CAULIFINDER

CAULIFINDER detects, reconstructs, annotates, groups, and classifies endogenous viral elements (EVEs) derived from the family Caulimoviridae in plant genomes to support evolutionary, taxonomic, and genomic analyses.

Key Features:

• Automated detection: Identifies caulimovirid EVEs within plant genome assemblies.
• Reconstruction and annotation: Reconstructs partial or complete caulimovirid sequences and provides annotations of their genomic features.
• Grouping by genomic features: Groups reconstructed EVEs based on their genomic characteristics to facilitate downstream analysis.
• Classification into genera: Assigns identified elements to officially recognized or tentative genera within the Caulimoviridae family.
• High-sensitivity annotation: Targets detection and annotation of caulimovirid EVEs that often occur at high copy numbers in tracheophyte plant genomes.
• Benchmarking: Validated using the Vitis vinifera reference genome with previously characterized caulimovirid EVEs.

Scientific Applications:

• Evolutionary analysis: Enables reconstruction of virus-host evolutionary histories from integrated caulimovirid EVEs.
• Virus taxonomy and classification: Supports assignment and refinement of Caulimoviridae genera for endogenous elements.
• Plant genome annotation: Supplies detailed annotations of caulimovirid EVEs for plant genome studies.
• Comparative genomics: Facilitates comparison of caulimovirid EVE content across tracheophyte plant genomes.

Methodology:

Implements two complementary workflows—one for reconstruction, annotation, and grouping of caulimovirid EVEs based on genomic features, and a second for classification of identified elements into officially recognized or tentative Caulimoviridae genera; benchmarked on the Vitis vinifera reference genome.