{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T09:38:35Z","timestamp":1791538715692,"version":"4.3.4"},"reference-count":30,"publisher":"Springer Science and Business Media LLC","issue":"3","license":[{"start":{"date-parts":[[2017,2,2]],"date-time":"2017-02-02T00:00:00Z","timestamp":1485993600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"The Netherlands Commission on Genetic Modification (COGEM)"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Plant Cell Rep"],"published-print":{"date-parts":[[2017,3]]},"DOI":"10.1007\/s00299-017-2098-z","type":"journal-article","created":{"date-parts":[[2017,2,2]],"date-time":"2017-02-02T16:18:04Z","timestamp":1486052284000},"page":"493-504","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":42,"title":["Re-sequencing transgenic plants revealed rearrangements at T-DNA inserts, and integration of a short T-DNA fragment, but no increase of small mutations elsewhere"],"prefix":"10.1007","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4495-1951","authenticated-orcid":false,"given":"Henk J.","family":"Schouten","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Henri","family":"vande Geest","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sofia","family":"Papadimitriou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marian","family":"Bemer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan G.","family":"Schaart","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marinus J. M.","family":"Smulders","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabino Sanchez","family":"Perez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elio","family":"Schijlen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2017,2,2]]},"reference":[{"key":"2098_CR1","doi-asserted-by":"crossref","first-page":"796","DOI":"10.1038\/35048692","volume":"408","author":"Arabidopsis Genome Initiative","year":"2000","unstructured":"Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796\u2013815","journal-title":"Nature"},{"key":"2098_CR2","doi-asserted-by":"crossref","first-page":"956","DOI":"10.1038\/ng.911","volume":"43","author":"J Cao","year":"2011","unstructured":"Cao J, Schneeberger K, Ossowski S et al (2011) Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet 43:956\u2013963","journal-title":"Nat Genet"},{"key":"2098_CR3","doi-asserted-by":"crossref","first-page":"990","DOI":"10.1111\/j.1365-313X.2010.04386.x","volume":"64","author":"KA Clark","year":"2010","unstructured":"Clark KA, Krysan PJ (2010) Chromosomal translocations are a common phenomenon in Arabidopsis thaliana T-DNA insert lines. Plant J 64:990\u20131001","journal-title":"Plant J"},{"key":"2098_CR4","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1046\/j.1365-313x.1998.00343.x","volume":"16","author":"SJ Clough","year":"2008","unstructured":"Clough SJ, Bent AF (2008) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 16:735\u2013743","journal-title":"Plant J"},{"key":"2098_CR5","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1007\/s00425-008-0868-0","volume":"229","author":"MJ Curtis","year":"2009","unstructured":"Curtis MJ, Belcram K, Bollmann SR, Tominey CM, HoVman PD, Mercier R, Hays JB (2009) Reciprocal chromosome translocation associated with TDNA-insert mutation in Arabidopsis: genetic and cytological analyses of consequences for gametophyte development and for construction of doubly mutant lines. Planta 229:731\u2013745","journal-title":"Planta"},{"key":"2098_CR6","first-page":"11","volume":"19","author":"J Doyle","year":"1987","unstructured":"Doyle J, Doyle JL (1987) Genomic plant DNA preparation from fresh tissue\u2014CTAB method. Phytochem Bull 19:11\u201315","journal-title":"Phytochem Bull"},{"key":"2098_CR7","first-page":"1","volume":"2150","author":"EFSA","year":"2011","unstructured":"EFSA (2011) Guidance for risk assessment of food and feed from genetically modified plants. EFSA J 2150:1\u201337","journal-title":"EFSA J"},{"issue":"2","key":"2098_CR8","doi-asserted-by":"crossref","first-page":"e0149515","DOI":"10.1371\/journal.pone.0149515","volume":"11","author":"SK