ARS | Publication request: The genome of melon (Cucumis melo L.). Genome amplification in the absence of recent duplication in an old widely cultivated species

Submitted to: Proceedings of the National Academy of Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 8, 2012
Publication Date: July 2, 2012
Citation: Garcia-Mas, J., Benjak, A., Sanserverino, W., Bourgeois, M., Mir, G., Gonzalez, V.M., Henaff, E., Camara, L., Cozzuto, L., Lowy, E., Alioto, T., Capella-Gutierrez, S., Blanca, J., Canizares, J., Ziarsolo, P., Gonzalez-Ibeas, D., Rodriguez-Moreno, L., Droege, M., Du, L., Alvarez-Tejado, M., Lorente-Galos, B., Mele, M., Yang, L., Weng, Y., Navarro, A., Marques-Bonet, T., Aranda, M.A., Nuez, F., Pico, B., Gabaldon, T., Roma, G., Guigo, R., Casacuberta, J.M., Arus, P., Puigdomenech, P. 2012. The genome of melon (Cucumis melo L.). Genome amplification in the absence of recent duplication in an old widely cultivated species . Proceedings of the National Academy of Sciences. 109(29):11872-11877.

Interpretive Summary: Using a whole genome shotgun approach based on 454 pyrosequencing and BAC-end Sanger sequences we obtained the genome sequence of the melon (Cucumis melo L.) double haploid line DHL92. We assembled 375 megabase pairs (Mb) representing 83.3 % of the estimated melon genome. The sequence was further refined after correction of homopolymer regions with Illumina reads. A major part of the assembly (87.5 %) was anchored to the melon genetic map giving 12 pseudochromosomes. At least 19.7 % of the assembled genome codes for transposons, and our data suggest that transposon amplification, after the separation between melon and the close relative cucumber (C. sativus L.), may in part explain the increased size of the melon genome. We predicted 27,427 protein-coding genes, which we analyzed from a phylogenomic perspective by reconstructing 22,218 phylogenetic trees. This allowed mapping of the orthology and paralogy relationships of sequenced plant genomes and investigation of patterns of recent and past gene family duplications. Our results indicate the absence of recent whole genome duplications in the melon lineage. Another particular feature of melon and other cucurbit genomes is the low number of predicted NBS-LRR disease resistance genes, suggesting the existence of alternative defense mechanisms in these species. By comparison of the melon (2n = 2x =24) and cucumber (2n = 2x =14) genomes, the high synteny between the closely related species was characterized. Finally, the DHL92 genome was compared with deep genome resequencing of its two parental lines, PI 161375 and ‘Piel de sapo’, which belong to the agrestis and melo subspecies respectively, demonstrating recombination events in DHL92 and allowing global quantification of the degree of sequence variability in the species, 1 SNP every 176 bp. The genome sequence presented here is a valuable tool for the improvement of breeding strategies in melon.

Technical Abstract: We report the genome sequence of melon (Cucumis melo L.), 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 when compared to the close relative cucumber. A low number of NBS-LRR 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 these and future investigations will facilitate the understanding of evolution of cucurbits and the improvement of breeding strategies.