TELR

TELR reconstructs and analyzes transposable element (TE) insertions from long-read sequencing data to characterize TE content, allele frequencies, and phylogenetic relationships in polyploid and structurally complex genomes.

Key Features:

• WGA-independent local assembly: Performs local assembly of long-read sequence data without relying on whole-genome assembly to resolve TEs in fragmented or structurally variable genomes, including tetraploid Drosophila S2R+ cell lines.
• TE identification and reconstruction: Identifies TE insertions and reconstructs full TE sequences and their genomic context from long reads.
• Allele frequency estimation: Estimates the allele frequency of TE insertions to quantify heterogeneity of TE content within a sample.
• Phylogenetic analysis of paralogs: Facilitates phylogenetic analysis of paralogous TE copies to infer lineage-specific expansions and relationships among TE copies.

Scientific Applications:

• Genome evolution in cell cultures: Analyze haplotype-specific TE insertions arising from somatic transposition to study mechanisms driving genome evolution in long-term animal cell cultures.
• TE dynamics in polyploid genomes: Investigate proliferation, distribution, and impact of TEs in polyploid and aneuploid genomes where WGA is problematic.
• Modeling somatic evolution: Apply to datasets such as Drosophila S2R+ to model evolutionary processes during extended somatic cell culture.

Methodology:

Uses long-read sequencing data to identify TE insertions, performs local assemblies of TE sequences independent of whole-genome assembly, estimates TE allele frequencies, and conducts phylogenetic analyses of paralogous TE copies.