Many of the world’s most important crops have unusually complex genomes, created by repeated replication and hybridization of their entire genomes. These so-called polyploid genomes contain multiple sets of chromosomes inherited from different ancestral species. But determining exactly how their genomes were assembled can be very difficult, especially if the original ancestral species is extinct or unknown.
New research introduces a genome-wide approach to unraveling these complex genetic histories. This method takes advantage of the evolutionary footprint left by long terminal repeat retrotransposons, a type of mobile DNA sequence. By comparing the similarity patterns of these elements across chromosomes, researchers can identify different subgenomes and estimate when major genome-binding events occurred. Applying this technique to cultivated octoploid strawberries revealed a gradual evolutionary history shaped by multiple rounds of allopolyploidization, providing new insights into how complex plant genomes form and diversify over millions of years.
Why polyploid genomes are difficult to decipher
Whole-genome duplication plays an important role in plant evolution, helping to drive innovation, adaptation, and the emergence of many crop species. In allopolyploid plants, chromosome sets are derived from different ancestral genomes. These chromosome groups, known as subgenomes, continue to evolve and interact long after initial hybridization has occurred.
Identifying their subgenomes is critical to understanding how species evolved. Traditional approaches often rely on comparing polyploid genomes to known diploid ancestors. The problem is that many ancestral species are extinct or have not yet been identified.
Transferable elements provide another source of information. Long terminal repeat retrotransposons accumulate in characteristic patterns within specific evolutionary lineages, preserving molecular evidence of past events. Although scientists have long recognized their potential value, reliable methods to translate those patterns into accurate subgenomic assignments remained limited. As a result, new tools are needed to reconstruct polyploid genome evolution without relying on known ancestral species.
Reconstructing genome history in new ways
Researchers from the U.S. Department of Agriculture and collaborating agencies describe such tools in the journal horticultural research. The research team has developed a bioinformatics framework that can reconstruct the evolutionary history of complex polyploid genomes.
To demonstrate this method, cultivated octoploid strawberries (Fragaria x anassa) were reexamined. Using a serial similarity matrix constructed from long terminal repeat retrotransposons, researchers elucidated the structure of the strawberry subgenome and uncovered multiple ancient genome fusion events that contributed to modern species. The discovery helps resolve long-standing questions about the evolutionary origins of strawberries.
This framework traces genome evolution through three major stages: before the ancestral species diverged, during their separate evolutionary histories, and after the genomes merged. Retrotransposons that expanded during the period of divergence retain signatures specific to particular subgenomes.
The researchers generated what they called a “serial similarity matrix” by calculating a similarity matrix of these elements across chromosomes and examining how they clustered at different similarity thresholds. This approach captures evolutionary signals accumulated over different time periods.
Testing the approach in crops
Before applying the technique to strawberries, the researchers tested it on well-studied allopolyploid crops such as teff and cotton. In both cases, this method was successful in identifying known subgenomes and separating events that occurred before and after polyploidization.
The researchers also evaluated approaches using artificially constructed polyploid genomes. These tests confirmed that this method is sensitive to both divergence time and amount of transposable element.
What the strawberry genome revealed
Applying this method to octoploid strawberries, they identified four distinct subgenomes, revealing evidence for three successive allopolyploidization events that occurred approximately 3.1 to 4.2 million years ago, 1.9 to 3.1 million years ago, and 800,000 to 1.9 million years ago.
This result confirms the close evolutionary relationship between the two subgenomes and species of strawberry. Fragaria Besca and Fragaria Izen. At the same time, this finding calls into question previous models that proposed additional diploid progenitor species.
This analysis suggests that some contributors to the strawberry genome may be extinct or remain unsampled, highlighting the complexity of polyploid genome evolution.
“This study demonstrates how transposable elements act as evolutionary timestamps embedded in plant genomes,” said one of the study’s senior authors. “By focusing on when and where these elements expanded, we can reconstruct genomic history even when direct ancestral references are lacking. This method provides a powerful new lens to study polyploid crops, moving beyond reliance on incomplete ancestry data and providing a more objective and reproducible framework for evolutionary genomics.”
Implications for crop research and breeding
Potential uses extend beyond strawberries. Many economically important crops, such as wheat, cotton, and sugarcane, are polyploid and have similarly complex evolutionary histories.
More precise identification of subgenomes has the potential to improve gene annotation, trait mapping, and comparative genomic studies. These advances, in turn, could support precision breeding efforts and help accelerate crop improvement.
By allowing genome evolution to be reconstructed without known ancestry, the continuous similarity matrix approach adds a valuable new tool for studying biodiversity, speciation, and adaptation. This framework may also be useful for studying other complex polyploid organisms and helps link evolutionary biology with practical agricultural research.
This research was supported by National Institute of Food and Agriculture (NIFA)–Specialty Crops Research Initiative (SCRI) grant 2022-51181-38241 to QY.
