Whole-genome sequencing reveals the molecular basis of sex determination in the dioecious wild yam Dioscorea tokoro

Kudoh, A.; Natsume, S.; Sugihara, Y.; Kato, H.; Abe, A.; Oikawa, K.; Shimizu, M.; Itoh, K.; Tsujimura, M.; Takano, Y.; Sakai, T.; Adachi, H.; Ohta, A.; Ohtsu, M.; Ishizaki, T.; Terachi, T.; Terauchi, R.

doi:10.1101/2025.04.28.650915

bioRxiv · 10.1101/2025.04.28.650915

Whole-genome sequencing reveals the molecular basis of sex determination in the dioecious wild yam Dioscorea tokoro

Kudoh, A.·Natsume, S.·Sugihara, Y.·Kato, H.·Abe, A.·Oikawa, K.·Shimizu, M.·Itoh, K.·Tsujimura, M.·Takano, Y.·Sakai, T.·Adachi, H.·Ohta, A.·Ohtsu, M.·Ishizaki, T.·Terachi, T.·Terauchi, R.

View original source ↗Export metadata ↓

Abstract

Dioecious plants, which have distinct male and female individuals, constitute [~]5% of angiosperm species and have emerged frequently and independently from hermaphroditic ancestors. Although recent molecular studies of sex determination have started to reveal the diversity of the genetic systems underlying dioecy, research on the evolution of dioecy is limited, especially in monocots. Here, we describe the molecular basis of sex determination in the monocot Dioscorea tokoro, a dioecious wild yam endemic to East Asia. Chromosome-scale and haplotype-resolved genome assemblies and linkage analysis suggested that this plant has a male heterogametic sex determination (XY) system, with sex determination regions located on chromosome 3. Sequence read coverage analysis of the sex chromosomes revealed X- and Y-specific regions in putative pericentromeric chromosome regions. Within the Y-specific region, we identified two candidate genes that are likely involved in sex determination: BLH9, encoding a homeobox protein, and HSP90, encoding a molecular chaperone. BLH9 has similar functions to AtBLH9 in Arabidopsis thaliana. BLH9 is thought to suppress female organ development, whereas HSP90 might be required for pollen development. These results shed light on the complex evolution of dioecy in plants. Author summarySexual reproduction is a nearly universal, indispensable feature of evolution in eukaryotes. The molecular mechanisms underlying sex determination vary depending on the taxon. However, most information about this process was derived from studies of model organisms and/or domesticated species. To elucidate the diversity and evolution of sex determination, we need to expand the taxonomic breadth of these investigations. Here, we focused on the monocot genus Dioscorea, which contains species with multiple sex-determination systems, suggesting that frequent evolutionary transitions occur between the different sex-determination systems. We investigated the genetics of sex determination in Dioscorea tokoro, a dioecious wild yam endemic to East Asia. Whole-genome assembly and genetic analysis, along with transcriptome analysis, suggested that this species employs a male heterogametic sex determination (XY) system, with two Y-chromosome-specific genes that might be involved in male and female differentiation. These findings enhance our understanding of the complex evolution of dioecy.

Explore related subjects

plant biology Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Kudoh, A., Natsume, S., Sugihara, Y., Kato, H., Abe, A., Oikawa, K., Shimizu, M., Itoh, K., Tsujimura, M., Takano, Y., Sakai, T., Adachi, H., Ohta, A., Ohtsu, M., Ishizaki, T., Terachi, T., Terauchi, R.. 2025-04-30. Whole-genome sequencing reveals the molecular basis of sex determination in the dioecious wild yam Dioscorea tokoro. https://doi.org/10.1101/2025.04.28.650915

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Analysis of SpCas9 on- and off-target effects in high efficiency multiplex editing in Arabidopsis

RNA-guided nucleases (RGNs), such as Cas9 from Streptococcus pyogenes (SpCas9), are widely used for plant genome editing. Previous surveys for off-targeting, the modification of unintended targets with similarity to the intended target, indicate high specificity of SpCas9 in plant cells. However, off-targeting has not been assessed for efficiency-optimized editing systems combined with extensive multiplexing, which might increase the likelihood of cleavage at unintended sites. We therefore analyzed Arabidopsis thaliana lines that had been extensively mutagenized using zCas9i and up to 29 gRNAs addressing >45 target sites over several rounds of editing. Genomes were sequenced by short- and long-read technologies, and genome-wide variants were catalogued. Our pipeline for variant calling reliably detected RGN-induced mutations at on-targets. When excluding these on-target modifications, variants were detected in edited lines at frequencies similar to those previously reported for spontaneous mutations. In further analyses, we did not find any evidence for an origin of these variants from RGN activity. Our data are thus consistent with high specificity of SpCas9. In contrast, we detected genomic reorganization events upon editing at two complex loci, RPP1 and RPP7, encompassing multiple homologous genes, and also identified an allele by WGS that had escaped detection by amplicon sequencing. We conclude that, while off-targets may efficiently be avoided by selection of specific gRNAs, on-target modifications may be more extensive than intended, especially at complex loci and/or during multiplexing.

