REXdb

REXdb catalogs LTR-retrotransposon protein domain sequences to support classification and comparative analysis of Ty1/copia and Ty3/gypsy elements in plants.

Key Features:

• Extensive Data Collection: Contains polyprotein domain sequences from 5,410 Ty1/copia and 8,453 Ty3/gypsy elements sampled across 80 species representing major groups of Viridiplantae.
• Phylogenetic Classification: Uses phylogenetic analyses of the conserved reverse transcriptase (RT), ribonuclease H (RH), and integrase (INT) domains to assign Ty1/copia and Ty3/gypsy elements to 16 and 14 lineages, respectively.
• Comprehensive Feature Characterization: Records additional polyprotein domains, extra open reading frames (ORFs), and primer binding sites and correlates their occurrence and types with phylogenetic lineages.
• Unified Annotation Framework: Integrates sequence and structural data to provide a consistent framework for annotating LTR-retrotransposons across diverse plant species.

Scientific Applications:

• Evolutionary analysis: Enables studies of the evolutionary dynamics and lineage diversification of LTR-retrotransposons in plant genomes.
• Phylogenetic inference: Supports reconstruction of relationships among retrotransposon families based on conserved polyprotein domains (RT, RH, INT).
• Genome annotation: Provides reference domain and structural information to inform annotation and classification of LTR-retrotransposons in genomic datasets.

Methodology:

Assembled a large dataset of polyprotein domain sequences from Ty1/copia and Ty3/gypsy elements, conducted phylogenetic analyses on RT, RH, and INT domains to define lineages, and characterized structural features which were correlated with the resulting phylogenies.