One Centromere Gene, Two Genomic Homes: Fly Study Reveals Surprising Stability of Cenp-C

Centromeres are among the most essential structures in the cell, yet they remain among the least intuitively understood features of the eukaryotic genome. These specialized chromosomal regions serve as the attachment points for spindle fibers during cell division, ensuring that chromosomes are segregated accurately into daughter cells. A failure at the centromere is not a minor glitch; it can lead to chromosome loss, aneuploidy, and cell death. Given this absolutely central role, evolutionary biologists have long expected the genes and DNA elements underpinning centromere function to be under intense constraint. A new study of fruit flies in the montium group of the genus Drosophila adds a fascinating twist to that expectation, showing that a single copy of a key centromere gene, Cenp-C, has been retained across species even as its physical location within the genome has shifted between different syntenic contexts.

The protein Cenp-C, short for centromere protein C, is a core component of the kinetochore, the multiprotein machine that assembles on centromeric DNA and physically links chromosomes to the microtubules of the mitotic spindle. In many organisms, Cenp-C acts as a bridge: one part of the protein recognizes centromeric chromatin marked by the histone variant CenH3, also known as CID in Drosophila, while other regions recruit the outer kinetochore proteins that make direct contact with spindle microtubules. Because of this pivotal structural role, Cenp-C has frequently been the subject of studies on rapid centromere evolution. Curiously, centromere-associated proteins are known to evolve unusually quickly at the sequence level, a pattern often attributed to an evolutionary arms race associated with female meiosis, where competing centromeres can bias their own transmission. The new work examines how gene copy number and genomic position for Cenp-C have fared over the evolutionary history of a diverse species group.

The montium group is a species-rich radiation within the subgenus Drosophila, comprising dozens of described species distributed largely across Asia and Australasia. These flies occupy varied ecological niches and have diverged over millions of years, making them an excellent natural laboratory for questions of comparative genomics. Unlike the classic laboratory workhorse Drosophila melanogaster, whose genome has been scrutinized for decades, many montium group species have only recently come under genomic analysis. This means that fundamental questions about the number of copies a gene occupies, and where in the genome those copies sit relative to their neighbors, can still yield genuinely novel findings. Gene duplication and loss are common outcomes of genome evolution, and duplicated copies of genes involved in chromosome segregation have been documented in other lineages, raising the question of whether centromere genes in montium flies show similar dynamism.

To address this, the researchers searched genome assemblies from multiple montium group species for homologs of Cenp-C, using sequence similarity searches and comparative genomic methods to identify candidate genes and verify their identity. A central concern in such surveys is distinguishing genuine functional gene copies from pseudogenes or assembly artifacts. The team examined whether each detected copy retained the hallmarks of a functional gene, including an intact open reading frame and conservation of the protein domains known to be important for kinetochore function, such as the N-terminal region that interacts with centromeric chromatin and the C-terminal cupin-fold domain characteristic of Cenp-C proteins across eukaryotes. The result was unambiguous: rather than a expanding family of paralogs, each species harbors a single Cenp-C gene, a pattern of strict retention of one copy per genome.

That single-copy retention is itself informative. In principle, a gene as central to chromosome segregation might tolerate or even benefit from duplication, as has been observed for kinetochore-associated genes in some plants and animals where duplications have been implicated in adaptation. Alternatively, strong purifying selection combined with dosage sensitivity could explain why extra copies are eliminated or fail to persist: the stoichiometry of kinetochore components matters, and too much or too little Cenp-C protein can disrupt the precise architecture of the centromere. The finding that montium flies uniformly carry exactly one copy suggests that dosage constraints and functional integration into the kinetochore complex have kept this gene locked at a copy number of one across the group’s diversification, mirroring the single-copy status of Cenp-C found in Drosophila melanogaster and other well-studied relatives.

The most striking result, however, concerns genomic location. In comparative genomics, synteny refers to the conservation of blocks of genes on chromosomes across species, reflecting shared ancestry. When genes remain in the same syntenic neighborhood over deep time, it often signals functional or regulatory constraints on rearrangement. The study found that the solitary Cenp-C gene in montium species is not anchored in a single conserved position. Instead, different species carry their Cenp-C gene in different syntenic locations, meaning that the gene has moved relative to its neighboring genes at some point in the group’s evolutionary history. Such movement can occur through several mechanisms, including chromosomal inversions, transpositions, or translocations, followed by loss of the original copy, leaving the gene resident in a new genomic neighborhood.

