Over the past decade, advances in sequencing technologies have enabled high-quality genome assemblies for many crops, including papaya. However, most genetic studies have relied on a single reference genome, which cannot capture the full spectrum of variation within a species. Increasing evidence from rice, soybean, and tomato shows that structural variations (SVs)—large insertions, deletions, and rearrangements—play crucial roles in agronomic traits and domestication. In papaya, previous work identified single-nucleotide polymorphisms and limited structural variants, but comprehensive population-scale SV maps remained lacking. Given the importance of papaya in tropical agriculture and breeding, deeper genomic exploration is needed to uncover hidden variation underlying key traits. Based on these challenges, it is necessary to conduct in-depth research using a pangenome framework to better capture genetic diversity.
A research team from the Guangdong Academy of Agricultural Sciences, in collaboration with JiguangGene Biotechnology Co., Ltd., reported (DOI: 10.1093/hr/uhaf282) the construction of a comprehensive papaya pangenome in Horticulture Research (2026). By assembling chromosome-level genomes of multiple representative cultivars and integrating them with existing references, the team generated graph-based and linear pangenome models. Their study identified more than 26,000 high-confidence SVs across 222 papaya accessions, revealing key functional gene variations associated with root development and domestication.
Using PacBio HiFi sequencing combined with Hi-C scaffolding, the researchers assembled four new high-quality papaya genomes and integrated them with two improved reference genomes. A syntelog-based pangenome grouped 120,273 genes into 24,453 syntelog groups, classifying them as core, dispensable, or private genes. The analysis revealed that dispensable genes were enriched in pathways related to photosynthesis and secondary metabolite biosynthesis, including terpene pathways associated with stress resistance and nutritional properties.
A graph-based pangenome was then constructed to detect structural variants more comprehensively. This model identified 12,213 structural “bubbles,” representing genomic insertions, deletions, and multiallelic variants. Population-scale SV genotyping of 222 accessions yielded 26,173 high-confidence SVs, many located in regulatory regions or overlapping coding sequences.
One particularly striking finding was a 94-base-pair deletion in the first intron of the RRG gene in the T3 cultivar. Although the coding sequence remained intact, expression of RRG was reduced by 9.5-fold compared to another cultivar. Cytological analysis showed fewer meristematic cells but increased cell elongation in T3 roots, leading to shorter roots. This demonstrates how subtle structural variation can significantly affect gene regulation and plant development.
“Our findings show that relying on a single reference genome underestimates the true genetic diversity of papaya,” said the corresponding author. “By integrating multiple high-quality genomes, we were able to uncover SVs that were previously invisible. The identification of functional SVs, such as the deletion affecting RRG, illustrates how pangenome approaches can directly connect genomic variation to agronomic traits. These resources will greatly facilitate gene discovery and precision breeding in papaya.”
The papaya pangenome provides a foundation for next-generation breeding strategies. Structural variants identified in this study can be incorporated into SV-based genome-wide association studies, potentially explaining missing heritability not captured by SNP analyses. The discovery of SVs under selection between wild and cultivated populations also sheds light on domestication and adaptive evolution. By combining graph-based and linear pangenome strategies, the study expands the catalog of inversions and translocations, offering breeders more precise molecular markers. Ultimately, these genomic insights may support the development of papaya varieties with improved yield, stress resistance, root architecture, and nutritional quality, benefiting tropical agriculture worldwide.
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References
DOI
10.1093/hr/uhaf282
Original Source URL
https://doi.org/10.1093/hr/uhaf282
Funding information
This work was supported by the General Program of the National Natural Science Foundation of China (grant 32572974), the ‘Young and Middle-aged Academic Leaders’ training fund project of Guangdong Academy of Agricultural Sciences (grant R2023PY-JX005), the Cultivation Project of Fruit Tree Research Institute, Guangdong Academy of Agricultural Sciences (grant 23107), and the Guangdong Province Rural Revitalization Strategy Special Fund-Seed Industry Revitalization Action Project (grant 2024-NPY-00-028), and the Guangzhou Municipal Science and Technology Project (grant 2024A04J6951).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.