Cucumber's genetic core: new insights into centromere structures
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Alignment of CENH3 homologs and localization of CsCENH3 protein and ChIPed DNA on cucumber chromosomes. a Multiple alignment of CsCENH3 (C. sativus), NtCENH3 (Nicotiana tabacum), AtCENH3 (A. thaliana), OsCENH3 (Oryza sativa) and ZmCENH3 (Zea mays). The protein structure is shown below the sequence. The peptide sequence used to generate anti-CsCENH3 is highlighted in a red box. b–g Immunostaining localization of CsCENH3. Interphase nuclei and metaphase chromosomes (blue) were stained with 4′,6-diamidino-2-phenylindole (DAPI). Immunofluorescence signals (c and d, f and g) are visible within the nucleus (d) and in the centromeric regions of the chromosomes (g). h–j FISH signal of DNA precipitated by ChIP using anti-CsCENH3 antibody. Somatic metaphase chromosomes (h and j) that were hybridized to CsCENH3 ChIPed DNA probes. FISH signals (i and j) are visible in the centromeres (j). Scale bars: 10 μm.
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The study provides significant insights into cucumber centromeres by identifying key centromeric satellite sequences and retrotransposons. Researchers found notable differences in centromeric DNA between wild and cultivated cucumbers, highlighting the impact of domestication. Using chromatin immunoprecipitation (ChIP) and sequencing, the study mapped CsCENH3-binding domains and discovered active genes with low transcription in these regions. This comprehensive characterization of cucumber centromeres advances our understanding of genome evolution and provides valuable information for improving genetic maps and breeding programs, potentially enhancing cucumber cultivation and genetic research.
Centromeres are crucial for chromosome segregation during cell division and consist of repetitive DNA sequences. Their structure and evolution vary widely among species, making them a significant research focus. In cucumbers, understanding these variations can provide valuable insights into genome organization and evolution. Due to these complexities and the lack of comprehensive studies in this area, a detailed investigation of cucumber centromeres is necessary to enhance our knowledge of their function and evolutionary dynamics, ultimately contributing to advancements in plant genetics and breeding strategies.
Researchers from the State Key Laboratory of Crop Genetics and Germplasm Enhancement at Nanjing Agricultural University published a study (DOI: 10.1093/hr/uhae127) on May 7, 2024, in Horticulture Research. The study investigates the centromeres of cucumber (Cucumis sativus) using chromatin immunoprecipitation (ChIP) techniques, uncovering centromeric satellite sequences and the prevalence of Ty1/Copia retrotransposons.
The study identified key components of cucumber centromeres, including the centromeric satellite sequence CentCs and Ty1/Copia long terminal repeat retrotransposons. Using ChIP sequencing, researchers mapped CsCENH3-binding domains and uncovered significant differences in centromeric DNA between wild and cultivated cucumbers. They found that the domestication process amplified centromeric DNA, as evidenced by higher CentCs content in cultivated varieties. Additionally, active genes with low transcription levels were identified within CsCENH3 nucleosome regions, marking the first comprehensive characterization of cucumber centromeres. These findings provide new insights into the evolutionary mechanisms of centromeres in the Cucumis genus and enhance our understanding of genome structure. The research also has practical implications, offering valuable information for improving genetic maps and breeding programs, which could lead to the development of superior cucumber varieties with desirable traits.
Dr. Qunfeng Lou, the corresponding author, stated, "This study marks a significant advancement in our understanding of cucumber centromeres. The identification of centromeric sequences and their variations between wild and cultivated cucumbers provides valuable insights into genome evolution and the domestication process. These findings have the potential to inform future research and breeding strategies."
The findings from this study have several important implications. The detailed characterization of cucumber centromeres enhances our understanding of genome structure and evolution, which is critical for genetic mapping and breeding programs. Additionally, the identification of centromeric sequences can aid in the development of new genetic tools and resources, facilitating the improvement of cucumber varieties with desirable traits. This research also contributes to the broader field of plant genomics, providing a framework for studying centromeres in other species.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhae127
Funding information
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.
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, 2022. 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.
Journal
Horticulture Research
Subject of Research
Not applicable
Article Title
Characterization of the CsCENH3 protein and centromeric DNA profiles reveal the structures of centromeres in cucumber
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