Chromosome-specific oligo-painting provides insights into the cytogenetic basis of karyotypic stasis in paleo-allotetraploid Cucurbita

Abstract

Post-polyploid karyotype evolution represents a crucial cytological mechanism contributing to angiosperm diversification and speciation. Many polyploids show extensive karyotypic reshuffling relative to their pre-ancestors. However, karyotypic stasis is gaining popularity as an alternative evolutionary pathway following polyploidization, whose underlying cytological mechanisms remain poorly understood. Here, we successfully developed a set of enhanced oligo-painting (EOP) probes specific to 20 chromosomes of Cucurbita (2n = 40), a paleo-polyploid with very small chromosomes and rich genetic diversity. The probes generated robust fluorescence in situ hybridization (FISH) signals across six Cucurbita and one sister outgroup species. Cross-species EOP results confirmed that Cucurbita genomes originated from a paleo-allotetraploid and maintained remarkably conserved chromosomal synteny without chromosome reshuffling, indicating karyotypic structural stasis during post-polyploid diploidization. Repositioning and amplification/elimination of rDNA loci (45S and 5S) across species caused significant morphological variations on seven out of 20 chromosomes. Six predicted centromeric monomers showed dramatic variations in localization and copy number along the phylogenetic relationships, highlighting the rapid turnover of centromere-associated sequences. In conclusion, our results suggest that Cucurbita genomes maintain karyotypic structural stasis during post-polyploid diploidization, with karyotype evolution instead being driven by rDNA repositioning and centromere turnover events, which constitute the cytogenetic basis for species divergence in Cucurbita. This finding highlights the more refined cytological evolutionary mechanisms underlying karyotypic stasis, providing new insights into post-polyploid karyotype evolution.

Acknowledgements

We thank the Bioinformatics Center at Nanjing Agricultural University for data analysis and Prof. Shuping Qu from Northeast Agricultural University for providing Cucurbita species seeds. This work was supported by the National Natural Science Foundation of China (32202488; 31430075), the Natural Science Foundation of Jiangsu Province (BK20221007), the National Key R&D Program of China (2021YFD1200200), the China Postdoctoral Science Foundation (2021M701744), Jiangsu Funding Program for Excellent Postdoctoral Talent (2022ZB348), and the Priority Academic Program Development of Jiangsu Higher Education Institutions.

Author contributions

Q.Z., Q.L., and J.C. conceived the research. Q.Z. designed and performed the experiments. Y.B. and Y.W. participated in the synthesis of oligo probes. C.C., and X.Y. contributed to Bioinformatic support. Q.Z. and J.C. wrote the manuscript. All authors read and approved the final manuscript.

Data availability

All data are available in the manuscript or supplementary materials.

Conflict of interest statement

The authors declare no conflicts of interest.

Supplementary data

Supplementary data is available at Horticulture Research online.

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