PlantRep

PlantRep provides a curated resource of 396,041,410 repeat sequences (206.04 gigabytes) from 459 plant genomes to enable comparative and evolutionary analyses of plant repetitive DNA.

Key Features:

• Extensive dataset: Contains 396,041,410 repeat sequences totaling 206.04 gigabytes derived from 459 diverse plant genomes.
• Phylogenetic classification: Repeats are systematically categorized into 15 clades: algae, bryophytes, lycophytes, ferns, gymnosperms, early angiosperms (ANA), magnolids, monocots, base eudicots, super rosids, fabids, malvids, super asterids, lamiids, and campanulids.
• Uniform annotation pipeline: Employs a consistent pipeline for re-annotation of repeat sequences to ensure comparability of structural and evolutionary characteristics across genomes.
• Comparative genomics resource: Provides annotations and classifications that facilitate cross-species analyses of repetitive element evolution and genome architecture.

Scientific Applications:

• Genome evolution studies: Enables analysis of evolutionary dynamics and the impact of repetitive elements on plant genome evolution and adaptation.
• Functional genomics: Supports investigation of the contribution of repeat sequences to gene structure and function.
• Comparative genomics: Facilitates systematic comparisons of repetitive element content and distribution across broad taxonomic groups.

Methodology:

A uniform annotation pipeline was applied to re-annotate repeat sequences across the 459 plant genomes.