PlantLTRdb

PlantLTRdb catalogs and annotates intact long terminal repeat retrotransposons (LTR-RTs) across plant genomes to support analysis of their classification, distribution, and genomic impacts.

Key Features:

• Extensive Data Coverage: Encompasses 150.18 Gbp across 3,079,469 pseudomolecules/scaffolds.
• Identification and Characterization: Identifies and annotates 520,194 intact LTR-RTs, including 29,462 autonomous and 490,732 nonautonomous elements, classified into Gypsy, Copia, BARE-2, TR-GAG, and unknown categories using homology-based and de novo structure-based methods.
• Functional Insights: Reports 36,236 LTR-RT–gene chimeras, 11,619 LTR-RTs within pseudo-genes, 50,026 genes located within 1 kbp of LTR-RTs, and 250,587 genes located between 1 and 10 kbp from LTR-RTs.
• Sequence similarity analyses: Supports BLAST analyses of plant LTR-RT sequences.

Scientific Applications:

• Structural variation analysis: Enables study of structural variations mediated by LTR-RT insertions in plant genomes.
• Genome organization studies: Facilitates analysis of LTR-RT contributions to genome architecture and distribution across pseudomolecules/scaffolds.
• Functional genomics: Supports investigation of LTR-RT impacts on genes, including formation of LTR-RT–gene chimeras and effects related to proximity.
• Marker development for molecular plant breeding: Aids development of LTR-RT target markers for molecular plant breeding and crop improvement strategies.

Methodology:

Integrates homology-based approaches with de novo structure-based analysis to identify and annotate autonomous and nonautonomous LTR-RTs and to perform age estimation of LTR-RT insertions.