Time- and Cost-Efficient Identification of T-DNA Insertion Sites through Targeted Genomic Sequencing

PLoS ONE

Volumn 8, Issue 8, 2013, Pages

  Lepage, Étienne ^a   Zampini, Éric ^a   Boyle, Brian ^b   Brisson, Normand ^a  

^a UNIVERSITÉ DE MONTRÉAL   (Canada)

^b UNIVERSITÉ LAVAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GYRASE INHIBITOR; TRANSFER DEOXYRIBONUCLEIC ACID; UNCLASSIFIED DRUG;

ARABIDOPSIS THALIANA; ARTICLE; ENZYME INHIBITION; FINANCIAL MANAGEMENT; GENE IDENTIFICATION; GENE INSERTION; GENE SEQUENCE; GENETIC SCREENING; GENETIC TRANSFORMATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENOME; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; TIME;

ARABIDOPSIS; DNA, BACTERIAL; GENE ORDER; GENOME, PLANT; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MUTAGENESIS, INSERTIONAL; MUTATION; PLANTS, GENETICALLY MODIFIED; TOPOISOMERASE II INHIBITORS;

EID: 84881497686     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0070912     Document Type: Article

References (20)

1. Alonso JM, Ecker JR, (2006) Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis. Nat Rev Genet 7: 524-536.
2. Alonso JM, Stepanova AN, Leisse TJ, Kim CJ, Chen H, et al. (2003) Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301: 653-657.
3. Robinson SJ, Tang LH, Mooney BA, McKay SJ, Clarke WE, et al. (2009) An archived activation tagged population of Arabidopsis thaliana to facilitate forward genetics approaches. BMC Plant Biol 9: 101.
4. Sessions A, Burke E, Presting G, Aux G, McElver J, et al. (2002) A high-throughput Arabidopsis reverse genetics system. Plant Cell 14: 2985-2994.
5. Ostergaard L, Yanofsky MF, (2004) Establishing gene function by mutagenesis in Arabidopsis thaliana. Plant J 39: 682-696.
6. Liu YG, Mitsukawa N, Oosumi T, Whittier RF, (1995) Efficient isolation and mapping of Arabidopsis thaliana T-DNA insert junctions by thermal asymmetric interlaced PCR. Plant J 8: 457-463.
7. Ochman H, Gerber AS, Hartl DL, (1988) Genetic applications of an inverse polymerase chain reaction. Genetics 120: 621-623.
8. Ji J, Braam J, (2010) Restriction site extension PCR: a novel method for high-throughput characterization of tagged DNA fragments and genome walking. PLoS One 5: e10577.
9. Williams-Carrier R, Stiffler N, Belcher S, Kroeger T, Stern DB, et al. (2010) Use of Illumina sequencing to identify transposon insertions underlying mutant phenotypes in high-copy Mutator lines of maize. Plant J 63: 167-177.
10. Urbanski DF, Malolepszy A, Stougaard J, Andersen SU, (2012) Genome-wide LORE1 retrotransposon mutagenesis and high-throughput insertion detection in Lotus japonicus. Plant J 69: 731-741.
11. Polko JK, Temanni MR, van Zanten M, van Workum W, Iburg S, et al. (2012) Illumina sequencing technology as a method of identifying T-DNA insertion loci in activation-tagged Arabidopsis thaliana plants. Mol Plant 5: 948-950.
12. Wall MK, Mitchenall LA, Maxwell A, (2004) Arabidopsis thaliana DNA gyrase is targeted to chloroplasts and mitochondria. Proc Natl Acad Sci U S A 101: 7821-7826.
13. Rowan BA, Oldenburg DJ, Bendich AJ, (2010) RecA maintains the integrity of chloroplast DNA molecules in Arabidopsis. J Exp Bot 61: 2575-2588.
14. Cappadocia L, Marechal A, Parent JS, Lepage E, Sygusch J, et al. (2010) Crystal structures of DNA-Whirly complexes and their role in Arabidopsis organelle genome repair. Plant Cell 22: 1849-1867.
15. Weigel D, Glazebrook J (2002) Arabidopsis: A Laboratory Manual. Cold Spring Harbor Lab Press, Cold Spring Harbor, NY.
16. Raherison E, Rigault P, Caron S, Poulin PL, Boyle B, et al. (2012) Transcriptome profiling in conifers and the PiceaGenExpress database show patterns of diversification within gene families and interspecific conservation in vascular gene expression. BMC Genomics 13: 434.
17. Parent JS, Lepage E, Brisson N, (2011) Divergent roles for the two PolI-like organelle DNA polymerases of Arabidopsis. Plant Physiol 156: 254-262.
18. Collin F, Karkare S, Maxwell A, (2011) Exploiting bacterial DNA gyrase as a drug target: current state and perspectives. Appl Microbiol Biotechnol 92: 479-497.
19. Barillot E, Lacroix B, Cohen D, (1991) Theoretical analysis of library screening using a N-dimensional pooling strategy. Nucleic Acids Res 19: 6241-6247.
20. Nacry P, Camilleri C, Courtial B, Caboche M, Bouchez D, (1998) Major chromosomal rearrangements induced by T-DNA transformation in Arabidopsis. Genetics 149: 641-650.