Genome of wild persimmon reveals secrets of early flowering and evolution
image: The morphology and homologous genome blocks for D. deyangensis. (A) Primary phenological growth stages of D. deyangensis including bud development stage, leaf development stage, flowering stage, and fruit development stage. (B) Flowering, setting fruit, and growing conditions in the first year of sowing. (C) Circos plot of major genomic characteristics. The outmost greenish circle comprises 60 pseudochromosomes. The features from outside to inside are (a) Chromosomes, (b) Copia density, (c) Gypsy density, (d) long terminal repeat retrotransposon density, (e) gene density, (f) GC content, and (g) the intrasubgenome syntenic regions. All distributions are drawn in a window size of 1 Mb. Syntenic blocks are represented by the inner lines. Each line represents a syntenic block. Image link: https://academic.oup.com/view-large/figure/512251981/uhaf001f1.tif?login=false
Credit: Horticulture Research
The genus Diospyros includes over 500 species, among which cultivated persimmon (D. kaki) holds great nutritional and economic importance. However, its complex hexaploid genome (2n = 6x = 90) and long juvenile period have long hindered molecular studies and breeding improvements. D. deyangensis, a wild tetraploid species native to Sichuan, China, displays unique traits such as a drastically shortened juvenile phase and distinct floral morphology. These biological advantages make it a valuable genetic resource for understanding persimmon evolution and shortening breeding cycles. Due to these challenges, it is necessary to conduct in-depth genomic and molecular studies on D. deyangensis to uncover the mechanisms underlying its rapid flowering and evolutionary adaptation.
Researchers from Northwest A&F University and their collaborators have successfully assembled a haplotype-resolved, chromosome-level genome of Diospyros deyangensis, providing the first genomic blueprint of a wild persimmon with rapid flowering ability. The study was published (DOI: 10.1093/hr/uhaf001) online in Horticulture Research on April 1, 2025. By combining PacBio HiFi, Oxford Nanopore, and Hi-C sequencing technologies, the team decoded a 3.01 Gb genome and revealed genetic clues to the species’ unique early-flowering trait and evolutionary divergence from cultivated persimmon.
The D. deyangensis genome, assembled with 60 pseudochromosomes, demonstrated exceptional completeness and phasing quality, achieving an N50 of 43.72 Mb and 97.5% BUSCO coverage. Comparative analyses indicated that the species underwent an additional whole-genome duplication after the ancestral eudicot hexaploidy event. Population resequencing of 63 accessions from 11 Diospyros species revealed that D. kaki evolved independently from its wild relatives rather than through hybridization. To identify genetic factors linked to its short juvenile phase, the researchers performed bulked segregant RNA sequencing (BSR-seq) in a backcross population of 399 seedlings. They pinpointed DdELF4 (EARLY FLOWERING 4) as a key flowering repressor gene. Overexpression of DdELF4 in Arabidopsis delayed flowering and suppressed FT gene expression, confirming its inhibitory function. These findings highlight DdELF4 as a potential target for manipulating flowering time in persimmon breeding and provide valuable genomic resources for future studies on polyploid fruit trees.
“Our genome assembly of Deyangshi fills a critical gap in persimmon genetics,” said Professor Tao Zhao, senior author of the study. “This wild species offers a natural model for studying rapid juvenile-to-adult transitions in perennial fruit trees. The discovery of DdELF4 not only enhances our understanding of flowering regulation but also provides molecular tools to shorten breeding cycles.
The D. deyangensis genome serves as a foundational resource for advancing genome-assisted breeding of persimmons and other woody fruit crops. By uncovering the genetic mechanisms of early flowering, this study paves the way for developing cultivars with reduced juvenile periods—an essential goal for improving breeding efficiency and accelerating variety innovation. Beyond horticultural applications, the research also contributes to evolutionary genomics, offering new perspectives on polyploidy, genome duplication, and speciation in perennial plants. The “Deyangshi” genome thus bridges the gap between wild diversity and cultivated improvement, supporting sustainable development of the global persimmon industry.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhaf001
Funding information
This research was supported by the National Natural Science Foundation of China (32272672), the Key Research and Development Program of Shaanxi Province, China (2022NY-11,2), and the Innovation Capability Support Program of Shaanxi Province, China (2022PT-25).
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, 2024. 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.