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The evolution and formation of centromeric repeats analysis in Vitis vinifera

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Abstract

Main conclusion

Six grape centromere-specific markers for cytogenetics were mined by combining genetic and immunological assays, and the possible evolution mechanism of centromeric repeats was analyzed.

Abstract

Centromeric histone proteins are functionally conserved; however, centromeric repetitive DNA sequences may represent considerable diversity in related species. Therefore, studying the characteristics and structure of grape centromere repeat sequences contributes to a deeper understanding of the evolutionary process of grape plants, including their origin and mechanisms of polyploidization. Plant centromeric regions are mainly composed of repetitive sequences, including SatDNA and transposable elements (TE). In this research, the characterization of centromere sequences in the whole genome of grapevine (Vitis vinifera L.) has been conducted. Five centromeric tandem repeat sequences (Vv1, Vv2, Vv5, Vv6, and Vv8) and one long terminal repeat (LTR) sequence Vv24 were isolated. These sequences had different centromeric distributions, which indicates that grape centromeric sequences may undergo rapid evolution. The existence of extrachromosomal circular DNA (eccDNA) and gene expression in CenH3 subdomain region may provide various potential mechanisms for the generation of new centromeric regions.

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Data availability

The datasets generated during and/or analyzed during the current study are available in the NCBI repository with accession number of PRJNA897873 and PRJNA907798.

Abbreviations

CenH3:

Centromeric specific histone H3 variant

eccDNA:

Extrachromosomal circular DNA

FPKM:

Fragments per kilobase of exon model per million mapped fragments

LTR:

Long terminal repeat

SatDNA:

Satellite DNA

TE:

Transposable element

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Acknowledgements

This study was supported by the National Natural Science Foundation of China (32272647), Jiangsu Agricultural Industry Technology System (JATS [2022] 457), and Priority Academic Program Development of Jiangsu Higher Education Institutions (RAPD). We are grateful to Zengjun Qi (the State Key Laboratory of Crop Genetic & Germplasm Enhancement) for FISH analysis instruction.

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Authors and Affiliations

  1. Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing, China

    Dan Pei, Xue Yu, Weihong Fu & Jinggui Fang

  2. Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, Nanjing, 210095, China

    Jinggui Fang

  3. College of Life Sciences, Zaozhuang University, Zaozhuang, 277000, China

    Xuhui Ma

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  1. Dan Pei
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  2. Xue Yu
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DP, WHF, and XY conducted the experiments and analyzed data. DP wrote the manuscript. JGF designed and coordinated this study. XHM revised the manuscript. All authors have read and approved the final manuscript.

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Correspondence to Jinggui Fang.

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Pei, D., Yu, X., Fu, W. et al. The evolution and formation of centromeric repeats analysis in Vitis vinifera. Planta 259, 99 (2024). https://doi.org/10.1007/s00425-024-04374-6

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