Graph-based pangenome analysis uncovers structural and functional impacts of allopolyploidization events
4 affiliations
- 1CIC bioGUNE, Bizkaia Technological Park, Building 800, 48160 Derio, Spain.
- 2Université de Strasbourg, CNRS, Inserm, IGBMC UMR 7104-UMR-S 1258, 67400 Illkirch, France.
- 3Institut Universitaire de France (IUF), 75231 Paris, France.
- 4Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
Abstract
The emergence of graph pangenomes has advanced the study of structural variants (SVs) across diverse species, yet the impact of complex ploidy on SV landscapes remains poorly explored. Brettanomyces bruxellensis, a yeast shaped by multiple allopolyploidization events, offers a compelling model due to its well-characterized genomic and phenotypic diversity. Here, we integrated subgenome-resolved assemblies with population-scale genomic and transcriptomic datasets to characterize SV distribution and functional impact at the species level. Leveraging a reference graph pangenome, we detected 5972 unique SVs across 1060 isolates. Allopolyploid genomes harbored significantly more SVs (320 on average) than diploids (116), reflecting hybridization's extensive impact on genome architecture. Functional association analysis revealed that 27.5% of SVs locally influence gene expression. Furthermore, a subset of SVs originating from ancestral divergence between subgenomes (hybridization-associated SVs) formed hotspots of structural diversity and disproportionately affect gene expression, with larger effect sizes than other SVs. These findings underscore allopolyploidization as a driver of structural and functional genomic diversification, highlighting the value of graph-based approaches in dissecting complex genome evolution.
Related
- Thermococcales pangenome uncovers new genera and modular evolution
- A Plasmodium falciparum Pangenome Resource to Drive Structural Variant Discovery and to assist Malaria Control
- Somatic structural variation discovery on cancer pangenome graphs
- Artificial hibernation uncovers distinct interaction dynamics in functional and pathological state change
- Graph-based pangenome of Venturia inaequalis, the apple scab fungus, reveals structural variants associated with population differentiation
BibTeX
@article{loegler2026graphbased,
title = {{Graph-based pangenome analysis uncovers structural and functional impacts of allopolyploidization events}},
author = {Victor Loegler and Anne Friedrich and Joseph Schacherer},
journal = {Science Advances},
year = {2026},
month = oct,
doi = {10.1126/sciadv.aea5812},
url = {https://www.science.org/doi/abs/10.1126/sciadv.aea5812},
note = {CC BY},
}
RIS
TY - JOUR
TI - Graph-based pangenome analysis uncovers structural and functional impacts of allopolyploidization events
AU - Victor Loegler
AU - Anne Friedrich
AU - Joseph Schacherer
PY - 2026
DA - 2026/10/30
JO - Science Advances
DO - 10.1126/sciadv.aea5812
UR - https://www.science.org/doi/abs/10.1126/sciadv.aea5812
AB - The emergence of graph pangenomes has advanced the study of structural variants (SVs) across diverse species, yet the impact of complex ploidy on SV landscapes remains poorly explored. Brettanomyces bruxellensis, a yeast shaped by multiple allopolyploidization events, offers a compelling model due to its well-characterized genomic and phenotypic diversity. Here, we integrated subgenome-resolved assemblies with population-scale genomic and transcriptomic datasets to characterize SV distribution and functional impact at the species level. Leveraging a reference graph pangenome, we detected 5972 unique SVs across 1060 isolates. Allopolyploid genomes harbored significantly more SVs (320 on average) than diploids (116), reflecting hybridization's extensive impact on genome architecture. Functional association analysis revealed that 27.5% of SVs locally influence gene expression. Furthermore, a subset of SVs originating from ancestral divergence between subgenomes (hybridization-associated SVs) formed hotspots of structural diversity and disproportionately affect gene expression, with larger effect sizes than other SVs. These findings underscore allopolyploidization as a driver of structural and functional genomic diversification, highlighting the value of graph-based approaches in dissecting complex genome evolution.
SN - 2375-2548
ER -