A whole-genome analysis of a transgenic rice seed-based edible vaccine against cedar pollen allergy

DNA Research

Volumn 20, Issue 6, 2013, Pages 623-631

  Kawakatsu, Taiji ^a   Kawahara, Yoshihiro ^a   Itoh, Takeshi ^a   Takaiwa, Fumio ^a  

^a NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

Author keywords

cedar pollen allergy; GM crop; transcriptome; transgenic rice; whole genome sequence

Indexed keywords

EDIBLE VACCINE; TRANSCRIPTOME;

ARTICLE; CELL CULTURE; CROP; CULTIVAR; DNA MODIFICATION; DNA TRANSFER; GENOME; GENOME ANALYSIS; JAPANESE CEDAR; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; POLLEN ALLERGY; RHIZOBIUM; SOMACLONAL VARIATION;

CEDAR POLLEN ALLERGY; GM CROP; TRANSCRIPTOME; TRANSGENIC RICE; WHOLE-GENOME SEQUENCE;

AGROBACTERIUM; ANTIGENS, PLANT; CEDRUS; GENOME, PLANT; MUTATION RATE; ORYZA SATIVA; PLANT PROTEINS; PLANTS, GENETICALLY MODIFIED; POLYMORPHISM, GENETIC; RHINITIS, ALLERGIC, SEASONAL; SEEDS; SEQUENCE ANALYSIS, DNA; TRANSCRIPTOME; VACCINES, EDIBLE;

EID: 84890445199     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dst036     Document Type: Article

References (33)