Guttikonda","year":"2016","unstructured":"Guttikonda SK, Marri P, Mammadov J, Ye L, Soe K et al (2016) Molecular characterization of transgenic events using Next Generation Sequencing approach. PLoS ONE 11(2):e0149515","journal-title":"PLoS ONE"},{"key":"2098_CR9","doi-asserted-by":"crossref","first-page":"1385","DOI":"10.1016\/j.cub.2011.07.002","volume":"21","author":"C Jiang","year":"2011","unstructured":"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\u20131390","journal-title":"Curr Biol"},{"key":"2098_CR10","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1016\/S1360-1385(02)02251-3","volume":"7","author":"M Karimi","year":"2002","unstructured":"Karimi M, Inz\u00e9 D, Depicker A (2002) GATEWAY\u2122 vectors for Agrobacterium-mediated plant transformation. Trends Plant Sci 7:193\u2013195","journal-title":"Trends Plant Sci"},{"key":"2098_CR11","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1093\/dnares\/dst036","volume":"20","author":"T Kawakatsu","year":"2013","unstructured":"Kawakatsu T, Kawahara Y, Itoh T, Takaiwa F (2013) A whole-genome analysis of a transgenic rice seed-based edible vaccine against cedar pollen allergy. DNA Res 20:623\u2013631","journal-title":"DNA Res"},{"key":"2098_CR12","doi-asserted-by":"crossref","first-page":"149","DOI":"10.3835\/plantgenome2012.10.0026","volume":"5","author":"D Kovalic","year":"2012","unstructured":"Kovalic D, Garnaat C, Guo L et al (2012) The use of next generation sequencing and junction sequence analysis bioinformatics to achieve molecular characterization of crops improved through modern biotechnology. The Plant Genome J 5:149\u2013163","journal-title":"The Plant Genome J"},{"key":"2098_CR13","unstructured":"Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997"},{"key":"2098_CR14","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754\u20131760","journal-title":"Bioinformatics"},{"key":"2098_CR15","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Handsaker B, Wysoker A et al (2009) The Sequence Alignment\/Map format and SAMtools. Bioinformatics 25:2078\u20132079","journal-title":"Bioinformatics"},{"key":"2098_CR16","doi-asserted-by":"crossref","first-page":"991","DOI":"10.1038\/nature06856","volume":"452","author":"R Ming","year":"2008","unstructured":"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\u2013996","journal-title":"Nature"},{"key":"2098_CR17","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1093\/pcp\/pcr172","volume":"53","author":"A Miyao","year":"2012","unstructured":"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\u2013264","journal-title":"Plant Cell Physiol"},{"key":"2098_CR18","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1007\/BF00224228","volume":"80","author":"E M\u00fcller","year":"1990","unstructured":"M\u00fcller E, Brown PTH, Hartke S, L\u00f6rz H (1990) DNA variation in tissue-culture-derived rice plants. Theor Appl Genet 80:673\u2013679","journal-title":"Theor Appl Genet"},{"key":"2098_CR19","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1093\/genetics\/149.2.641","volume":"149","author":"P Nacry","year":"1998","unstructured":"Nacry P, Camilleri C, Courtial B et al (1998) Major chromosomal rearrangements induced by T-DNA transformation in Arabidopsis. Genetics 149:641\u2013650","journal-title":"Genetics"},{"key":"2098_CR20","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1126\/science.1180677","volume":"327","author":"S Ossowski","year":"2010","unstructured":"Ossowski S, Schneeberger K, Lucas-Lledo JI et al (2010) The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327:92\u201394","journal-title":"Science"},{"key":"2098_CR21","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1016\/j.tifs.2015.07.009","volume":"45","author":"K Pauwels","year":"2015","unstructured":"Pauwels K, De Keersmaecker SCJ, de Schrijver D, du Jardin P, Roosens NHC, Herman P (2015) Next-generation sequencing as a tool for the molecular characterisation and risk assessment of genetically modified plants: added value or not? Trends Food Sci Techn 45:319\u2013326","journal-title":"Trends Food Sci