Centromeres act as the control centers of chromosomes, ensuring accurate genetic inheritance during cell division, yet they remain among the least understood genomic regions due to their repetitive structure. Researchers have now generated a near-complete genome assembly of allotetraploid elephant grass, providing the first comprehensive resolution of all centromeres in this species. The study reveals how repetitive DNA, mobile genetic elements, and epigenetic regulation collectively shape centromere evolution following genome duplication. While centromeric DNA sequences diversify rapidly, their functional epigenetic features remain highly conserved, suggesting that chromosome stability is maintained through epigenetic mechanisms even as genetic architecture undergoes continuous evolutionary change.
Centromeres are essential chromosomal regions responsible for accurate segregation of genetic material during mitosis and meiosis. Despite their conserved biological function, centromere DNA evolves rapidly and varies widely among species, making these regions difficult to assemble using conventional sequencing technologies. The challenge is even greater in allopolyploid plants, whose genomes arise from hybridization between distinct ancestral species and often undergo large-scale chromosomal rearrangements. Elephant grass (Pennisetum purpureum) is an important forage and bioenergy crop formed through such genome merging events, yet previous genome assemblies lacked complete centromeric information. Because of these challenges, deeper investigation into the genetic and epigenetic organization of centromeres in polyploid plants has become essential.
Researchers from the Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity at Minjiang University, the State Key Laboratory of Crop Gene Resources and Breeding at the Chinese Academy of Agricultural Sciences, the Center for Plant Biology at Tsinghua University, the National Engineering Research Center for Sugarcane at Fujian Agriculture and Forestry University, Jiangsu Academy of Agricultural Sciences, and Anhui Normal University reported a near-complete genome assembly of Pennisetum purpureum ‘Purple’ in the journal Horticulture Research. The study was published (DOI: 10.1093/hr/uhaf301) on November 7, 2025, with a corrected and typeset version released in February 2026. By integrating PacBio HiFi sequencing with Hi-C chromatin interaction data, the team successfully resolved all 14 centromeres, enabling detailed investigation of centromere evolution following allopolyploid genome formation.
The researchers constructed a high-quality genome assembly of approximately 2.0 Gb with greatly improved continuity and accuracy compared with previous references. The new assembly resolved nearly all telomeric regions and closed most genomic gaps, enabling detailed characterization of centromere structure for the first time.
Analyses revealed that unequal expansion of long terminal repeat retrotransposons reshaped chromosome architecture differently between the two subgenomes. These mobile elements contributed to structural divergence after hybridization, driving genome evolution at large scales. Meanwhile, centromeric satellite repeats known as CentP showed rapid sequence diversification across chromosomes and subgenomes.
Despite this extensive genetic variation, epigenetic features remained remarkably stable. The centromere-specific histone variant CENH3 consistently marked functional centromeres, and chromatin modification patterns showed similar enrichment profiles across both subgenomes. These findings indicate that centromere identity depends more on epigenetic regulation than on fixed DNA sequences.
The study also uncovered dynamic interactions between satellite repeats and centromeric retrotransposons. Newly inserted retrotransposons increased local sequence variability but were gradually removed through homogenization processes, suggesting an evolutionary cycle that balances structural innovation with functional stability.
“Our results demonstrate that centromeres are evolutionarily dynamic yet functionally robust,” the researchers explained. “Although their DNA sequences change rapidly after genome duplication, conserved epigenetic regulation ensures reliable chromosome inheritance.” The team emphasized that resolving complete centromeres provides critical insight into how complex plant genomes stabilize after hybridization events. Understanding this balance between genetic flexibility and epigenetic conservation may help explain the evolutionary success of polyploid crops and guide future genomic research in agriculturally important species.
The near-complete genome provides a valuable foundation for crop improvement, evolutionary biology, and genome engineering. Elephant grass is widely cultivated for forage production and emerging bioenergy applications, and improved genomic resolution will accelerate gene discovery and molecular breeding efforts. Insights into centromere organization may also enhance chromosome engineering strategies and improve precision in genome editing technologies. More broadly, the findings advance understanding of how hybrid genomes maintain stability despite rapid sequence evolution. By revealing how epigenetic mechanisms preserve chromosome function amid genetic change, the study offers new perspectives for developing resilient crops capable of adapting to environmental and agricultural challenges.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhaf301
Funding information
This work was supported by funds from the National Natural Science Foundation of China (32001605), the Natural Science Foundation of Fujian Province, China (2025 J01332), and the Open Project of State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources (SKLCUSA-b202408).
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.
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