PRBB Computational Genomics Seminars Rosa Fernández

19/03/202612:00R_473.10_AULAPRBB Computational Genomics SeminarsRosa FernándezMetazoa Phylogenomics and Genome Evolution Lab, IBE (CSIC-UPF)Breaking bad: phylogeny-aware investigation of macrosynteny amidst extensive genomic rearrangementsAbstract:Reconstructing ancestral chromosome architecture is fundamental for understanding genome evolution, but current methods often fail in lineages with extensive rearrangements, whole-genome duplications, or rapid genome evolution. We present LINGUINE, a phylogeny-aware pipeline for robust inference of ancestral linkage groups. By using orthogroups instead of single-copy genes, modeling syntenic blocks with a Hidden Markov framework, and explicitly resolving paralogy generated by genome duplications, LINGUINE improves marker density and avoids artifacts common in existing approaches. The method reconstructs ancestral states iteratively along the species tree, integrating information from all descendant lineages to remain robust to missing data and atypical genome evolution. This paralogy-aware framework also enables the detection of candidate whole-genome duplication events in rapidly evolving clades, where current methods often fail.