SCORPiOs

SCORPiOs reconstructs and corrects gene phylogenies in clades affected by whole-genome duplications (WGDs) by integrating local synteny, species-tree constraints, and gene-sequence evolution to resolve paralogy and orthology relationships.

Key Features:

• Synteny-guided correction: Uses conserved duplicated syntenic regions produced by WGDs to inform paralogy and orthology assignments.
• Detection of misplaced or missing duplications: Identifies gene trees where WGD-derived duplication events are absent or incorrectly placed.
• WGD- and species-tree–aware reconstruction: Reconstructs optimized gene trees consistent with known WGD events, the species tree, local synteny context, and gene-sequence evolution.
• Complement to sequence-based methods: Integrates synteny information to complement sequence-based phylogenetic inference and improve tree accuracy.
• Empirical validation on teleosts and Ensembl: Detected inconsistencies in almost one-fourth of teleost gene phylogenies in Ensembl and proposed improved trees for 2,387 of 3,394 families (≈70%).
• Improved congruence with biology: Produces synteny-guided phylogenies that are more congruent with species trees and expected expression conservation patterns than state-of-the-art methods.

Scientific Applications:

• Teleost WGD phylogeny reconstruction: Applied to the 320-million-year-old teleost WGD to resolve gene-family evolutionary histories.
• Comparative genomics in polyploid taxa: Provides more accurate phylogenies for studies of duplicate gene retention and loss in ancient polyploid lineages.
• Timing of rediploidization: Facilitates investigations into the timing of genome rediploidization after WGD events.
• Functional consequences of WGDs: Enables study of functional divergence and expression conservation among WGD paralogs.

Methodology:

SCORPiOs identifies gene trees with missing or incorrectly placed duplications, leverages duplicated syntenic regions produced by WGDs, and reconstructs optimized gene trees consistent with known WGD events, the species tree, local synteny contexts, and gene-sequence evolution, thereby complementing sequence-based phylogenetic methods.