How inverted repeats shape sex determination in a woody tree

How do plants decide to be male or female? In dioecious species, sex is often controlled by small genomic regions called sex-determining regions (SDRs). But in many plants, these regions remain difficult to resolve due to complex repetitive sequences and structural variations. Now, researchers have constructed a haplotype-resolved female genome of Vernicia montana — a dioecious woody tree with a ZW sex-determination system — and pinpointed a ~61.4-kb W-specific SDR. Their findings challenge the conventional view that sex determination requires a novel "master sex gene," instead pointing to structural remodeling that reshapes the regulatory landscape of existing genes.

Sex determination has evolved repeatedly across flowering plants, yet the molecular mechanisms remain poorly understood in many species. In dioecious plants, sex-determining regions (SDRs) often harbor key genes that suppress one sexual function while promoting the other. However, these regions are notoriously difficult to sequence: they are frequently enriched in repetitive elements, structural variants, and haplotype-specific insertions or inversions that obscure collinearity and complicate the identification of causal genes. Moreover, beyond the discovery of sex-linked markers, an important unresolved question is how structural remodeling within SDRs reshapes local regulatory landscapes and contributes to the stabilization of sex-specific developmental programs. Based on these challenges, there is a need for high-quality, haplotype-resolved female genomes to accurately pinpoint SDRs and understand their evolutionary dynamics.

A research team from Huanggang Normal University, Central South University of Forestry and Technology, and the Hubei Academy of Agricultural Sciences has published (DOI: 10.1093/hr/uhag149) their findings in Horticulture Research on April 16, 2026. Using PacBio HiFi sequencing and Hi-C scaffolding, the researchers constructed a chromosome-level, haplotype-resolved female genome assembly of Vernicia montana, a dioecious woody oilseed tree native to China. Their integrated population-scale coverage-based genome-wide association study of 178 natural individuals identified a highly localized sex-associated signal on ChrB02.

The team’s coverage-based GWAS revealed that all significant sex-associated signals were tightly clustered within a narrow ~77.5-kb interval on ChrB02. Fine-scale structural analysis further resolved a core W-specific SDR spanning approximately 61.4 kb. Strikingly, while the flanking regions remained highly conserved between the two haplotypes — with over 99% sequence identity — the SDR itself exhibited a complex mosaic of structural features: duplications, fragmented syntenic blocks, inversions, and multiple haplotype-specific sequences (NOTAL segments) that could not be aligned between haplotypes. PCR validation confirmed multiple female-specific segments within this structurally heterogeneous region.

Only two protein-coding genes were found at the SDR boundaries: VmBASS4.2 and VmCET2.2, each with a homologous allele on the other haplotype. Notably, VmBASS4.2 showed pronounced developmental dynamics and broad reproductive expression, and is positioned adjacent to major structural rearrangements within the SDR. When the team overexpressed VmBASS4.2 in Arabidopsis thaliana, the transgenic plants exhibited reduced stigma receptivity and increased floral and silique abortion. This suggested that VmBASS4.2 is a dosage-sensitive regulator of reproductive development — but not a novel sex-determination gene per se.

The authors said that their findings suggest sex determination in V. montana is not driven by the emergence of a novel sex-determining gene, but instead is associated with local inverted-repeat-mediated structural remodeling that reshapes the regulatory landscape of pre-existing boundary genes such as VmBASS4.2. They explained that this study proposes an inverted-repeat-mediated SDR evolution model, providing a framework linking local structural architecture to regulatory divergence during the early evolution of homomorphic sex chromosomes in plants.

This research has practical applications for forestry and breeding. Vernicia montana is widely cultivated as an ornamental tree and for high-quality tung oil production. The female-specific PCR markers validated in this study can be used for early sex identification, enabling breeders to select trees of desired sex without waiting years for flowering. More broadly, the inverted-repeat-mediated SDR evolution model proposed here offers a new conceptual framework for understanding how sex chromosomes evolve in plants — not through the invention of new genes, but through structural remodeling that repurposes existing ones. This challenges the conventional "master gene" paradigm and opens new avenues for studying sex determination in other dioecious species.

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References

DOI

10.1093/hr/uhag149

Original Source URL

https://doi.org/10.1093/hr/uhag149

Funding information

National Natural Science Foundation of China (Grant Nos. 32230073, 32401637, 32171843); Hubei Provincial Natural Science Foundation (Grant No. 2024AFB006); Hubei Provincial Outstanding Young and Middle-aged Science and Technology Innovation Teams (Grant No. T2023025); Postgraduate Scientific Research Innovation Project of Hunan Province (Project Nos. CX20200700).

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.