TDNAscan

TDNAscan identifies Transfer (T)-DNA insertions from next-generation sequencing (NGS) data and determines insertion orientation, zygosity, and genomic annotation to enable causal-gene identification in forward genetic screens.

Key Features:

• NGS-based detection: Uses next-generation sequencing (NGS) data to detect T-DNA insertions.
• Complete and truncated insertion detection: Detects both complete and truncated Transfer (T)-DNA insertions.
• Orientation determination: Determines the orientation of T-DNA insertions within the genome.
• Zygosity calling: Determines the zygosity (homozygous or heterozygous state) of T-DNA insertions.
• Genomic annotation: Provides detailed annotation of T-DNA insertion sites in their genomic context.
• Application to forward genetics: Designed for analysis of mutants derived from forward genetic screens.

Scientific Applications:

• Mapping insertion sites: Mapping T-DNA insertion sites in genomes from forward genetic screens.
• Causal-gene identification: Identification of genes disrupted by complete or truncated T-DNA insertions for mutant phenotype analysis.
• Demonstrated case study: Applied to Arabidopsis thaliana hlb3 mutant analysis, identifying the recessive mutation as a class II FORMIN gene.

Methodology:

Leverages next-generation sequencing (NGS) data to detect complete and truncated T-DNA insertions, determine insertion orientation and zygosity, and provide genomic annotation.