Characterization of the CsCENH3 protein and centromeric DNA profiles reveal the structures of centromeres in cucumber

Abstract

Centromeres in eukaryotes mediate the accurate segregation of chromosomes during cell division. They serve as essential functional units of chromosomes and play a core role in the process of genome evolution. Centromeres are composed of satellite repeats and highly repetitive centromeric retrotransposons (CRs), which vary greatly even among closely related species. Cucumber (Cucumis sativus ) is a globally cultivated and economically important vegetable and the only species in the Cucumis genus with seven pairs of chromosomes. Therefore, studying the centromeres of the Cucumis subgenus may yield valuable insights into its genome structure and evolution. Using chromatin immunoprecipitation (ChIP) techniques, we isolated centromeric DNA from cucumber reference line 9930. Our investigation into cucumber centromeres uncovered the centromeric satellite sequence, designated as CentCs, and the prevalence of Ty1/Copia long terminal repeat retrotransposons. In addition, active genes were identified in the CsCENH3 nucleosome regions with low transcription levels. To the best of our knowledge, this is the first time that characterization of centromeres has been achieved in cucumber. Meanwhile, our results on the distribution of CentCs and CsCRs in the subgenus Cucumis indicate that the content of centromeric repeats in the wild variants was significantly reduced compared with the cultivated cucumber. The results provide evidence for centromeric DNA amplification that occurred during the domestication process from wild to cultivated cucumber. Furthermore, these findings may offer new information for enhancing our understanding of phylogenetic relationships in the Cucumis genus.

Acknowledgements

This work was financially supported by National Key R&D Program of China (2021YFD1200200), the Province Key Research and Development Program (BE2021357), the National Natural Science Foundation of China (32272730), and the Fund for Seed Industry Revitalization Project (JBGS (2021)070) and the Project Funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions.

Author contributions

Q.F.L. and J.F.C. conceived and designed the experiments; Y.W., F.Z., and Y.G.L. performed the experiments; Y.W. conducted the bioinformatics analysis and wrote the manuscript. X.Q.Y., Y.H.W., X.B.F., and Q.Z.Z. revised the manuscript. All authors have read and agreed to the final version of the manuscript.

Data availability

The data used to support the study findings are included within the article. The CsCENH3-associated DNA and input DNA (genome DNA) datasets were submitted to the National Center for Biotechnology Information (NCBI) (accession number PRJNA1046282).

Conflict of interest

The authors declare no competing interests.

Supplementary data

Supplementary data are available at Horticulture Research online.

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