was retrotransposed in A. thaliana, and most of the retrotransposed copies were found in centromeric repeats of A. thaliana, suggesting targeted integration. The targeted integration is especially surprising because the centromeric repeat sequences differ considerably between A. lyrata and A. thaliana. Our results revealed unexpectedly dynamic controls for evolution of the transposon-rich heterochromatic regions.

SUBMITTER: Tsukahara S

PROVIDER: S-EPMC3323881 | biostudies-literature | 2012 Apr

REPOSITORIES: biostudies-literature

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Centromere-targeted de novo integrations of an LTR retrotransposon of Arabidopsis lyrata.

Tsukahara Sayuri S Kawabe Akira A Kobayashi Akie A Ito Tasuku T Aizu Tomoyuki T Shin-i Tadasu T Toyoda Atsushi A Fujiyama Asao A Tarutani Yoshiaki Y Kakutani Tetsuji T

Genes & development 20120319 7

The plant genome evolves with rapid proliferation of LTR-type retrotransposons, which is associated with their clustered accumulation in gene-poor regions, such as centromeres. Despite their major role for plant genome evolution, no mobile LTR element with targeted integration into gene-poor regions has been identified in plants. Here, we report such targeted integrations de novo. We and others have previously shown that an ATCOPIA93 family retrotransposon in Arabidopsis thaliana is mobilized wh ...[more]

PMID: 22431508

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Project description:BackgroundLTR retrotransposons are a class of mobile genetic elements containing two similar long terminal repeats (LTRs). Currently, LTR retrotransposons are annotated in eukaryotic genomes mainly through the conventional homology searching approach. Hence, it is limited to annotating known elements.ResultsIn this paper, we report a de novo computational method that can identify new LTR retrotransposons without relying on a library of known elements. Specifically, our method identifies intact LTR retrotransposons by using an approximate string matching technique and protein domain analysis. In addition, it identifies partially deleted or solo LTRs using profile Hidden Markov Models (pHMMs). As a result, this method can de novo identify all types of LTR retrotransposons. We tested this method on the two pairs of eukaryotic genomes, C. elegans vs. C. briggsae and D. melanogaster vs. D. pseudoobscura. LTR retrotransposons in C. elegans and D. melanogaster have been intensively studied using conventional annotation methods. Comparing with previous work, we identified new intact LTR retroelements and new putative families, which may imply that there may still be new retroelements that are left to be discovered even in well-studied organisms. To assess the sensitivity and accuracy of our method, we compared our results with a previously published method, LTR_STRUC, which predominantly identifies full-length LTR retrotransposons. In summary, both methods identified comparable number of intact LTR retroelements. But our method can identify nearly all known elements in C. elegans, while LTR_STRUCT missed about 1/3 of them. Our method also identified more known LTR retroelements than LTR_STRUCT in the D. melanogaster genome. We also identified some LTR retroelements in the other two genomes, C. briggsae and D. pseudoobscura, which have not been completely finished. In contrast, the conventional method failed to identify those elements. Finally, the phylogenetic and chromosomal distributions of the identified elements are discussed.ConclusionWe report a novel method for de novo identification of LTR retrotransposons in eukaryotic genomes with favorable performance over the existing methods.

Dataset Information

Centromere-targeted de novo integrations of an LTR retrotransposon of Arabidopsis lyrata.

Publications

Centromere-targeted de novo integrations of an LTR retrotransposon of Arabidopsis lyrata.

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