Unraveling evolutionary pathways: allopolyploidization and introgression in polyploid Prunus (Rosaceae)
Si-Yu Xie1,2,3, Xiao-Hua Lin1,2,3, Jun-Ru Wang1
1College of Life Sciences & Herbarium of Northwest A&F University, Northwest A&F University, Yangling, 712100, China.
The Plant Journal : for Cell and Molecular Biology
|July 4, 2025
Summary
Allopolyploidization, not incomplete lineage sorting, drove the evolution of polyploid Prunus. Geological events like Himalayan uplift spurred rapid diversification and hybridization in this economically important genus.
Area of Science:
- Evolutionary Biology
- Genomics
- Plant Science
Background:
- Allopolyploidization, a key driver of evolution, involves hybridization and whole-genome duplication (WGD).
- Polyploid Prunus (Rosaceae) is agriculturally significant, making it a valuable model for studying allopolyploidy.
- Understanding the evolutionary dynamics of polyploidization is crucial for crop improvement and biodiversity conservation.
Purpose of the Study:
- To develop and apply a comprehensive analytical framework for detecting whole-genome duplication (WGD) events in polyploid Prunus.
- To evaluate the relative contributions of allopolyploidization and incomplete lineage sorting (ILS) to lineage diversification in Prunus.
- To investigate the role of geological events in driving the diversification of the Maddenia clade within Prunus.
Main Methods:
- Deep genome skimming (DGS) data was employed for comprehensive genomic analysis.
- A novel tool, DGS-Tree2GD, was developed for accurate detection of WGD events.
- Phylogenomic discordance analyses and methods to assess ILS were utilized.
Main Results:
- Allopolyploidization was identified as the dominant factor in the origin and diversification of polyploid Prunus, overshadowing ILS.
- The uplift of the Himalayas during the Middle to Late Miocene was inferred as a critical factor promoting rapid diversification of the Maddenia clade.
- Extensive hybridization and allopolyploidization, including introgression between specific clades, were facilitated by this geological event.
Conclusions:
- The developed analytical framework is robust and effective for identifying WGD events and understanding allopolyploidization mechanisms.
- Geological history, specifically the Himalayan uplift, significantly influenced the evolutionary trajectory and diversification of polyploid Prunus.
- This study provides critical insights into the genomic and evolutionary processes shaping agriculturally important plant lineages.
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