plant biology↗

bioRxiv2026

Seeding paradise: germination ecophysiology of Xyris paradisiaca Wand. (Xyridaceae), an endangered endemic species from Central Brazil

Seed ecophysiology is essential for understanding plant regeneration and developing effective conservation and ecological restoration strategies, yet knowledge remains scarce for most threatened Cerrado species. We characterised the germination niche, desiccation tolerance and storage behaviour of Xyris paradisiaca (Xyridaceae), an Endangered species endemic to Central Brazil, to assess whether its restricted distribution is associated with narrow germination requirements and to inform seed-based conservation. Germination was tested across light regimes, constant temperatures, decreasing water potentials and short-duration heat shocks, while thermal- and hydro-time models were used to quantify thermal and hydric thresholds. Seeds exhibited an absolute light requirement but broad abiotic tolerances. Germination remained >87% between 15 and 40 {degrees}C, with estimated cardinal temperatures of Tb = 8.94 {degrees}C, To = 33.13 {degrees}C and Tc = 45.53 {degrees}C. Germination remained similar to the control down to -0.6 MPa and exceeded 40% at -1.0 MPa, with a median base water potential of {Psi}b = -1.03 MPa. Germination also remained high after 1-min heat shocks up to 200 {degrees}C. Seeds were desiccation tolerant, with 100% germination after drying and a viability loss index of -0.04, and germination remained >90% after 24 months of ambient storage. Thus, the highly restricted distribution of X. paradisiaca is not driven by a narrow physiological germination niche. Its broad environmental tolerances, desiccation tolerance and favourable storage behaviour also highlight its unexplored potential for seed-based restoration, propagation and ex situ conservation.

plant biology↗

bioRxiv2026

Planted origin of shade trees: a robust determinant of cocoa yield among smallholder farmers in Cote d'Ivoire

CONTEXT: While the agroeconomic literature on the determinants of cocoa yield among West African smallholders is abundant, it remains dominated by descriptive studies or work conducted at an aggregated regional scale, leaving open the question of the role of shade-tree management practices at the scale of the individual plantation. OBJECTIVE: This study tests whether shade-tree management practices and the farmer's socio-demographic profile explain variation in cocoa yield, using a nationwide sample of 409 plantations covering, for the first time, the three major Ivorian production zones (loops) (98, 151 and 160 plantations for loops 1, 2 and 3, respectively). METHODS: A univariate screening of 27 variables, a mixed model with a random intercept by village, a production-function specification, LASSO variable selection, and a random forest were applied, all evaluated by 5-fold cross-validation. RESULTS AND CONCLUSIONS: The five approaches converge on a robust result: the deliberately planted origin of shade trees (as opposed to a residual or spontaneous origin) is the strongest and most stable determinant of yield, with a mean gap of 332 versus 183 kg/ha/year. This effect withstands four successive robustness checks: it remains significant after simultaneous adjustment for age, plantation size, production zone, technical extension, and farmer education; it is not driven by a handful of extreme plantations; it holds within each of the three production zones taken separately rather than in only one of them; and, taken in isolation, it retains a positive out-of-sample predictive power (cross-validated R2=8776; 0.05). A second group of robust determinants of more modest magnitude emerges for agricultural technical extension (ANADER/CNRA/SATMACI) and farmer education level; shade-tree alignment shows a signal in the same direction, consistent with recent independent work in Cote d'Ivoire, but becomes statistically marginal once adjusted for these other factors. The full multivariate model reaches a cross-validated R2 of around 0.07-0.08. SIGNIFICANCE: This signal, undetectable in an analysis restricted to loop 1 alone (n=98) for lack of statistical power, confirms the value of nationwide sampling for detecting modest but real agronomic determinants, and argues for integrating shade-tree origin into agroforestry extension programmes.

plant biology↗