Plant Genetics Research Reveals Dynamic and Diverse Centromere Behavior

Cell division is an essential process by which living organisms grow, replenish lost cells, and regenerate dead and damaged tissues. When a parent cell divides into two daughter cells, 'chromosomes'-the structures that organize and store genetic information-are duplicated to generate two copies. These copies are distributed equally so that the daughter cells are genetically identical. The arms of the chromosome or 'sister chromatids,' typically oriented in an 'X' shape, are held together at the center by a clip-like structure known as the 'centromere.' The chromatids are separated or pinched off at the centromere for the even distribution of genetic information to the daughter cells during cell division.

There has been a long-standing belief that tandem DNA repeat sequences, also known as 'satellites,' are necessary to stabilize centromeres. However, recent advancements in genomic sequencing have revealed significant inter-species diversity, suggesting that the stereotypical satellite-bearing centromere may not be the only form of centromere. Furthermore, studies in plants have shown that centromeres can dynamically shift positions, even at an inter-individual level.

Diving deeper, Associate Professor Kiyotaka Nagaki from the Institute of Plant Science and Resources, and Professor Koichiro Ushijima, from the Graduate School of Environmental and Life Science, Okayama University, Japan, sought to analyze variations in the size, stability, and migration of centromeres using Allium species, including onion and garlic, as a model system.

Their findings were published online in The Plant Cell on June 10, 2025. "Owing to their large size and small number of chromosomes, garlic, Welsh onion, and onion are valuable models in cytogenetic education and research. The reference genome sequences of these species were recently released. We, therefore, attempted to determine the exact location of the centromere using an antibody produced in our previous study," explains Associate Prof. Nagaki.

The centromere interacts with the nucleosome (DNA-protein complex unit) containing the centromere-specific histone H3 variant (CENH3) and initiates chromosome segregation during cell division. The researchers used a CENH3-targeted antibody to map centromere regions in the genome of eight Welsh onion cultivars (a cultivated plant variety with desirable features). Next, compared the CENH3-bound genomic sequences with the reference sequence to identify tandem repeats. Their analysis revealed a single CENH3 peak on each chromosome. The centromere regions ranged from 0.9 Mb (mega base = 1 million base pairs) to 2.6 Mb and overlapped with the tandem repeats, suggesting a stable centromere position with significant variations in size.

On the contrary, centromere mapping of six onion and three shallot cultivars showed multiple CENH3 peaks per chromosome, with significant variations among the different cultivars. Interestingly, unlike in the Welsh onions, the researchers noted that CENH3 distribution shifted from the position of the ancient centromeres (mapped to satellite sequences) by up to 28.0 Mb. Furthermore, they observed inter-individual differences in the same cultivar, suggesting the potential role of epigenomic mechanisms (reversible genomic changes) rather than structural rearrangements.

So far, the researchers have found that while Welsh onions present with uniform centromere positions but in varying lengths, onions exhibit centromere migration. Next, they examined how these properties manifest in 'Wakegi'-a hybrid of Welsh onion and shallot. Notably, only one CENH3 peak was noted per chromosome without polymorphisms (genomic variations). The absence of centromere migration in the hybrid variety suggested that hybridization may improve centromere stability.

Finally, centromere mapping in garlic revealed strikingly larger CENH3-distributed regions. The representative gigantic centromeres were 5.5 times larger than those of Welsh onion and twice as large as the sizes of the centromeres of bread wheat, the largest centromeres measured to date. Interestingly, garlic presented stable centromeres despite lacking satellite-type repeat sequences altogether, calling into question the need for tandem repeats in centromere stability.

Overall, these findings suggest that centromeres may not be static after all, as earlier believed, but vary significantly in their organization, size, and position/mobility even between closely related species.

Associate Prof. Nagaki concludes with the long-term implications of their work by saying, "If centromeres can be artificially shifted in the future, this could alter the expression of adjacent genes, which can help improve the breeding and cultivation of food crops."