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

Author
item GARCIA-MAS, JORDI - University Of Barcelona
item BENJAK, ANDREJ - University Of Barcelona
item SANSERVERINO, WALTER - University Of Barcelona
item BOURGEOIS, MICHAEL - University Of Barcelona
item MIR, GISELA - University Of Barcelona
item GONZALEZ, VICTOR - University Of Barcelona
item HENAFF, ELIZABETH - University Of Barcelona
item CAMARA, LUCA - Center For Genomic Regulation (CRG)
item COZZUTO, LUCA - Center For Genomic Regulation (CRG)
item LOWY, ERNESTO - Center For Genomic Regulation (CRG)
item ALIOTO, TYLER - University Of Barcelona
item CAPELLA-GUTIERREZ, SALVADOR - Center For Genomic Regulation (CRG)
item BLANCA, JOSE - University Of Valencia
item CANIZARES, JOAQUIN - University Of Valencia
item ZIARSOLO, PELLO - University Of Valencia
item GONZALEZ-IBEAS, DANIEL - Centro De Edafologia Y Biologia Aplicada Del Segura (CEBAS)
item RODRIGUEZ-MORENO, LUIS - Centro De Edafologia Y Biologia Aplicada Del Segura (CEBAS)
item DROEGE, MARCUS - Roche Diagnostics
item DU, LEI - Roche Diagnostics
item ALVAREZ-TEJADO, MIGUEL - Roche Applied Science
item LORENTE-GALOS, BELEN - Pompeu Fabra University
item MELE, MARTA - Center For Genomic Regulation (CRG)
item YANG, LUMING - University Of Wisconsin
item Weng, Yiqun
item NAVARRO, ARCADI - Pompeu Fabra University
item MARQUES-BONET, TOMAS - Pompeu Fabra University
item ARANDA, MIGUEL - Centro De Edafologia Y Biologia Aplicada Del Segura (CEBAS)
item NUEZ, FERNANDO - University Of Valencia
item PICO, BELEN - University Of Valencia
item GABALDON, TONI - Center For Genomic Regulation (CRG)
item ROMA, GUGLIELMO - Center For Genomic Regulation (CRG)
item GUIGO, RODERIC - Center For Genomic Regulation (CRG)
item CASACUBERTA, JOSEP - University Of Barcelona
item ARUS, PERE - University Of Barcelona
item PUIGDOMENECH, PERE - University Of Barcelona

Submitted to: Proceedings of the National Academy of Sciences (PNAS)
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/8/2012
Publication Date: 7/2/2012
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.