Why would a gene move at all, given the strong constraints apparently acting on its copy number and sequence? One possibility is that the rearrangements were not driven by selection on Cenp-C itself but were incidental consequences of other chromosomal changes, with the gene simply being swept along and re-established in a new location. Chromosomal inversions are famously common in Drosophila evolution and often carry adaptive significance related to local adaptation or reproductive isolation, and a gene caught within an inverted segment can end up relocated without any direct selection acting on its position. Alternatively, local gene order may be more fluid in this genomic region than is typical, allowing the kind of positional shuffling observed. Distinguishing between these scenarios will require denser sampling of species and higher-quality genome assemblies, since rearrangement breakpoints can be difficult to place precisely with fragmented assemblies.

Beyond its intrinsic interest for centromere biology, the finding has practical implications for the growing number of researchers using montium group species as models. Comparative genomic analyses frequently rely on synteny to anchor gene predictions, order scaffolds, and infer orthology. Knowing that Cenp-C, a gene of considerable interest in chromosome biology, does not maintain a fixed syntenic position in this group is a useful caution against assuming positional conservation for every single-copy gene. It also highlights the broader point that gene copy number and gene position are under partly independent evolutionary pressures: one can be rigidly conserved while the other is labile. For centromere researchers, the study provides a natural experiment on the evolutionary flexibility of a gene that sits at the heart of the chromosome segregation machinery.

The work also speaks to a larger question in genome evolution: how do essential genes survive the constant churn of rearrangements, duplications, and transposable element activity that characterizes eukaryotic genomes? The montium group answer appears to be through a combination of strong selective maintenance of a single functional copy and tolerance of positional change. As genome assemblies for non-model Drosophila species continue to improve, fueled by long-read sequencing technologies and initiatives aimed at high-quality reference genomes across the tree of life, studies like this one will become increasingly feasible for many more gene families and species groups. The retention of a single Cenp-C gene in shifting syntenic locations is a vivid reminder that conservation in biology is rarely absolute: evolution preserves what function demands, while remaining remarkably creative about how and where that function is encoded in the genome. For one of the most conserved machines in the cell, the fly genome has found more than one place to call home.

The shifting position of Cenp-C in montium genomes also fits a broader pattern long recognized in centromere biology, sometimes called the centromere paradox. Centromeres perform the same essential task in every dividing cell, yet both their DNA sequences and their associated proteins evolve rapidly, often faster than the genomic average. In Drosophila, centromeres are defined not by a specific DNA sequence but by epigenetic marking with the histone variant CenH3, or CID, which means the underlying sequence can change substantially without abolishing function. That flexibility may extend to the genes that service centromeres, since what matters is the presence of the protein in the right cellular context rather than its residence at a particular chromosomal address.

It is worth noting that Drosophila centromeres are unusually compact and gene-poor compared with those of many other eukaryotes, so Cenp-C itself is not embedded within centromeric DNA but encoded elsewhere in the genome and recruited to the kinetochore through protein interactions. This separation of gene location from gene function may help explain why positional changes are tolerated. As long as the gene is expressed at the right time and level, its genomic neighborhood may be largely irrelevant to kinetochore assembly.

The study also illustrates how species groups beyond the standard model organism can sharpen evolutionary inference. Because montium species span a range of divergence times, patterns of copy number and synteny can be traced across multiple branches rather than inferred from a single reference genome. As more high-quality assemblies accumulate, similar surveys of other kinetochore genes could reveal whether single-copy retention with positional mobility is a general feature of the centromere apparatus, or a peculiarity of Cenp-C shaped by its dosage-sensitive role at the heart of chromosome segregation.

Subject of Research: Evolutionary retention of a single Cenp-C centromere gene across shifting syntenic locations in montium group Drosophila species

Article Title: Retention of a single Cenp-C gene in different syntenic locations in the montium group of Drosophila species

Article References: Soares, R. F., Chang, C.-H., Koerich, L. B., Malik, H. S., & Kuhn, G. C. S. (2026). Retention of a single Cenp-C gene in different syntenic locations in the montium group of Drosophila species. Heredity. https://doi.org/10.1038/s41437-026-00882-1

Image Credits: AI Generated

DOI: 10.1038/s41437-026-00882-1

Keywords: Cenp-C, centromere, kinetochore, Drosophila, montium group, synteny, comparative genomics, gene copy number, chromosomal rearrangement, chromosome segregation, genome evolution, purifying selection