A new study offers the clearest view yet of that transition. A research team from Northeast Forestry University and BGI Research assembled chromosome-level genomes for two closely related Magnoliales species with opposite centromere designs: Myristica fragrans, the nutmeg tree, whose chromosomes are holocentric, and Cananga odorata, the ylang-ylang, whose chromosomes follow the classic monocentric plan. By comparing the two assemblies with an integrated battery of genomic, epigenomic and phylogenetic analyses, the researchers were able to isolate the molecular changes that accompany the shift from a single centromere per chromosome to a distributed one. The work was published in the Journal of Systematics and Evolution.

The scale of the assemblies alone represents a technical achievement. The team generated a 637-million-base-pair genome for M. fragrans spanning 22 chromosomes and a 717-million-base-pair genome for C. odorata spanning 8 chromosomes, with completeness scores between 97.5 and 98.6 percent on the BUSCO benchmark of conserved single-copy genes. Hi-C contact maps, which chart how chromatin folds in three-dimensional space, confirmed that each C. odorata chromosome carries a single prominent heterochromatic block — the cytological signature of a conventional centromere. M. fragrans, by contrast, showed no such concentrated signal. Two independent computational centromere-prediction tools independently recapitulated the pattern, calling one centromeric locus per chromosome in the ylang-ylang genome and multiple loci per chromosome in nutmeg.

Interestingly, the regions associated with centromeric function in both species were not chemically alien to one another. In each genome, centromere-associated regions correlated positively with methylation of cytosines in the CG and CHG sequence contexts, and both fell within the so-called B compartments of chromatin, the heterochromatic zones that are generally transcriptionally silent. Whatever else changed during the holocentric transition, the deep epigenetic identity of centromeric DNA appears to have been conserved. The differences emerged elsewhere in the chromosome landscape, and they were dramatic.

Transposable elements — the jumping genes that make up a large fraction of most plant genomes — turned out to be the most conspicuous point of divergence. C. odorata displayed tightly clustered heterochromatin and a dominant plateau of LTR/Gypsy-family retrotransposons, including the Tekay, Athila and SIRE lineages, heaped around its concentrated centromeric regions. M. fragrans instead showed a dispersed chromatin organization studded with multiple discrete peaks of LTR/Copia elements, particularly the Ale and SIRE families. The methylation mark mCHH, which in plants typically fortifies heterochromatin against transposon activity, was depleted within the centromeric regions of nutmeg but enriched around those of ylang-ylang — a mirror-image pattern in the epigenetic armor of two sister lineages.

Tandem repeat satellite DNA, long regarded as the canonical stuff of centromeres, told a similarly divergent story. The two major tandem-repeat families in the nutmeg genome, designated MF_351 and MF_269, preferentially localized to the chromosome termini, where they carried elevated levels of CG and CHG methylation — a positioning that suggests they may contribute to structural stability at the chromosome ends rather than to a concentrated centromere. In ylang-ylang, tandem repeats accumulated predominantly in euchromatic, gene-rich regions, with negligible occupancy of heterochromatin. In other words, holocentricity in Myristica did not arise simply by enlarging a conventional centromere; the entire repeat landscape was rearranged.

Detective work at the evolutionary timescale helped rule out the most obvious suspect. Phylogenomic analysis and comparisons of synonymous substitution rates, so-called Ks analyses, showed that the two species share an ancient whole-genome duplication, dubbed LAURb, that occurred roughly 115 million years ago. Crucially, that duplication is shared, meaning it predates the split between the holocentric and monocentric lineages and cannot by itself explain the transition. The team also found evidence that M. fragrans and the related species M. yunnanensis experienced two distinct waves of transposon expansion, pointing instead to repeat dynamics as a lineage-specific driver.

The proteins that physically attach chromosomes to the spindle machinery offered few dramatic answers. CENH3, the core kinetochore histone that epigenetically defines centromeric identity, is highly conserved between the two species, differing only in subtle lineage-specific substitutions within the centromere-recognition loop 1 and the flexible N-terminal tail. An elongated N-terminus in NASP, another centromere-associated protein, turned out to be a Magnoliales-wide feature rather than a signature of holocentricity, and the researchers detected no large-scale structural changes in any of the other core kinetochore proteins. The machinery of chromosome segregation, in short, appears essentially intact on both sides of the divide.

