Melon genome sequence

A consortium of nine research groups, coordinated by CRAG scientists (CSIC Professor Pere Puigdomenech and IRTA Researcher Jordi García-Mas), reported the genome sequence of melon (Cucumis melo), an important horticultural crop worldwide. Melon belongs to the cucurbitaceae family, which contains other important crops as cucumber (Cucumis sativus), watermelon (Citrulus lanatus) and zucchini (Cucurbita pepo).

375 Mb of the double-haploid melon line DHL92 were assembled in 1,599 scaffolds, and 27,427 protein-coding genes were predicted from the assembly. 87% of the genome assembly was anchored to 12 pseudochromosomes by using a SNP genetic map. The phylome of melon was also obtained: 22,218 phylogenetic trees containing melon genes and ortologous and paralogous sequences from 22 plant species. An exhaustive analysis of the genome sequence did not show recent whole-genome duplications in the melon lineage since the known ancient eudicot gamma triplication. Data also suggested that transposon amplification around 2 My ago may explain the increased size of the melon genome (450 Mb) compared with the close relative cucumber (350 Mb). The genomes of cucumber (2n=2x=14) and melon (2n=2x=24) were compared, suggesting that chromosome fusions followed by rearrangements happened in the cucumber lineage from an x=12 ancestor to yield the current x=7 cucumber. The DHL92 genome was also compared with that of its parental lines, the Piel de sapo line T111 and the Korean accession PI 161375, allowing a preliminary quantification of sequence variability in the species.

Cucurbit species are of high commercial interest, especially in the Mediterranean, Asian, and African countries. Diseases that affect them, such as the mosaic virus in the case of cucumber or fungi can cause important losses. The availability of the genome sequence will allow the improvement of melon breeding strategies, by accelerating the discovery of the genes related with agronomically important traits such as fruit quality and disease resistance. The use of the genome sequence in future investigations will also facilitate the understanding of the evolution of the cucurbit family.

The research was performed in the framework of the MELONOMICS project, a public-private initiative that was launched in 2009. The genome sequence of melon was the first example of the sequencing of a eukaryote genome performed and coordinated in Spain.


Melon Genome
Melon genome sequence

Reference work

Garcia-Mas J., Benjak A., Sanseverino W., Bourgeois M., Mir G., Gonzalez V.M., Henaff E., Camara F., Cozzuto L., Lowy E., Alioto T., Capella-Gutierrez S., Blancae J., Canizares J., Ziarsolo P., Gonzalez-Ibeas D., Rodriguez-Moreno L., Droege M., Du L., Alvarez-Tejado M., Lorente-Galdos B., Melec M., Yang L., Weng Y., Navarro A., Marques-Bonet T., Aranda M.A., Nuez F., Pico B., Gabaldon T., Roma G., Guigoc R., Casacuberta J.M., Arus P., Puigdomenech P.
The genome of melon (Cucumis melo L.)
(2012) Proceedings of the National Academy of Sciences of the United States of America, vol. 109 (29), pp. 11872-11877