GABI-Kat

GABI-Kat provides a sequence-indexed collection of T-DNA insertion lines and mapped flanking sequence tags (FSTs) to support reverse genetics and functional genomics in Arabidopsis thaliana.

Key Features:

• Extensive database: Approximately 71,000 T-DNA insertion lines cataloged, covering insertions in 62.5% of the 27,206 nuclear protein-coding genes of Arabidopsis thaliana.
• Flanking Sequence Tags (FSTs): A comprehensive collection of FSTs adjacent to T-DNA insertions, newly mapped using an optimized procedure to improve insertion site localization.
• New FST generation: Re-analysis of lines with previously weak FST yields produced approximately 20,000 additional FSTs.
• TAIRv10 integration: All insertion data aligned to the TAIRv10 genome sequence and annotation dataset.
• Allele-specific data: Insertion allele-specific data are reported for 9,545 confirmed lines.
• Data integrity improvements: Identification of FST groups that point to the same insertion site in multiple lines and correction of problematic FST-to-line links using new wet-lab data.

Scientific Applications:

• Reverse genetics: Identification and selection of sequence-indexed T-DNA insertion alleles to disrupt target genes in Arabidopsis thaliana.
• Gene knockout studies: Use of mapped insertion lines and FSTs to generate and confirm loss-of-function alleles.
• Functional genomics: Genome-wide analysis of gene function using large-scale insertional mutagenesis data.
• Gene regulatory network analysis: Investigation of genetic interactions and regulatory relationships using allele-specific insertion data.

Methodology:

Mapping of FSTs using an optimized procedure; re-analysis of lines with weak FST yields to generate new FSTs; alignment and annotation of insertion data against the TAIRv10 genome sequence dataset.