AGORA

AGORA reconstructs ancestral gene content and chromosomal gene order to enable high-resolution studies of genome and karyotype evolution across vertebrates, plants, fungi, metazoans, and protists.

Key Features:

• Ancestral Genome Reconstruction: Reconstructs both gene content and chromosomal gene order, producing near-complete reconstructions for 183 of 624 studied ancestral genomes.
• High-Resolution Evolutionary Analysis: Compares successive ancestral genomes along phylogenetic trees to estimate intra- and interchromosomal rearrangements with high resolution across major vertebrate clades.
• Integration with Genomicus: Integrated with the Genomicus database to support gene order comparison studies using curated genomic data.
• Validation Against References: Validates reconstructed genomes by alignment to descendant extant genomes and by comparison with reference cytogenetic and in silico reconstructions.

Scientific Applications:

• Molecular Evolution Studies: Enables tracing of small-scale sequence modifications through evolutionary timelines across diverse clades.
• Genome and Karyotype Evolution: Provides comprehensive chronological views of genome and karyotype evolution across multiple clades without relying on a single extant species as reference.
• Rearrangement Dynamics: Facilitates estimation and comparison of intra- and interchromosomal rearrangement patterns across lineages.

Methodology:

AGORA employs advanced algorithms that analyze phylogenetic relationships and leverage comparative genomics to reconstruct ancestral gene content and chromosomal organization, compare successive ancestral genomes along phylogenies to infer rearrangements, and validate reconstructions by alignment to descendant genomes and comparison with cytogenetic and in silico references.