1. Van Montagu, M. 2011, It is a long way to GMagriculture, Ann. Rev. Plant Biol., 62, 1-23.
2. Clive J. 2011, Global Status of Commercialized Biotech/ GM Crops: 2011, ISAAA Brief, ISAAA, Ithaca, NY.
3. Wakasa, Y., Takagi, H., Hirose, S., et al. 2013, Oralimmunotherapy with transgenic rice seed containing destructed Japanese cedar pollen allergens, Cry j 1 and Cry j 2, against Japanese cedar pollinosis. Plant Biotechnol. J., 11, 66-76.
4. Labra, M., Savini, C., Bracale, M., et al. 2001, Genomic changes in transgenic rice (Oryza sativa L) plants produced by infecting calli with Agrobacterium tumefaciens. Plant Cell Rep., 20, 325-30.
5. Labra, M., Vannini, C., Grassi, F., et al. 2004, Genomic stability in Arabidopsis thaliana transgenic plants obtained by floral dip, Theor. Appl. Genet., 109, 1512-8.
6. Gelvin, S.B. 2010. Plant proteins involved in Agrobacterium-mediated genetic transformation, Ann. Rev. Phytopathol., 48, 45-68.
7. Ming, R., Hou, S., Feng, Y., et al. 2008, The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature, 452, 991-6.
8. Batista, R., Saibo, N., Lourenco, T. and Oliveira, M.M. 2008, Microarray analyses reveal that plant mutagenesis may induce more transcriptomic changes than transgene insertion. Proc. Natl Acad. Sci. USA., 105, 3640-45.
9. Tada, Y., Utsumi, S.andTakaiwa, F.2003,Foreigngeneproducts can be enhanced by introduction into low storage protein mutants. Plant Biotechnol. J., 1, 411-22.
10. Iida, S., Kusaba, M. and Nishio, T. 1997, Mutants lacking glutelin subunits in rice: Mapping and combination of mutated glutelin genes, Theor. Appl. Genet., 94, 177-83.
11. Martin, M. 2011, Cutadapt removes adapter sequences from high-Throughput sequencing reads, EMBnet J., 17, 10-2.
12. Takaiwa, F., Kikuchi, S. and Oono, K. 1987, A rice glutelin gene family - a major type of glutelin messenger-RNAs can be divided into 2 classes. Mol. Genet. Genomics., 208, 15-22.
13. Sakai, H., Lee, S.S., Tanaka, T., et al. 2013, Rice Annotation Project Database (RAP-DB): An integrative and interactive database for rice genomics. Plant Cell Physiol., 54, e6.
14. Anders, S. and Huber, W. 2010, Differential expression analysis for sequence count data,Genome Biol., 11, R106.
15. Yamamoto, T.,Nagasaki, H., Yonemaru, J., et al. 2010, Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms. BMC Genomics, 11, 267.
16. Ulker, B., Li, Y.,Rosso, M.G., Logemann,E., Somssich, I.E.and Weisshaar, B. 2008, T-DNA-mediated transfer of Agrobacterium tumefaciens chromosomal DNA into plants, Nature Biotechnol., 26, 1015-7.
17. Kim, S.R. and An, G. 2012, Bacterial transposons are cotransferred with T-DNA to rice chromosomes during Agrobacterium-mediated transformation. Mol. Cells, 33, 583-9.
18. Wood,D.W., Setubal, J.C., Kaul, R., et al. 2001, The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science, 294, 2317-23.
19. Li, H. and Durbin, R. 2009, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, 25, 1754-60.
20. Sabot, F., Picault, N., El-Baidouri, M., et al. 2011, Transpositional landscape of the rice genome revealed by paired-end mapping of high-Throughput re-sequencing data. Plant J Cell Mol. Biol., 66, 241-6.
21. Miyao, A., Nakagome, M., Ohnuma, T., et al. 2012, Molecular spectrum of somaclonal variation in regenerated rice revealed by whole-genome sequencing. Plant Cell Physiol., 53, 256-64.
22. Jiang, C., Mithani, A., Gan, X., et al. 2011, Regenerant Arabidopsis lineages display a distinct genome-wide spectrum of mutations conferring variant phenotypes. Curr. Biol., 21, 1385-90.
23. Hurwitz, B.L., Kudrna, D., Yu, Y., et al. 2010, Rice structural variation: A comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza. Plant J Cell Mol Biol, 63, 990-1003.
24. Ossowski, S., Schneeberger, K., Lucas-Lledo, J.I., et al. The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science, 327, 92-4.
25. Greene, E.A., Codomo, C.A., Taylor, N.E., et al. 2003, Spectrum of chemically induced mutations from a large-scale reverse-genetic screen in Arabidopsis, Genetics, 164, 731-40.
26. Morita, R., Kusaba, M., Iida, S., Yamaguchi, H., Nishio, T. and Nishimura, M. 2009, Molecular characterization of mutations induced by gamma irradiation in rice Genes Genet. Syst., 84, 361-70.
27. Arai-Kichise, Y., Shiwa, Y., Nagasaki, H., et al. 2011, Discovery of genome-wide DNA polymorphisms in a landrace cultivar of Japonica rice by whole-genome sequencing. Plant Cell Physiol., 52, 274-82.
28. Hayashi, S., Wakasa, Y., Takahashi, H., Kawakatsu, T. and Takaiwa, F. 2012, Signal transduction by IRE1-mediated splicing of bZIP50 and other stress sensors in the endoplasmic reticulum stress response of rice. Plant J., 69, 946-56.
29. Oono, Y., Wakasa, Y., Hirose, S., Yang, L., Sakuta, C. and Takaiwa, F. 2010, Analysis of ER stress in developing rice endosperm accumulating beta-Amyloid peptide. Plant Biotechnol. J., 8, 691-718.
30. Li, T., Liu, B., Spalding, M.H.,Weeks, D.P. and Yang, B. 2012, High-efficiency TALEN-based gene editing produces disease-resistant rice. Nat. Biotechnol., 30, 390-92.
31. Terada, R., Urawa, H., Inagaki, Y., Tsugane, K. and Iida, S. 2002,Efficient genetargeting byhomologousrecombination in rice. Nat. Biotechnol., 20, 1030-34.
32. Ozawa, K.,Wakasa, Y., Ogo, Y.,Matsuo, K., Kawahigashi, H. and Takaiwa, F. 2012, Development of an efficient Agrobacterium-mediated gene targeting system for rice and analysis of rice knockouts lacking granule-bound starch synthase (Waxy) and beta1,2-xylosyltransferase. Plant Cell Physiol., 53, 755-61.
33. Robinson, J.T., Thorvaldsdottir, H., Winckler, W., et al. 2011, Integrative genomics viewer. Nat. Biotechnol., 29, 24-6.