The genome of melon (Cucumis melo L.)

Abstract

We report the genome sequence of melon, an important horticultural crop worldwide. We assembled 375 Mb of the double-haploid line DHL92, representing 83.3% of the estimated melon genome. We predicted 27,427 protein-coding genes, which we analyzed by reconstructing 22,218 phylogenetic trees, allowing mapping of the orthology and paralogy relationships of sequenced plant genomes. We observed the absence of recent whole-genome duplications in the melon lineage since the ancient eudicot triplication, and our data suggest that transposon amplification may in part explain the increased size of the melon genome compared with the close relative cucumber. A low number of nucleotide-binding site-leucine-rich repeat disease resistance genes were annotated, suggesting the existence of specific defense mechanisms in this species. The DHL92 genome was compared with that of its parental lines allowing the quantification of sequence variability in the species. The use of the genome sequence in future investigations will facilitate the understanding of evolution of cucurbits and the improvement of breeding strategies.

Fig. 1.

The DHL92 melon genome. (A) Physical map of the 12 melon pseudochromosomes, represented clockwise starting from center above. Blocks represent scaffolds anchored to the genetic map. Scaffolds without orientation are in green. The physical location of SNP markers from the SC × PS genetic map is represented. (B) Distribution of ncRNAs (orange). (C) Distribution of predicted genes (light green). (D) Distribution of transposable elements (blue). (E) Distribution of NBS–LRR R-genes (brown). (F) Melon genome duplications. Duplicated blocks are represented as dark-green connecting lines.

Fig. 2.

LTR retrotransposon insertion during melon genome evolution. All LTR retrotransposon families with 10 or more copies were considered. Combined number of insertions for all families is displayed. Red arrow indicates when the melon and cucumber lineages diverged.

Fig. 3.

Comparative genomics of 23 fully sequenced plant species where phylogeny is based on maximum-likelihood analysis of a concatenated alignment of 60 widespread single-copy proteins. Different background colors indicate taxonomic groupings within the species used to make the tree. Bars represent the total number of genes for each species (scale on the top). Bars are divided to indicate different types of homology relationships. Green: widespread genes that are found in at least 25 of the 28 species, including at least one out-group. Orange: widespread but plant-specific genes that are found in at least 20 of the 23 plant species. Gray: Species-specific genes with no (detectable) homologs in other species. Brown: genes without a clear pattern. The thin purple line under each bar represents the percentage of genes with a least one paralog in each species. The thin dark gray line represents the percentage of melon genes that have homologs in a given species.

Fig. 4.

Comparative analysis of the melon and cucumber genomes. (A) Alignment of melon (x = 12) and cucumber (x = 7) genomes. (B) Alignment of melon LG IV and LG VI with cucumber chromosome 3. Direct blocks are represented in red and inverted blocks in green. (C) Alignment of melon LG I with cucumber chromosome 7. Direct blocks are represented in red and inverted blocks in green. (D) Genome expansion in melon LG IV distal region of 8.5 Mb (Upper) compared with cucumber chromosome 3 distal region of 5 Mb (Lower). Blocks of the same color correspond to syntenic regions.