A haplotype-resolved female genome of the oilseed tree Vernicia montana locates its entire sex-determining region in a 77-kilobase window with only two genes at the edges.

The textbook account of sex determination is a master gene: a locus that appears, takes control of a developmental switch, and defines a sex chromosome around itself. A study in Horticulture Research on the woody oilseed tree Vernicia montana finds something harder to fit into that picture.

The species is dioecious — individual trees are male or female — with a ZW system in which females carry the heterogametic pair, as in birds and butterflies rather than mammals. The team assembled a chromosome-level, haplotype-resolved female genome using PacBio HiFi sequencing and Hi-C scaffolding, which means the two copies of each chromosome were reconstructed separately rather than merged into a consensus.

That separation is what makes the rest possible. A sex-determining region is by definition a place where the two haplotypes differ, and a collapsed assembly hides exactly the structure being looked for.

The work was carried out by researchers at Huanggang Normal University, Central South University of Forestry and Technology, and the Hubei Academy of Agricultural Sciences.

Seventy-seven kilobases

A coverage-based genome-wide association study across 178 natural individuals placed every significant sex-associated signal inside a single interval of about 77.5 kilobases on chromosome B02. The core W-specific sex-determining region spans roughly 61.4 kilobases.

That is a very small region, and the contrast with its surroundings is the striking part. The flanking sequence is more than 99 per cent identical between the two haplotypes, while the sex-determining region itself contains duplications, inversions, fragmented syntenic blocks and haplotype-specific sequence. PCR validation confirmed multiple female-specific segments within it.

A sharp boundary between near-identical flanks and a structurally scrambled core is the signature of suppressed recombination. Once recombination stops in a region — typically because an inversion prevents the chromosomes from pairing properly there — the sequence inside begins to accumulate rearrangements and lineage-specific DNA while everything outside continues to be homogenised by crossing over. The 99 per cent identity next door dates the suppression as recent.

Two genes, at the edges

The gene content is where the result becomes awkward for the master-gene model. Only two protein-coding genes sit at the boundaries of the region — VmBASS4.2 and VmCET2.2 — and each has a homologous allele on the other haplotype.

Neither is therefore a new gene. Both exist in two copies, one per haplotype, which rules out the scenario in which a female-specific gene appeared and took over the developmental decision.

The functional test went to VmBASS4.2, overexpressed in Arabidopsis thaliana. The result was reduced stigma receptivity and increased floral and silique abortion — effects on female reproductive function, which is the right direction for a gene implicated in sex determination in a ZW system.

The authors’ own characterisation is careful: they describe it as a dosage-sensitive reproductive regulator rather than a novel sex-determination gene. The distinction is that the gene’s effect depends on how much of it is made, so a structural change that alters its regulation could shift a developmental outcome without any change to the protein.

Structure instead of sequence

From that the authors propose a mechanism: sex determination here arises from inverted-repeat-mediated structural remodelling that alters the regulation of existing genes, rather than from a new master sex gene.

Inverted repeats — the same sequence present in both orientations — are the agent in that account, because they predispose a region to looping, inversion and duplication. A rearrangement of that kind can move a gene relative to its regulatory elements, change its copy number, or place it in a different chromatin context, all without altering what the gene encodes.

If that is right, the sex-determining region is better understood as a regulatory accident that became heritable than as the arrival of a switch. It is also a model that would be easy to miss with conventional sequencing, since the evidence for it is structural and a collapsed assembly discards structure.

The functional evidence is a step removed, and worth being clear about. VmBASS4.2 was tested by overexpression in Arabidopsis — a different species, a hermaphrodite, with no sex chromosomes at all. That a gene overexpressed in a model plant impairs female reproductive function is consistent with the proposed role and does not demonstrate what the gene does at native dosage in a Vernicia tree, which is the experiment the species’ long generation time makes hard.

The practical output

The applied result is simpler than the biology. The female-specific PCR markers identified in the sex-determining region could allow sex to be determined early in breeding.

For a dioecious tree that matters a great deal. Vernicia is grown for tung oil, and an orchard needs a controlled ratio of females to males — but a seedling cannot be sexed by looking at it, and waiting for a tree to flower means years of growing plants that may turn out to be the wrong sex. A PCR test on a leaf converts that wait into an afternoon.

Two gaps in the release are worth noting. It names no individual authors, and it contains no direct quotations from any researcher — the authors’ views appear only as paraphrase, so the interpretation reported here is the release’s summary of their argument rather than their own words.

The paper was published on 16 April 2026, which is some months before the release. The work was funded by the National Natural Science Foundation of China (32230073, 32401637 and 32171843), the Hubei Provincial Natural Science Foundation (2024AFB006), the Hubei Provincial Outstanding Young and Middle-aged Science and Technology Innovation Teams programme (T2023025) and the Postgraduate Scientific Research Innovation Project of Hunan Province (CX20200700). The authors declare no competing interests.

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Notes

1. “Haplotype-resolved genome assembly of female Vernicia montana elucidates its W-specific sex-determination region.” Horticulture Research, 2026. DOI: 10.1093/hr/uhag149. The release does not name the paper’s authors.
2. Nanjing Agricultural University The Academy of Science. “How inverted repeats shape sex determination in a woody tree.” EurekAlert!, 5 October 2026. https://www.eurekalert.org/news-releases/1146488.

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