Chromosome-scale genomes of two wild flowering cherrys (Cerasus itosakura and C. jamasakura) provide insights into structural evolution in Prunus

Fujiwara, K.; Toyoda, A.; Katsuki, T.; Sato, Y.; Biswa, B. B.; Kishida, T.; Tsuruta, M.; Nakamura, Y.; Mochizuki, T.; Kimura, N.; Kawamoto, S.; Ohta, T.; Nonomura, K.-I.; Niki, H.; Yano, H.; Umehara, K.; Suzuki, C.; Koide, T.

doi:10.1101/2025.08.30.673203

bioRxiv · 10.1101/2025.08.30.673203

Chromosome-scale genomes of two wild flowering cherrys (Cerasus itosakura and C. jamasakura) provide insights into structural evolution in Prunus

Fujiwara, K.·Toyoda, A.·Katsuki, T.·Sato, Y.·Biswa, B. B.·Kishida, T.·Tsuruta, M.·Nakamura, Y.·Mochizuki, T.·Kimura, N.·Kawamoto, S.·Ohta, T.·Nonomura, K.-I.·Niki, H.·Yano, H.·Umehara, K.·Suzuki, C.·Koide, T.

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Abstract

Flowering cherries (genus Cerasus) are iconic trees in Japan, celebrated for their cultural and ecological significance. Despite their prominence, high-quality genomic resources for wild Cerasus species have been limited. Here, we report chromosome-level genome assemblies of two representative Japanese cherries: Cerasus itosakura, a progenitor of the widely cultivated C. xyedoensis Somei-yoshino, and Cerasus jamasakura, a traditional popular wild species endemic to Japan. Using deep PacBio long-read and Illumina short-read sequencing, combined with reference-guided scaffolding based on near-complete C. speciosa genome, we generated assemblies of 259.1 Mbp (C. itosakura) and 312.6 Mbp (C. jamasakura), with both >98% BUSCO completeness. Consistent with their natural histories, C. itosakura showed low heterozygosity, while C. jamasakura displayed high genomic diversity. Comparative genomic analyses revealed structural variations, including large chromosomal inversions. Notably, the availability of both the previously published C. speciosa genome and our new C. itosakura genome enabled the reconstruction of proxy haplotypes for both parental lineages of Somei-yoshino. Comparison with the phased genome of Somei-yoshino revealed genomic discrepancies, suggesting that the cultivar may have arisen from genetically distinct or admixed individuals, and may also reflect intraspecific diversity. Our results offer genomic foundations for evolutionary and breeding studies in Cerasus and Prunus.

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Fujiwara, K., Toyoda, A., Katsuki, T., Sato, Y., Biswa, B. B., Kishida, T., Tsuruta, M., Nakamura, Y., Mochizuki, T., Kimura, N., Kawamoto, S., Ohta, T., Nonomura, K.-I., Niki, H., Yano, H., Umehara, K., Suzuki, C., Koide, T.. 2025-08-31. Chromosome-scale genomes of two wild flowering cherrys (Cerasus itosakura and C. jamasakura) provide insights into structural evolution in Prunus. https://doi.org/10.1101/2025.08.30.673203

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