PlantLAI

PlantLAI computes the LTR Assembly Index (LAI) to quantify plant and algal genome assembly quality by measuring long terminal repeat retrotransposon (LTR-RT) assembly completeness.

Key Features:

• LAI metric: Computes the LTR Assembly Index (LAI) as a quantitative measure where higher LAI values correlate with superior genome assembly.
• Large-scale assessment: Evaluates 1,664 plant and algal genomes encompassing over 55 million pseudomolecules/scaffolds totaling approximately 988 gigabase-pairs using an LAI workflow.
• LTR-RT discovery: Identifies 46,583,551 LTR retrotransposons across superfamilies, including 2,263,188 Copia, 2,933,052 Gypsy, and 1,387,311 unknown-superfamily elements.
• Quality classification: Classifies genomes into draft, reference, and gold categories based on LAI values (476 diploid genomes as draft, 472 genomes as reference, 135 genomes as gold).
• Data repository: Provides a repository of LAI assessments and associated genome assembly information to address gaps in existing assembly reports.

Scientific Applications:

• Comparative genomics: Enables comparative assessment of assembly completeness across plant and algal genomes using LAI values.
• Evolutionary biology: Supports analyses of genome structure and transposable element dynamics via comprehensive LTR-RT catalogs.
• Functional genomics: Informs selection of assemblies suitable for downstream gene annotation and functional analyses based on assembly quality.

Methodology:

Uses an LAI workflow that identifies LTR-RTs across Copia, Gypsy, and unknown superfamilies and classifies genomes into quality categories based on computed LAI values.