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Pangenomes as a framework for adaptive radiation, speciation, and adaptation.

Nicolò Tellini1,2, Ole K Tørresen2, David Edwards3

  • 1CNRS, INSERM, IRCAN, Côte d'Azur University, Nice, France.

American Journal of Botany
|December 5, 2025
PubMed
Summary

Pangenomes reveal core and accessory genomic regions, offering deeper insights into evolutionary diversification. Analyzing these regions enhances our understanding of adaptation, speciation, and hybridization processes.

Keywords:
accessory genomeadaptive radiationgenome adaptationpangenomeplant evolutionspeciationstructural variation

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Area of Science:

  • Evolutionary Biology
  • Genomics
  • Bioinformatics

Background:

  • Understanding the genomic basis of biological diversification is a key challenge in evolutionary biology.
  • Traditional genomic studies often rely on single reference genomes, which can bias analyses by overlooking genetic variation.
  • Pangenomes, representing multiple individuals within a lineage, allow differentiation between core (shared) and accessory (variable) genomic regions.

Purpose of the Study:

  • To propose that analyzing genes within both core and accessory genomic regions can deepen the understanding of diversification.
  • To highlight the limitations of single reference genomes in capturing the full genetic diversity of a lineage.
  • To suggest pangenome and accessory region analysis as a method for gaining deeper insights into evolutionary processes.

Main Methods:

  • Development and application of pangenome construction techniques.
  • Comparative genomic analysis to identify core and accessory regions.
  • Gene association studies linking genomic regions to diversification processes.

Main Results:

  • Pangenome analysis effectively distinguishes core from accessory genomic regions.
  • Accessory regions harbor genetic variants crucial for lineage-specific adaptations.
  • Identifying genes in both core and accessory regions provides a more comprehensive view of diversification.

Conclusions:

  • Pangenome and accessory region analysis are essential for a complete understanding of evolutionary diversification.
  • This approach overcomes the limitations of single reference genomes.
  • Future research should leverage pangenomes to explore adaptation, speciation, and hybridization in greater detail.