Telomere-to-telomere and gap-free reference genome assembly of the kiwifruit Actinidia chinensis

Abstract

Kiwifruit is an economically and nutritionally important fruit crop with extremely high contents of vitamin C. However, the previously released versions of kiwifruit genomes all have a mass of unanchored or missing regions. Here, we report a highly continuous and completely gap-free reference genome of Actinidia chinensis cv. ‘Hongyang’, named Hongyang v4.0, which is the first to achieve two de novo haploid-resolved haplotypes, HY4P and HY4A. HY4P and HY4A have a total length of 606.1 and 599.6 Mb, respectively, with almost the entire telomeres and centromeres assembled in each haplotype. In comparison with Hongyang v3.0, the integrity and contiguity of Hongyang v4.0 is markedly improved by filling all unclosed gaps and correcting some misoriented regions, resulting in ∼38.6–39.5 Mb extra sequences, which might affect 4263 and 4244 protein-coding genes in HY4P and HY4A, respectively. Furthermore, our gap-free genome assembly provides the first clue for inspecting the structure and function of centromeres. Globally, centromeric regions are characterized by higher-order repeats that mainly consist of a 153-bp conserved centromere-specific monomer (Ach-CEN153) with different copy numbers among chromosomes. Functional enrichment analysis of the genes located within centromeric regions demonstrates that chromosome centromeres may not only play physical roles for linking a pair of sister chromatids, but also have genetic features for participation in the regulation of cell division. The availability of the telomere-to-telomere and gap-free Hongyang v4.0 reference genome lays a solid foundation not only for illustrating genome structure and functional genomics studies but also for facilitating kiwifruit breeding and improvement.

Acknowledgements

This work was supported by funds from the National Natural Science Foundation of China (31972474, 90717110) and Hubei Natural Science Fund for Distinguished Young Scholars (2020CFA062).

Author contributions

Y. Liu and J.Y. conceived the ideas for this paper. Y. Liu, Y. Wu, and H.X. prepared the materials. J.Y., Q.C., Y. Z. Wang, Y. Lin, H.Q., Y. L. Wang, and S.Z. analyzed the data and drew the figures. X.W., S.C., and W.H. provided good guidance for data analysis. J.Y., Y.Y., and C.Y. designed the web server. J.Y., Y. Liu, and Y. Wang wrote the paper. L.Z. and S.W. edited the paper. All authors read and approved the final manuscript.

Data availability

The raw reads generated in this study have been deposited in the NCBI sequence read archive (SRA) with the accession number PRJNA869178 (http://www.ncbi.nlm.nih.gov/bioproject/PRJNA869178). The custom Perl scripts are all publicly available on GitHub (https://github.com/aaranyue/).

Conflict of interest

The authors declare that they have no competing interests for this research.

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