In a groundbreaking development that promises to reshape our understanding of one of the world’s most important crops, researchers have unveiled a highly detailed, haplotype-resolved, chromosome-level genome assembly of the hexaploid sweetpotato (Ipomoea batatas). This feat not only illuminates the complex genomic architecture of sweetpotato but also sheds light on its elusive evolutionary origins, an endeavor that has challenged scientists for decades. By dissecting the genome into phased chromosomes, the team has revealed a mosaic composition derived from wild relatives, challenging traditional assumptions about sweetpotato’s subgenomic structure and offering new avenues for breeding improvement.
Sweetpotato has long been recognized for its remarkable agricultural and nutritional significance, especially in regions vulnerable to food insecurity. As a staple crop in many parts of Africa, Asia, and the Americas, its role in biofortification, nutritional security, and climate resilience cannot be overstated. Despite this importance, the sweetpotato genome has proven notoriously difficult to decode, primarily due to its hexaploid nature—possessing six sets of chromosomes—as well as extensive heterozygosity and the intertwining of genetic material from different wild progenitors.
By utilizing advanced sequencing technologies combined with sophisticated computational techniques for genome phasing, the research consortium succeeded in assembling the sweetpotato genome at the chromosome level from a highly heterozygous African cultivar known as ‘Tanzania.’ The phased assembly allows for the resolution of individual haplotypes, effectively untangling the complex web of genetic contributions from multiple ancestral species. This reveals an unprecedented view into the intricacies of sweetpotato’s genome organization and evolutionary history.
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One of the most striking findings is the mosaic nature of the sweetpotato genome. Rather than existing as distinct, separate subgenomes corresponding neatly to each ancestral species, the DNA sequences contributed by different wild relatives are interspersed and intricately intertwined along the chromosomes. This genomic patchwork defies the classical model of allopolyploid genome evolution, where subgenomes typically maintain structural integrity and limited recombination.
The study identifies two primary wild progenitors contributing to sweetpotato’s hexaploid genome. The first is Ipomoea aequatoriensis, a wild tetraploid species native to the coastal regions of Ecuador. This species accounts for a substantial fraction of the hexaploid genome, suggesting a significant evolutionary role. The second key ancestor is the wild tetraploid Ipomoea batatas 4×, found in Central America, which similarly contributes to a large proportion of the genome. The co-existence of these two wild tetraploid lineages within a single hexaploid genome highlights the complex evolutionary path sweetpotato has undergone.
The researchers hypothesize that the interspersed genomic pattern can be attributed to non-preferential recombination events among sweetpotato’s haplotypes. Unlike typical allopolyploids, in which subgenomes exhibit preferential pairing and limited cross-haplotype exchange, sweetpotato’s haplotype chromosomes seem to undergo frequent recombination without bias. This process leads to a mosaic architecture rather than well-defined, easily delineated subgenomes. Such genomic plasticity may underpin sweetpotato’s remarkable resilience and adaptability in diverse environments.
This new genome assembly offers valuable resources that accelerate the breeding and genetic improvement of sweetpotato. By providing a phased and chromosome-level understanding of the crop’s genome, breeders can now more precisely target genes associated with desirable traits such as drought tolerance, disease resistance, and nutrient enrichment. Given sweetpotato’s critical role in food security and nutritional programs globally, this enhanced genetic insight is timely and has wide-reaching agricultural implications.
The research also provides clues for addressing climate-related challenges. Sweetpotato’s adaptability to varied and often challenging environments is one of its key strengths. Better understanding the genome structure and the mosaic amalgamation of wild progenitor genetic material offers a foundation for dissecting the genetic basis of this adaptability. Consequently, future breeding strategies could more effectively harness natural variation present in the genome’s wild-derived segments, enabling the development of cultivars suited to changing climates.
Technically, the study leverages cutting-edge sequencing platforms combined with algorithms capable of phasing polyploid genomes. The complexity of hexaploid genomes makes phasing—resolving which variants occur together on a single chromosome—a daunting task. Achieving this for sweetpotato set a major milestone, made possible through innovations in long-read sequencing, chromatin conformation capture methods, and computational phasing approaches that can parse through heterozygosity and repetitive regions.
The implications of this work extend beyond sweetpotato itself. Many polyploid crops, including staples like wheat and cotton, possess complex genome structures. The successful haplotype-resolved assembly of sweetpotato sets a precedent and methodological benchmark for other polyploid genome projects. It offers new perspectives on how polyploid genomes can evolve unique, interwoven genomic architectures rather than conforming to classical models of subgenome partitioning.
From a more fundamental evolutionary biology perspective, the mosaic structure of the sweetpotato genome challenges established views on polyploid genome stabilization. The widely accepted view is that polyploid genomes usually resolve into subgenomes from each progenitor with limited inter-subgenomic recombinant exchange to maintain genome integrity. Sweetpotato defies this expectation, showcasing extensive recombinational blending, hinting at a unique mode of polyploid genome evolution that may enhance genetic diversity and plasticity.
The study also raises intriguing questions about the origins and domestication of sweetpotato. Its genome composition suggests that domestication involved complex hybridization events between multiple wild species followed by extensive recombination, rather than a simple, linear evolutionary trajectory. Future investigations integrating population genomics and phenotypic analyses will likely further clarify the routes through which sweetpotato adapted to human cultivation and diverse ecological niches.
This comprehensive genome resource will undoubtedly serve as a cornerstone for future functional genomics studies aimed at dissecting sweetpotato traits at a molecular level. By having a phased genome map, scientists can now undertake allele-specific expression studies, pinpoint regulatory elements with precision, and explore epigenetic modifications across haplotypes. These advances will be crucial in linking genotype to phenotype and enhancing crop improvement programs.
Importantly, the methodological framework used to achieve this genome assembly is applicable to other understudied polyploid crops that contribute to global food security, especially in developing countries. The ability to untangle complex genomes with high heterozygosity and polyploidy opens the door to accelerated genetic improvement efforts for a variety of crops with similar genomic challenges.
In conclusion, this landmark study not only delivers a highly resolved sweetpotato genome but also deepens our understanding of its intricate evolutionary past and genome architecture. The revelations about mosaic haplotypes and intertwined ancestral genome contributions demand a paradigm shift in how scientists view polyploid genome evolution and stability. As sweetpotato continues to be a cornerstone of global agricultural systems, this new knowledge provides a powerful platform for breeding innovations aimed at tackling both food security and climate resilience challenges in the coming decades.
Subject of Research: Genetic architecture and evolutionary origins of the hexaploid sweetpotato (Ipomoea batatas) through haplotype-resolved chromosome-level genome assembly.
Article Title: Phased chromosome-level assembly provides insight into the genome architecture of hexaploid sweetpotato.
Article References:
Wu, S., Sun, H., Zhao, X. et al. Phased chromosome-level assembly provides insight into the genome architecture of hexaploid sweetpotato. Nat. Plants (2025). https://doi.org/10.1038/s41477-025-02079-6
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