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.

Figure 1

Overview of the Kuizilikjiz genome assembly. A Hi-C interaction map for each chromosomal pseudo-molecule at 100 kb resolution. The interaction intensity color bar represents the heat map intensity scale. B Collinearity between the genetic map and genome assembly. Scatter plots represent the positions of SNPs in the Kuizilikjiz genome assembly and genetic map constructed using Kuizilikjiz as the female parent. C Features of the assembly. The blue shadow at the top represents the coverage density of HiFi reads mapped onto the assembled genome. The rectangles in the middle represent the contigs anchored onto each chromosome. The orange shadow at the bottom represents the coverage density of paired-end reads mapped onto the assembled genome. The red vertical bars at the ends of each chromosome represent the telomeres. The red horizontal bars on the contigs represent centromeres. The purple horizontal bars under the contigs represent the locations of 45S rDNA. The green horizontal bars under the contigs represent the locations of 5S rDNA. The black triangles under the contigs represent the locations of unclosed gaps.

Figure 2

Circos plot of Kuizilikjiz genome annotation. Quantitative tracks (labeled a–g) are aggregated in a 500-kb window. (a) This track represents the chromosome. The highlighted rectangular blocks represent the centromeres. (b) This track represents the density of annotated genes. (c) This track represents the density of repeat sequences. (d) This track represents the density of Gypsy. (e) This track represents the density of Copia. (f) This track represents the density of transposable elements. (g) This track represents the locations of transcription factors. Photograph in the center shows the fruit of Kuizilikjiz.

Figure 3

Comparative genomics analysis. A Syntenic analysis among the Kuizilikjiz genome and the other five published melon genomes. B Numbers and locations of variants detected between Kuizilikjiz and the other five published melon genomes, comprising Charmono, DHL92, Harukei-3, IVF77, and Payzawat. C Neighbor-joining phylogenetic tree of Kuizilikjiz genome and the other five published melon genomes with 1000 bootstrap replicates based on SNP data. D Percentages of genes lifted from Kuizilikjiz to the other five published melon genomes. All mapped genes include the valid and invalid mapped genes. E Flower plots of the unmapped (left), invalid (middle) and valid (right) mapped genes between the Kuizilikjiz genome and the other five published melon genomes.

Figure 4

Meta-QTL analysis based on the Kuizilikjiz genome. A Numbers and classifications of published QTLs in melon. B Numbers and locations of projected and filtered QTLs on the Kuizilikjiz chromosomes. C Distribution of LOD scores for all published QTLs in melon. D Distribution of PVE (%) for all published QTLs in melon. E Locations of the 20 meta-QTLs and their initial QTLs in the Kuizilikjiz genome.