TEF

TEF detects active transposable elements and their insertion sites in next-generation sequencing (NGS) data by focusing on target site duplications (TSDs) and analyzing junction sequences to discover novel transposition events, including insertions into loci containing older TEs.

Key Features:

• Detection without known sequences: TEF enables detection of TE transpositions without prior knowledge of the TE sequence, addressing limitations of tools such as Transposon Insertion Finder (TIF).
• Focus on Target Site Duplications (TSDs): By concentrating on TSDs, TEF identifies both TE ends and their insertion sites, including insertions into regions containing older TEs.
• Dual algorithmic approach: TEF implements two complementary algorithms: grouping sequences by shared TSDs with direct k-mer comparisons of NGS reads (avoiding similarity searches), and junction mapping of TE end sequence candidates to determine insertion sites.
• Genotype verification: TEF verifies genotypes of detected transpositions by analyzing junctions between TE ends and non-insertion sequences within NGS reads.
• Library independence: TEF operates independently of predefined transposable element libraries, enabling discovery of insertions from unknown TEs.
• Validation through PCR: Detected insertions have been validated by polymerase chain reaction (PCR) confirmation in rice test cases.

Scientific Applications:

• Genome-wide discovery of novel TE insertions: TEF enables identification of new transposition events from NGS data across genomes, as demonstrated in rice.
• Studies of genome dynamics and evolution: TEF supports analyses of TE-mediated genetic variation and genome evolution in organisms including rice, Arabidopsis, and Drosophila.
• Plant genetics and evolutionary biology: TEF facilitates investigations in plant genetics and evolutionary biology by revealing novel TE insertions in species such as rice and Arabidopsis.

Methodology:

Grouping sequences by shared TSDs with direct k-mer comparisons of NGS reads (no similarity searches), junction mapping of TE end sequence candidates to determine insertion sites, and analysis of read junctions between TE ends and non-insertion sequences for genotype verification.