Establishment of a Lotus japonicus gene tagging population using the exon-targeting endogenous retrotransposon LORE1

Plant Journal

Volumn 69, Issue 4, 2012, Pages 720-730

  Fukai, Eigo ^a,b   Soyano, Takashi ^a   Umehara, Yosuke ^a   Nakayama, Shinobu ^b   Hirakawa, Hideki ^b   Tabata, Satoshi ^b   Sato, Shusei ^b   Hayashi, Makoto ^a  

^a NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

^b KAZUSA DNA RESEARCH INSTITUTE   (Japan)

Author keywords

gene tagging; Lotus japonicus; Lotus Retrotransposons 1; pyrosequencing; retrotransposon; symbiosis

Indexed keywords

GENE TAGGING; LOTUS JAPONICUS; LOTUS RETROTRANSPOSONS 1; PYROSEQUENCING; RETROTRANSPOSON; SYMBIOSIS;

BIOLOGY; PLANTS (BOTANY);

GENES;

PRIMER DNA;

ARTICLE; DNA SEQUENCE; EXON; GENE EXPRESSION REGULATION; GENE TARGETING; GENETICS; LONG TERMINAL REPEAT; LOTUS; METHODOLOGY; MUTATION; RETROPOSON; SYMBIOSIS;

DNA PRIMERS; EXONS; GENE TARGETING; LOTUS; MUTAGENESIS, INSERTIONAL; MUTATION; RETROELEMENTS; SEQUENCE ANALYSIS, DNA; SYMBIOSIS; TERMINAL REPEAT SEQUENCES;

LOTUS CORNICULATUS VAR. JAPONICUS;

EID: 84856727215     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/j.1365-313X.2011.04826.x     Document Type: Article

References (47)

