Songtao Jiu, Yahui Lei, Linlin Fang, Yue Huang, Wenbo Chen, et al. (2026).
Pangenome and resequencing analyses reveal flowering evolution and genetic control in Cerasus.
Nature Communications. 10.1038/s41467-026-72832-8
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Pangenome and resequencing analyses reveal flowering evolution and genetic control in Cerasus
Why this matters: A new 21-accession Cerasus pangenome pinpoints AGL9 as a key accelerator of post-dormancy flowering, opening a path to dissect and engineer bloom timing in cherries.
Background
Prunus subgenus Cerasus includes over 70 species of ornamental, edible, and medicinal cherries. Despite their economic and cultural importance, genomic resources have been sparse, limiting study of structural variation and the genetic control of phenological traits such as flowering time — a trait highly relevant to climate adaptation and breeding.
The authors set out to build a representative pangenome for Cerasus and use it to identify regulators of flowering progression after dormancy.
Methods
- Assembled 8 new genomes spanning wild and cultivated Cerasus species.
- Combined with 13 previously published genomes to construct a pangenome covering 21 accessions / 17 species.
- Collected phenological data on flowering time across accessions.
- Integrated comparative genomics, transcriptomics, and population genetic analyses to nominate candidate flowering-time genes.
- Functionally tested PavAGL9 via ectopic expression (heterologous) and transient overexpression in cherry.
- Probed regulatory and protein interactions using promoter binding assays (PavBPC6 → PavAGL9 promoter) and protein–protein interaction assays (PavAGL9 with PavSEP1 and PavPMADS2).
Key findings
- The pangenome provides the first broad structural-variation framework for Cerasus.
- Phenological surveys reveal substantial inter-species variation in flowering time.
- AGAMOUS-LIKE 9 (AGL9) emerges as strongly associated with flowering progression.
- Both ectopic and transient overexpression of PavAGL9 accelerate post-dormancy flowering progression.
- PavBPC6 binds the PavAGL9 promoter and represses its transcription, defining a negative regulatory module upstream of AGL9.
- PavAGL9 physically interacts with PavSEP1 and PavPMADS2, consistent with a MADS-box complex acting in floral organ development.
Limitations and open questions
The abstract does not detail quantitative effect sizes, environmental replication of phenology data, or how broadly the BPC6–AGL9 module operates across the 17 species sampled. The functional assays focus on Prunus avium (Pav) gene copies; the extent to which structural variants identified pangenome-wide causally drive interspecific flowering-time differences remains to be established.
Original abstract
Prunus subgenus Cerasus contains numerous species with ornamental, edible, and medicinal value. However, limited genomic resources have constrained systematic analyses of structural variation and the genetic basis of key phenological traits in this group. Here, we assemble eight genomes from diverse Cerasus species. Together with 13 published genomes, we construct a pangenome of 21 accessions representing 17 species. Phenological observations reveal substantial variation in flowering time. Integrating comparative genomics, transcriptomics, and population genetic analyses highlight candidate regulators of flowering time. We find that AGAMOUS-LIKE 9 (AGL9) is strongly associated with flowering progression. Both ectopic expression and transient overexpression of PavAGL9 can accelerate post-dormancy flowering progression. We reveal that PavBPC6 binds the PavAGL9 promoter and represses its transcription, indicating a negative regulatory role. Furthermore, PavAGL9 interacts physically with PavSEP1 and PavPMADS2, suggesting synergistic roles in floral organ development. Our pangenome resource establishes a comprehensive genomic framework for Cerasus and provides insights into the regulation of flowering progression. Prunus subgenus Cerasus comprises over 70 species with ornamental, edible, and medicinal value. Here, the authors assemble eight genomes from wild and cultivated Cerasus species, construct pangenome together with 13 public genomes, and uncover the evolutionary origin and genetic determinants of flower development.
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