Techn"},{"key":"2098_CR22","doi-asserted-by":"crossref","first-page":"i333","DOI":"10.1093\/bioinformatics\/bts378","volume":"28","author":"T Rausch","year":"2012","unstructured":"Rausch T, Zichner T, Schlattl A et al (2012) DELLY: structural variant detection by integrated paired-end and split-read analysis. Bioinformatics 28:i333\u2013i339","journal-title":"Bioinformatics"},{"key":"2098_CR23","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1111\/j.1365-313X.2011.04492.x","volume":"66","author":"F Sabot","year":"2011","unstructured":"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. The Plant J 66:241\u2013246","journal-title":"The Plant J"},{"key":"2098_CR24","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s11248-014-9843-7","volume":"24","author":"J Schnell","year":"2014","unstructured":"Schnell J, Steele M, Bean J, Neuspiel M, Girard C, Dormann N, Pearson C, Savoie A, Bourbonni\u00e8re L, Macdonald P (2014) A comparative analysis of insertal effects in genetically engineered plants: considerations for pre-market assessments. Transgenic Res 24:1\u201317","journal-title":"Transgenic Res"},{"key":"2098_CR25","doi-asserted-by":"crossref","first-page":"1527","DOI":"10.1104\/pp.126.4.1527","volume":"126","author":"FE Tax","year":"2001","unstructured":"Tax FE, Vernon DM (2001) T-DNA-associated duplication\/translocations in Arabidopsis. Implications for mutant analysis and functional genomics. Plant Physiol 126:1527\u20131538","journal-title":"Plant Physiol"},{"key":"2098_CR26","first-page":"1718","volume":"6","author":"D Wahler","year":"2013","unstructured":"Wahler D, Schauser L, Bendiek J, Grohmann L (2013) Next-Generation Sequencing as a tool for detailed molecular characterisation of genomic inserts and flanking regions in genetically modified plants: a pilot study using a rice event unauthorised in the EU. Food Anal. Methods 6:1718\u20131727","journal-title":"Methods"},{"key":"2098_CR27","first-page":"1","volume":"2006","author":"D Weigel","year":"2005","unstructured":"Weigel D, Glazebrook J (2005) Transformation of Agrobacterium using electroporation. CSH protocols 2006:1\u201313","journal-title":"CSH protocols"},{"key":"2098_CR28","doi-asserted-by":"crossref","first-page":"2839","DOI":"10.1038\/srep02839","volume":"3","author":"L Yang","year":"2013","unstructured":"Yang L, Wang C, Holst-Jensen A et al (2013) Characterization of GM events by insert knowledge adapted re-sequencing approaches. Sci Rep 3:2839","journal-title":"Sci Rep"},{"key":"2098_CR29","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1101\/gr.3436305","volume":"15","author":"K Yogeeswaran","year":"2005","unstructured":"Yogeeswaran K, Frary A, York TL, Amenta A (2005) Comparative genome analyses of Arabidopsis spp.: inferring chromosomal rearrangement events in the evolutionary history of A. thaliana. Genome Res 15:505\u2013515","journal-title":"Genome Res"},{"key":"2098_CR30","first-page":"1","volume":"8","author":"GM Zastrow-Hayes","year":"2015","unstructured":"Zastrow-Hayes GM, Lin H, Sigmund AL, Hoffman JL, Alarcon CM, Hayes KR, Richmond TA, Jeddeloh JA, May GD, Beatty MK (2015) Southern-by-sequencing: a robust screening approach for molecular characterization of genetically modified crops. Plant Genome 8:1\u201315","journal-title":"Plant Genome"}],"container-title":["Plant Cell Reports"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s00299-017-2098-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s00299-017-2098-z\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s00299-017-2098-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,7,23]],"date-time":"2022-07-23T08:59:30Z","timestamp":1658566770000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s00299-017-2098-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,2,2]]},"references-count":30,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2017,3]]}},"alternative-id":["2098"],"URL":"https:\/\/doi.org\/10.1007\/s00299-017-2098-z","relation":{},"ISSN":["0721-7714","1432-203X"],"issn-type":[{"value":"0721-7714","type":"print"},{"value":"1432-203X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,2,2]]}}}