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Plant J. 2016 Oct;88(2):306-317. doi: 10.1111/tpj.13243. Epub 2016 Sep 27.

The LORE1 insertion mutant resource.

Author information

1
Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark.
2
Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria.
3
Division of Plant Sciences, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannon-dai, Tsukuba, 305-8602, Japan.
4
Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan.
5
Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.

Abstract

Long terminal repeat (LTR) retrotransposons are closely related to retroviruses, and their activities shape eukaryotic genomes. Here, we present a complete Lotus japonicus insertion mutant collection generated by identification of 640 653 new insertion events following de novo activation of the LTR element Lotus retrotransposon 1 (LORE1) (http://lotus.au.dk). Insertion preferences are critical for effective gene targeting, and we exploit our large dataset to analyse LTR element characteristics in this context. We infer the mechanism that generates the consensus palindromes typical of retroviral and LTR retrotransposon insertion sites, identify a short relaxed insertion site motif, and demonstrate selective integration into CHG-hypomethylated genes. These characteristics result in a steep increase in deleterious mutation rate following activation, and allow LORE1 active gene targeting to approach saturation within a population of 134 682 L. japonicus lines. We suggest that saturation mutagenesis using endogenous LTR retrotransposons with germinal activity can be used as a general and cost-efficient strategy for generation of non-transgenic mutant collections for unrestricted use in plant research.

KEYWORDS:

Lotus japonicus ; DNA methylation; Long terminal repeat retrotransposon; mutagenesis; palindrome

PMID:
27322352
DOI:
10.1111/tpj.13243
[Indexed for MEDLINE]
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