1. Andersson, R., Enroth, S., Rada-Iglesias, A., Wadelius, C., and, Komorowski, J., (2009) Nucleosomes are well positioned in exons and carry characteristic histone modifications. Genome Res. 19, 1732-1741.
2. Brady, T.L., Schmidt, C.L., and, Voytas, D.F., (2008) Targeting integration of the Saccharomyces Ty5 retrotransposon. Methods Mol. Biol. 435, 153-163.
3. Bushman, F.D., (2003) Targeting survival: integration site selection by retroviruses and LTR-retrotransposons. Cell, 115, 135-138. (Pubitemid 37329577)
4. Carpenter, R., and, Coen, E.S., (1990) Floral homeotic mutations produced by transposon-mutagenesis in Antirrhinum majus. Genes Dev. 4, 1483-1493.
5. Chatterjee, A.G., Leem, Y.E., Kelly, F.D., and, Levin, H.L., (2009) The chromodomain of Tf1 integrase promotes binding to cDNA and mediates target site selection. J. Virol. 83, 2675-2685.
6. Chodavarapu, R.K., Feng, S., Bernatavichute, Y.V., et al. (2010) Relationship between nucleosome positioning and DNA methylation. Nature, 466, 388-392.
7. Clough, S.J., and, Bent, A.F., (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16, 735-743.
8. Ellinghaus, D., Kurtz, S., and, Willhoeft, U., (2008) LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics, 9, 18.
9. Feuillet, C., Leach, J.E., Rogers, J., Schnable, P.S., and, Eversole, K., (2011) Crop genome sequencing: lessons and rationales. Trends Plant Sci. 16, 77-88.
10. Fukai, E., Dobrowolska, A.D., Madsen, L.H., Madsen, E.B., Umehara, Y., Kouchi, H., Hirochika, H., and, Stougaard, J., (2008) Transposition of a 600 thousand-year-old LTR retrotransposon in the model legume Lotus japonicus. Plant Mol. Biol. 68, 653-663.
11. Fukai, E., Umehara, Y., Sato, S., Endo, M., Kouchi, H., Hayashi, M., Stougaard, J., and, Hirochika, H., (2010) Derepression of the plant chromovirus LORE1 induces germline transposition in regenerated plants. PLoS Genet. 6, e1000868.
12. Gao, X., Hou, Y., Ebina, H., Levin, H.L., and, Voytas, D.F., (2008) Chromodomains direct integration of retrotransposons to heterochromatin. Genome Res. 18, 359-369. (Pubitemid 351347079)
13. Gorinsek, B., Gubensek, F., and, Kordis, D., (2004) Evolutionary genomics of chromoviruses in eukaryotes. Mol. Biol. Evol. 21, 781-798. (Pubitemid 38529721)
14. Grandbastien, M.A., Spielmann, A., and, Caboche, M., (1989) Tnt1, a mobile retroviral-like transposable element of tobacco isolated by plant cell genetics. Nature, 337, 376-380.
15. Hancock, C.N., Zhang, F., Floyd, K., Richardson, A.O., Lafayette, P., Tucker, D., Wessler, S.R., and, Parrott, W.A., (2011) The Rice (Oryza sativa) MITE mPing is an Effective Insertional Mutagen in Soybean (Glycine max). Plant Physiol. 157, 552-562.
16. Handberg, K., and, Stougaard, J., (1992) Lotus japonicus, an autogamous, diploid legume species for classical and molecular-genetics. Plant J. 2, 487-496.
17. Hayashi, M., Miyahara, A., Sato, S., et al. (2001) Construction of a genetic linkage map of the model legume Lotus japonicus using an intraspecific F2 population. DNA Res. 8, 301-310. (Pubitemid 33617883)
18. Hirochika, H., (1993) Activation of tobacco retrotransposons during tissue culture. EMBO J. 12, 2521-2528. (Pubitemid 23194203)
19. Hirochika, H., Sugimoto, K., Otsuki, Y., Tsugawa, H., and, Kanda, M., (1996) Retrotransposons of rice involved in mutations induced by tissue culture. Proc. Natl Acad. Sci. USA, 93, 7783-7788. (Pubitemid 26277115)
20. Hossain, M.S., Umehara, Y., and, Kouchi, H., (2006) A novel fix-symbiotic mutant of Lotus japonicus, Ljsym105, shows impaired development and premature deterioration of nodule infected cells and symbiosomes. Mol. Plant Microbe Interact. 19, 780-788.
21. Imaizumi, R., Sato, S., Kameya, N., Nakamura, I., Nakamura, Y., Tabata, S., Ayabe, S., and, Aoki, T., (2005) Activation tagging approach in a model legume, Lotus japonicus. J. Plant. Res. 118, 391-399. (Pubitemid 41831856)
22. Inagaki, Y., Hisatomi, Y., Suzuki, T., Kasahara, K., and, Iida, S., (1994) Isolation of a Suppressor-Mutator/Enhancer-like transposable element, Tpn1, from Japanese morning glory bearing variegated flowers. Plant Cell, 6, 375-383.
23. Ingouff, M., Rademacher, S., Holec, S., Soljic, L., Xin, N., Readshaw, A., Foo, S.H., Lahouze, B., Sprunck, S., and, Berger, F., (2010) Zygotic resetting of the HISTONE 3 variant repertoire participates in epigenetic reprogramming in Arabidopsis. Curr. Biol. 20, 2137-2143.
24. Kanamori, N., Madsen, L.H., Radutoiu, S., et al. (2006) A nucleoporin is required for induction of Ca2+ spiking in legume nodule development and essential for rhizobial and fungal symbiosis. Proc. Natl Acad. Sci. USA, 103, 359-364. (Pubitemid 43122405)
