A collection of sequenced and mapped Ds transposon insertion sites in Arabidopsis thaliana.
Insertional mutagenesis is a powerful tool for generating knockout mutations that facilitate associating biological functions with as yet uncharacterized open reading frames (ORFs) identified by genomic sequencing or represented in EST databases. We have generated a collection of Dissociation (Ds) transposon lines with insertions on all 5 Arabidopsis chromosomes. Here we report the insertion sites in 260 independent single-transposon lines, derived from four different Ds donor sites. We amplified and determined the genomic sequence flanking each transposon, then mapped its insertion site by identity of the flanking sequences to the corresponding sequence in the Arabidopsis genome database. This constitutes the largest collection of sequence-mapped Ds insertion sites unbiased by selection against the donor site. Insertion site clusters have been identified around three of the four donor sites on chromosomes 1 and 5, as well as near the nucleolus organizers on chromosomes 2 and 4. The distribution of insertions between ORFs and intergenic sequences is roughly proportional to the ratio of genic to intergenic sequence. Within ORFs, insertions cluster near the translational start codon, although we have not detected insertion site selectivity at the nucleotide sequence level. A searchable database of insertion site sequences for the 260 transposon insertion sites is available at http://sgio2.biotec.psu.edu/sr. This and other collections of Arabidopsis lines with sequence-identified transposon insertion sites are a valuable genetic resource for functional genomics studies because the transposon location is precisely known, the transposon can be remobilized to generate revertants, and the Ds insertion can be used to initiate further local mutagenesis.
Raina
Surabhi
S
Life Sciences Consortium and Biotechnology Institute, Pennsylvania State University, University Park 16802, USA.
Mahalingam
Ramamurthy
R
Chen
Fuqiang
F
Fedoroff
Nina
N
D017360:Arabidopsis / Q000235:genetics*; D001665:Binding Sites / Q000235:genetics; D002874:Chromosome Mapping; D004251:DNA Transposable Elements / Q000235:genetics*; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D018745:Genome, Plant; D016254:Mutagenesis, Insertional; D016366:Open Reading Frames / Q000235:genetics; D030821:Plants, Genetically Modified; D017422:Sequence Analysis, DNA
D004251:DNA Transposable Elements; D018744:DNA, Plant