The LORE1 insertion mutant resource.
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.
Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark.
Anna
A
Małolepszy
Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark.
Terry
T
Mun
Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark.
Niels
N
Sandal
Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark.
Vikas
V
Gupta
Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria.
Manu
M
Dubin
Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark.
Dorian
D
Urbański
Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark.
Niraj
N
Shah
Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark.
Asger
A
Bachmann
Division of Plant Sciences, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannon-dai, Tsukuba, 305-8602, Japan.
Eigo
E
Fukai
Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan.
Hideki
H
Hirakawa
Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan.
Satoshi
S
Tabata
Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark.
Marcin
M
Nadzieja
Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark.
Katharina
K
Markmann
Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark.
Junyi
J
Su
Division of Plant Sciences, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannon-dai, Tsukuba, 305-8602, Japan.
Yosuke
Y
Umehara
Division of Plant Sciences, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannon-dai, Tsukuba, 305-8602, Japan.
Takashi
T
Soyano
Division of Plant Sciences, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannon-dai, Tsukuba, 305-8602, Japan.
Akira
A
Miyahara
Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.
Shusei
S
Sato
Division of Plant Sciences, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannon-dai, Tsukuba, 305-8602, Japan.
Makoto
M
Hayashi
Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark.
Jens
J
Stougaard
Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark.
Stig U
SU
Andersen
D019175:DNA Methylation / Q000235:genetics; D000070116:Lotus / Q000235:genetics*; D016254:Mutagenesis, Insertional; D009154:Mutation / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism*; D018626:Retroelements / Q000235:genetics*; D020079:Terminal Repeat Sequences / Q000235:genetics*
D010940:Plant Proteins; D018626:Retroelements

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