The synthesis that emerges is one of lineage-specific rewiring rather than a single master event. According to first author Jinyin Xing, comparing a holocentric species with a closely related monocentric one at chromosome-level resolution was precisely what allowed the team to dissect the genomic changes underlying what he calls this remarkable reorganization. The evidence converges on remodeling of repetitive DNA and epigenetic states as the proximate cause of the centromere’s dispersion in Myristica, while whole-genome duplication and major kinetochore protein evolution can be largely excluded as sufficient explanations.

Beyond resolving a longstanding puzzle in chromosome biology, the study delivers a resource with practical and conceptual reach. Chromosome-level reference genomes for nutmeg and ylang-ylang — both economically and culturally significant species — will support breeding, conservation and comparative work in a lineage that anchors some of the earliest branches of flowering plant evolution. More broadly, the comparative framework demonstrates how holocentricity, one of the most striking alternative solutions to the problem of chromosome inheritance, can emerge through the slow accumulation of repeat and chromatin changes rather than through a single evolutionary leap. For a structure as fundamental as the centromere, that lesson — that even the most essential genomic architecture is negotiable over deep time — is a reminder of how inventive evolution can be with the rules of life.

Subject of Research: Comparative genomics of monocentric-to-holocentric centromere transition in Magnoliales plants

Article Title: Chromosome-level genomes of two Magnoliales species provide new insights into the holocentric transition

Article References: Chromosome-level genomes of two Magnoliales species provide new insights into the holocentric transition. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: centromere evolution, holocentric chromosomes, Magnoliales, comparative genomics, Myristica fragrans, Cananga odorata, transposable elements, DNA methylation, CENH3, whole-genome duplication, genome assembly, Journal of Systematics and Evolution

The central obstacle has always been polyploidy. While bread wheat itself is a hexaploid with six chromosome sets, Thinopyrum ponticum goes several steps further, packing ten sets into each cell nucleus. Distinguishing its individual chromosomes under the microscope has been a long-standing headache for cytogeneticists, because many of them look alike with conventional staining techniques. Without a reliable reference karyotype, a map that identifies each chromosome by its unique visual signature, researchers could not confidently determine which wild chromosome had been added to, or swapped into, a wheat line during wide hybridization. That uncertainty slowed every introgression program, since breeders could not easily verify whether the resistance gene they were chasing had actually landed in the plant they were testing.

To break through this bottleneck, the team combined two complementary fluorescence in situ hybridization approaches. The first, non-denaturing FISH, or ND-FISH, uses short synthetic oligonucleotide probes that bind to repetitive DNA sequences without requiring the harsh DNA denaturation step of traditional FISH. This gentler method preserves chromosome morphology and produces crisp, reproducible banding patterns that act like barcodes for individual chromosomes. The second technique, bulked oligonucleotide pool-based FISH painting, takes the barcode concept further. Instead of a single probe, it deploys hundreds or thousands of oligonucleotides designed from chromosome-specific sequences, flooding the preparation with fluorescent labels that effectively paint an entire chromosome in a distinctive color. Together, the two methods allowed the researchers to assign each of the fifty chromosomes of Thinopyrum ponticum to a recognizable identity, establishing a reference karyotype for the species.

With the karyotype in hand, the team turned the platform loose on a real breeding material: the wheat–Thinopyrum ponticum partial amphiploid known as Agrotana. Partial amphiploids are hybrids that carry the complete wheat genome plus a full set of chromosomes from the wild donor, and they serve as genetic bridges from which breeders extract useful chromosome segments. Using their new probes, the researchers could cytogenetically analyze Agrotana chromosome by chromosome, confirming its constitution and spotting any structural rearrangements that had crept in during its creation. This kind of precise audit was previously impossible at this level of resolution for a decaploid donor, and it demonstrates that the platform works not just on pristine laboratory material but on the messy, recombined genomes that breeders actually handle.

One of the more intriguing findings came from immunostaining experiments focused on centromeres, the specialized structures that anchor chromosomes to the spindle apparatus during cell division. The team examined the localization of CENH3, the centromere-specific histone variant that epigenetically defines functional centromeres, and found that the Thinopyrum chromosomes maintain normal centromeric histone localization even in the wheat nuclear background. Equally notable, the alien chromosomes displayed distinct DNA methylation patterns compared with their wheat counterparts. These epigenetic signatures matter because centromere identity determines whether a chromosome segregates faithfully during meiosis; a chromosome whose centromere fails can be lost from a population. The observation suggests that Thinopyrum chromatin retains its functional integrity when placed inside wheat, good news for breeders hoping the donated chromosomes will behave stably across generations.

