Deciphering octoploid strawberry evolution with serial LTR similarity matrices for subgenome partition

Authors: LYU, HAOMIN - Hawaii Agricultural Research Center; OU, SHUJUN - Ohio University; YIM, WON CHEOL - University Of Nevada; Yu, Qingyi

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/11/2025
Publication Date: 5/21/2025
Citation: Lyu, H., Ou, S., Yim, W., Yu, Q. 2025. Deciphering octoploid strawberry evolution with serial LTR similarity matrices for subgenome partition. Horticulture Research. 12(8). Article uhaf132. https://doi.org/10.1093/hr/uhaf132.
DOI: https://doi.org/10.1093/hr/uhaf132

Interpretive Summary: Polyploidization, or whole genome duplication (WGD), has been recognized as one of the major factors driving plant evolution. Nearly all seed plants have undergone at least one ancient WGD event. Advancements in sequencing technologies and genome assembly algorithms now allow high-quality, chromosome-level assemblies of polyploid genomes. However, accurately delineating these assemblies into subgenomes remains a challenging task, especially in case where known diploid ancestors are absent. In this study, we introduce a bioinformatics pipeline for precise subgenome partition in allopolyploid genomes, particularly those lacking information on diploid progenitors. Our method utilizes the similarities of long terminal repeats (LTRs) to construct a Serial of Similarity Matrix (SSM), facilitating the effective clustering of chromosomes within the allopolyploid genome. We validated this approach using well-studied allopolyploidy genomes, tested it on an artificially constructed allotetraploid genome, and applied it to distinguish the subgenomes of the octoploid strawberry (F. × ananassa Duchesne) genome. Our findings elucidate the intricate evolutionary processes underlying allopolyploidization in this agriculturally important crop species.

Technical Abstract: Polyploidization has been recognized as a major force in plant evolution. With the continuous progress in sequencing technologies and genome assembly algorithms, high-quality chromosome-level assemblies of polyploid genomes have become increasingly attainable. However, accurately delineating these assemblies into subgenomes remains a challenging task, especially in case where known diploid ancestors are absent. In this study, we introduce a novel approach that leverages long terminal repeat retrotransposons (LTR-RTs) coupled with the Serial Similarity Matrix (SSM) method to assign genome assemblies to subgenomes, particularly beneficial for those without known diploid progenitor genomes. The SSM method helps identify subgenome-specific LTRs and facilitate the inference of the timing of allopolyploidization events. We validated the efficacy of the SSM approach using well-studied allopolyploidy genomes, Eragrostis tef and Gossypium hirsutum, alongside an artificially created allotetraploid genome by merging two closely related diploid species, Glycine max and G. soja. Our results demonstrated the robustness of the method and its effectiveness in assigning chromosomes to subgenomes. We then applied the SSM method to the octoploid strawberry genome. Our analysis revealed three allopolyploidization events in the evolutionary trajectory of the octoploid strawberry genome, shedding light on the evolutionary process of the origin of the octoploid strawberry genome and enhancing our understanding of allopolyploidization in this complex species.