Telomere-to-telomere genome assembly of melon (Cucumis melo L. var. inodorus) provides a high-quality reference for meta-QTL analysis of important traits

Abstract

Melon is an important horticultural crop with extensive diversity in many horticultural groups. To explore its genomic diversity, it is necessary to assemble more high-quality complete genomes from different melon accessions. Meanwhile, a large number of QTLs have been mapped in several studies. Integration of the published QTLs onto a complete genome can provide more accurate information for candidate gene cloning. To address these problems, a telomere-to-telomere (T2T) genome of the elite melon landrace Kuizilikjiz ( Cucumis melo L. var. inodorus) was de novo assembled and all the published QTLs were projected onto it in this study. The results showed that a high-quality Kuizilikjiz genome with the size of 379.2 Mb and N50 of 31.7 Mb was de novo assembled using the combination of short reads, PacBio high-fidelity long reads, Hi-C data, and a high-density genetic map. Each chromosome contained the centromere and telomeres at both ends. A large number of structural variations were observed between Kuizilikjiz and the other published genomes. A total of 1294 QTLs published in 67 studies were collected and projected onto the T2T genome. Several clustered, co-localized, and overlapped QTLs were determined. Furthermore, 20 stable meta-QTLs were identified, which significantly reduced the mapping intervals of the initial QTLs and greatly facilitated identification of the candidate genes. Collectively, the T2T genome assembly together with the numerous projected QTLs will not only broaden the high-quality genome resources but also provide valuable and abundant QTL information for cloning the genes controlling important traits in melon.

Acknowledgements

This work was supported by the Key R&D Project of Hubei Province (2021BBA101), the Fundamental Research Funds for the Central Universities (2662020YLPY024), the Key R&D Project of Xinjiang Academy of Agricultural Sciences (xjkcpy-2022006), the Tianshan Innovation Team (2022D14015), and the China Agriculture Research System (CARS-25).

Author contributions

Q.K. and X.Z. conceived the project. W.Y. and J.C. prepared the materials. M.W., Y.H., C.M., H.W., and Q.Z. performed the data analysis. M.W. drafted the manuscript. Q.K. revised the manuscript. All authors have read and approved the final version of the paper.

Data availability

All raw sequencing data generated in this project, including HiFi, Hi-C, and Illumina, were deposited at NCBI (https://www.ncbi. nlm.nih.gov/) under BioProject accession numbers PRJNA979338 and PRJNA952861. The assembly and annotation files were sub- mitted to the National Genomics Data Center (https://ngdc.cncb. ac.cn/). The accession number for the Kuizilikjiz genome assem- bly reported in this paper is SAMC2920780 under the project PRJCA018418.

Conflict of interest

The authors declare that they have no conflicts of interest.

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