The group-6 chromosomes of Thinopyrum species are particularly prized because they harbor several superior resistance genes against devastating wheat diseases. To get at this genetic treasure, the researchers performed microdissection of the 6J^S^S chromosome, physically cutting it out of a metaphase spread with a fine glass needle under the microscope. The tiny quantity of DNA recovered was then amplified and sequenced, generating a chromosome-specific genomic resource. Such single-chromosome sequencing sidesteps the enormous challenge of assembling the full decaploid genome, in which ten homoeologous copies of many genes would confound standard assembly algorithms. Instead, the sequenced 6J^S^S DNA provides a clean dataset for comparative genome analysis, allowing researchers to align it against wheat and other Triticeae genomes to identify syntenic regions and candidate resistance genes.

The sequencing effort also opens the door to targeted functional gene discovery and marker development. With the 6J^S^S sequence in hand, scientists can design molecular markers that specifically track this chromosome arm through breeding populations, ensuring that resistance genes are retained while as much unwanted alien DNA as possible is discarded. The data have been deposited in the figshare repository, making the resource freely available to the international wheat community. This kind of open sharing matters in a field where breeding programs in different countries often work on parallel introgression lines and can waste years rediscovering what another group has already characterized.

To validate the specificity of Thinopyrum introgressions in various wheat derivatives, the team also examined seed storage protein profiles. Storage proteins, such as glutenins, are encoded by genes on particular chromosomes, and the presence of Thinopyrum-specific protein bands serves as an independent biochemical confirmation that alien chromatin is present and expressed. This orthogonal line of evidence complements the cytogenetic data, giving breeders two independent ways to verify their material. The approach echoes a long tradition in wheat genetics, where seed protein electrophoresis has been used since the era before molecular markers to confirm chromosome additions and substitutions.

The broader significance of this work lies in what it enables for global food security. Wheat faces relentless pressure from rusts, powdery mildew, fusarium head blight, salinity, and heat, and the genetic uniformity of modern cultivars leaves crops vulnerable to epidemics. Wild relatives such as Thinopyrum ponticum, which thrives in saline and alkaline soils and shrugs off multiple fungal diseases, represent a reservoir of resilience that conventional crossing within wheat cannot supply. Previous successes, including the stem rust resistance genes Sr26 and Sr61 and the powdery mildew gene Pm51, all trace back to Thinopyrum ponticum or its relatives, and each required laborious cytogenetic detective work to characterize. A standardized platform that makes such characterization routine could compress decades of trial and error into a few breeding cycles.

The study also contributes to basic science, offering a window into how chromosomes from a decaploid species coexist with the wheat genome. Questions about centromere specification, epigenetic compatibility, and chromosome rearrangement during wide hybridization are fundamental to understanding genome evolution in the Triticeae tribe, which includes wheat, barley, and rye. By providing a reference karyotype, chromosome-specific sequence data, and validated probes, the platform transforms Thinopyrum ponticum from a black box into a tractable experimental system. For breeders, the message is straightforward: the tools now exist to identify exactly which wild chromosome carries a desired trait, to track it precisely through crosses, and to deploy it in new varieties with confidence. As climate change intensifies both biotic and abiotic stresses on wheat production, that capability may prove to be one of the most valuable additions to the breeder’s arsenal in years.

Subject of Research: Molecular cytogenetic characterization of Thinopyrum ponticum chromatin for wheat improvement

Article Title: An integrated molecular cytogenetic platform enables precise characterization of Thinopyrum ponticum chromatin and its structural modifications in wheat background

Article References: Jiang, C., Wan, M., Wang, J., Ren, Y., Yang, E., Li, G., Zhang, P., & Yang, Z. (2026). An integrated molecular cytogenetic platform enables precise characterization of Thinopyrum ponticum chromatin and its structural modifications in wheat background. Theoretical and Applied Genetics, 139(10), Article 278. https://doi.org/10.1007/s00122-026-05392-6

Image Credits: AI Generated

DOI: 10.1007/s00122-026-05392-6

Keywords: Thinopyrum ponticum, wheat breeding, cytogenetics, ND-FISH, Oligo-FISH painting, chromosome microdissection, polyploidy, karyotype, disease resistance, introgression, centromere, CENH3