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Distribution of 1000 sequenced T‐DNA tags in the Arabidopsis genome
Author(s) -
Szabados László,
Kovács Izabella,
Oberschall Attila,
Ábrahám Edit,
Kerekes Irén,
Zsigmond Laura,
Nagy Réka,
Alvarado Martha,
Krasovskaja Inga,
Gál Mónika,
Berente Anikó,
Rédei George P.,
Haim Amit Ben,
Koncz Csaba
Publication year - 2002
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1046/j.1365-313x.2002.01417.x
Subject(s) - biology , genetics , intergenic region , genome , gene , gene density , arabidopsis , dna , genome evolution , mutant
Summary Induction of knockout mutations by T‐DNA insertion mutagenesis is widely used in studies of plant gene functions. To assess the efficiency of this genetic approach, we have sequenced PCR amplified junctions of 1000 T‐DNA insertions and analysed their distribution in the Arabidopsis genome. Map positions of 973 tags could be determined unequivocally, indicating that the majority of T‐DNA insertions landed in chromosomal domains of high gene density. Only 4.7% of insertions were found in interspersed, centromeric, telomeric and rDNA repeats, whereas 0.6% of sequenced tags identified chromosomally integrated segments of organellar DNAs. 35.4% of T‐DNAs were localized in intervals flanked by ATG and stop codons of predicted genes, showing a distribution of 62.2% in exons and 37.8% in introns. The frequency of T‐DNA tags in coding and intergenic regions showed a good correlation with the predicted size distribution of these sequences in the genome. However, the frequency of T‐DNA insertions in 3′‐ and 5′‐regulatory regions of genes, corresponding to 300 bp intervals 3′ downstream of stop and 5′ upstream of ATG codons, was 1.7–2.3‐fold higher than in any similar interval elsewhere in the genome. The additive frequency of insertions in 5′‐regulatory regions and coding domains provided an estimate for the mutation rate, suggesting that 47.8% of mapped T‐DNA tags induced knockout mutations in Arabidopsis .