25. Kaneko, T., Nakamura, Y., Sato, S., et al. (2000) Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. DNA Res. 7, 381-406.
26. Madsen, L.H., Fukai, E., Radutoiu, S., Yost, C.K., Sandal, N., Schauser, L., and, Stougaard, J., (2005) LORE1, an active low-copy-number TY3-gypsy retrotransposon family in the model legume Lotus japonicus. Plant J. 44, 372-381.
27. Mathieu, M., Winters, E.K., Kong, F., et al. (2009) Establishment of a soybean (Glycine max Merr. L) transposon-based mutagenesis repository. Planta, 229, 279-289.
28. Mazier, M., Botton, E., Flamain, F., Bouchet, J.P., Courtial, B., Chupeau, M.C., Chupeau, Y., Maisonneuve, B., and, Lucas, H., (2007) Successful gene tagging in lettuce using the Tnt1 retrotransposon from tobacco. Plant Physiol. 144, 18-31. (Pubitemid 46941600)
29. Miyao, A., Tanaka, K., Murata, K., Sawaki, H., Takeda, S., Abe, K., Shinozuka, Y., Onosato, K., and, Hirochika, H., (2003) Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome. Plant Cell, 15, 1771-1780. (Pubitemid 37078333)
30. Miyao, A., Iwasaki, Y., Kitano, H., Itoh, J., Maekawa, M., Murata, K., Yatou, O., Nagato, Y., and, Hirochika, H., (2007) A large-scale collection of phenotypic data describing an insertional mutant population to facilitate functional analysis of rice genes. Plant Mol. Biol. 63, 625-635.
31. Murashige, T., and, Skoog, F., (1962) A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol. Plant. 15, 473-497.
32. Ohmido, N., Ishimaru, A., Kato, S., Sato, S., Tabata, S., and, Fukui, K., (2010) Integration of cytogenetic and genetic linkage maps of Lotus japonicus, a model plant for legumes. Chromosome Res. 18, 287-299.
33. Sandal, N., Petersen, T.R., Murray, J., et al. (2006) Genetics of symbiosis in Lotus japonicus: recombinant inbred lines, comparative genetic maps, and map position of 35 symbiotic loci. Mol. Plant Microbe Interact. 19, 80-91. (Pubitemid 43011201)
34. Sato, S., Nakamura, Y., Kaneko, T., et al. (2008) Genome structure of the legume, Lotus japonicus. DNA Res. 15, 227-239.
35. Sessions, A., Burke, E., Presting, G., et al. (2002) A high-throughput Arabidopsis reverse genetics system. Plant Cell, 14, 2985-2994. (Pubitemid 36029127)
36. Stiller, J., Martirani, L., Tuppale, S., Chian, R.-J., Chiurazzi, M., and, Gresshoff, P.M., (1997) High frequency transformation and regeneration of transgenic plants in the model legume Lotus japonicus. J. Exp. Bot. 48, 1357-1365. (Pubitemid 27378026)
37. Tadege, M., Wen, J., He, J., et al. (2008) Large-scale insertional mutagenesis using the Tnt1 retrotransposon in the model legume Medicago truncatula. Plant J. 54, 335-347. (Pubitemid 351503122)
38. Tsukahara, S., Kobayashi, A., Kawabe, A., Mathieu, O., Miura, A., and, Kakutani, T., (2009) Bursts of retrotransposition reproduced in Arabidopsis. Nature, 461, 423-426.
39. Urbański, D.F., Małolepszy, A., Stougaard, J., and, Andersen, S.U., (2011) Genome-wide LORE1 retrotransposon mutagenesis and high-throughput insertion detection in Lotus japonicus. Plant J. doi:.
40. Uren, A.G., Mikkers, H., Kool, J., et al. (2009) A high-throughput splinkerette-PCR method for the isolation and sequencing of retroviral insertion sites. Nat. Protoc. 4, 789-798.
41. Vandenbussche, M., Janssen, A., Zethof, J., et al. (2008) Generation of a 3D indexed Petunia insertion database for reverse genetics. Plant J. 54, 1105-1114. (Pubitemid 351794026)
42. Vollbrecht, E., Duvick, J., Schares, J.P., et al. (2010) Genome-wide distribution of transposed Dissociation elements in maize. Plant Cell, 22, 1667-1685.
43. Walbot, V., (2000) Saturation mutagenesis using maize transposons. Curr. Opin. Plant Biol. 3, 103-107. (Pubitemid 30157012)
44. Williams-Carrier, R., Stiffler, N., Belcher, S., Kroeger, T., Stern, D.B., Monde, R.A., Coalter, R., and, Barkan, A., (2010) Use of Illumina sequencing to identify transposon insertions underlying mutant phenotypes in high-copy Mutator lines of maize. Plant J. 63, 167-177.
45. Wu, X., Li, Y., Crise, B., Burgess, S.M., and, Munroe, D.J., (2005) Weak palindromic consensus sequences are a common feature found at the integration target sites of many retroviruses. J. Virol. 79, 5211-5214. (Pubitemid 40464269)
46. Yano, K., Shibata, S., Chen, W.L., et al. (2009) CERBERUS, a novel U-box protein containing WD-40 repeats, is required for formation of the infection thread and nodule development in the legume-Rhizobium symbiosis. Plant J. 60, 168-180.
47. Yokota, K., Fukai, E., Madsen, L.H., et al. (2009) Rearrangement of actin cytoskeleton mediates invasion of Lotus japonicus roots by Mesorhizobium loti. Plant Cell, 21, 267-284.