Journal
PLANT JOURNAL
Volume 88, Issue 2, Pages 306-317Publisher
WILEY
DOI: 10.1111/tpj.13243
Keywords
Long terminal repeat retrotransposon; mutagenesis; palindrome; DNA methylation; Lotus japonicus
Categories
Funding
- Danish National Research Foundation [DNRF79]
- ERC [268523]
- Funding Program for Next Generation World-Leading Researchers from Japan Society for the Promotion of Science [GS029]
- Danish Council for Independent Research \ Technology and Production Sciences [10-081677]
- European Research Council (ERC) [268523] Funding Source: European Research Council (ERC)
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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.
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