The Melon Genome

  • Josep Casacuberta
  • Pere Puigdomènech
  • Jordi Garcia-MasEmail author
Part of the Plant Genetics and Genomics: Crops and Models book series (PGG, volume 20)


The availability of next-generation sequencing technologies in the past years has allowed unprecedented access to draft genome sequences for the main crops and plants. These genome sequences offer new possibilities for studying genome evolution, for understanding the biological processes controlling important traits and for improving plant breeding. Among them, the genome of melon (Cucumis melo L.), one of the main cucurbit crops, was released in 2012. Since the publication of the reference genome of the double haploid line DHL92 v3.5, the genome assembly and annotation have been improved in new genome versions. The melon genome has been useful for performing several comparative analysis with other cucurbit genomes, for analysing the genome structure and extant variability and for the isolation and characterization of several important genes.


Genome sequence Melon Next-generation sequence Genome structure Resequencing 

Literature Cited

  1. Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000;408:796–815.CrossRefGoogle Scholar
  2. Argyris JM, Pujol M, Martín-Hernández AM, Garcia-Mas J. Combined use of genetic and genomics resources to understand virus resistance and fruit quality traits in melon. Physiol Plant. 2015a;155:4–11.CrossRefPubMedGoogle Scholar
  3. Argyris JM, Ruiz-Herrera A, Madriz-Masis P, Sanseverino W, Morata J, Pujol M, et al. Use of targeted SNP selection for an improved anchoring of the melon (Cucumis melo L.) scaffold genome assembly. BMC Genomics. 2015b;16:4.CrossRefPubMedPubMedCentralGoogle Scholar
  4. Arumuganathan K, Earle ED. Nuclear DNA content of some important plant species. Plant Mol Biol Report. 1991;9:208–18.CrossRefGoogle Scholar
  5. Blanca JM, Canizares J, Ziarsolo P, Esteras C, Mir G, Nuez F, et al. Melon transcriptome characterization: simple sequence repeats and single nucleotide polymorphisms discovery for high throughput genotyping across the species. Plant Genome. 2011;4:118–31.CrossRefGoogle Scholar
  6. Clepet C, Joobeur T, Zheng Y, Jublot D, Huang M, Truniger V, et al. Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon. BMC Genomics. 2011;12:252.CrossRefPubMedPubMedCentralGoogle Scholar
  7. Cohen S, Itkin M, Yeselson Y, Tzuri G, Portnoy V, Harel-Beja R, et al. The PH gene determines fruit acidity and contributes to the evolution of sweet melons. Nat Commun. 2014;5:4026.CrossRefPubMedGoogle Scholar
  8. Diaz A, Fergany M, Formisano G, Ziarsolo P, Blanca J, Fei Z, et al. A consensus linkage map for molecular markers and quantitative trait loci associated with economically important traits in melon (Cucumis melo L.). BMC Plant Biol. 2011;11:111.CrossRefPubMedPubMedCentralGoogle Scholar
  9. Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, et al. Real-time DNA sequencing from single polymerase molecules. Science. 2009;323:133–8.CrossRefPubMedGoogle Scholar
  10. Esteras C, Formisano G, Roig C, Diaz A, Blanca J, Garcia-Mas J, et al. SNP genotyping in melons: genetic variation, population structure, and linkage disequilibrium. Theor Appl Genet. 2013;126:1285–303.CrossRefPubMedGoogle Scholar
  11. Feder A, Burger J, Gao S, Lewinsohn E, Katzir N, Schaffer AA, et al. A Kelch domain-containing F-box coding gene negatively regulates flavonoid accumulation in muskmelon. Plant Physiol. 2015;169:1714–26.PubMedPubMedCentralGoogle Scholar
  12. Garcia-Mas J, Benjak A, Sanseverino W, Bourgeois M, Mir G, Gonzalez VM, et al. The genome of melon (Cucumis melo L.). Proc Natl Acad Sci U S A. 2012;109:11872–7.CrossRefPubMedPubMedCentralGoogle Scholar
  13. González V, Aventín N, Centeno E, Puigdomènech P. Interspecific and intraspecific gene variability in a 1-Mb region containing the highest density of NBS-LRR genes found in the melon genome. BMC Genomics. 2014;15:1131.CrossRefPubMedPubMedCentralGoogle Scholar
  14. Gonzalez VM, Rodriguez-Moreno L, Centeno E, Benjak A, Garcia-Mas J, Puigdomenech P, et al. Genome-wide BAC-end sequencing of Cucumis melo using two BAC libraries. BMC Genomics. 2010;11:618.CrossRefPubMedPubMedCentralGoogle Scholar
  15. Gonzalo MJ, Oliver M, Garcia-Mas J, Monfort A, Dolcet-Sanjuan R, Katzir N, et al. Simple-sequence repeat markers used in merging linkage maps of melon (Cucumis melo L.). Theor Appl Genet. 2005;110:802–11.CrossRefPubMedGoogle Scholar
  16. Hénaff E, Zapata L, Casacuberta JM, Ossowski S. Jitterbug: somatic and germline transposon insertion detection at single-nucleotide resolution. BMC Genomics. 2015;16:768.CrossRefPubMedPubMedCentralGoogle Scholar
  17. Huang S, Li R, Zhang Z, Li L, Gu X, Fan W, et al. The genome of the cucumber, Cucumis sativus L. Nat Genet. 2009;41:1275–81.CrossRefPubMedGoogle Scholar
  18. International Rice Genome Sequencing Project. The map-based sequence of the rice genome. Nature. 2005;436:793–800.CrossRefGoogle Scholar
  19. Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature. 2007;449:463–7.CrossRefPubMedGoogle Scholar
  20. Li D, Cuevas HE, Yang L, Li Y, Garcia-Mas J, Zalapa J, et al. Syntenic relationships between cucumber (Cucumis sativus L.) and melon (C. melo L.) chromosomes as revealed by comparative genetic mapping. BMC Genomics. 2011;12:396.CrossRefPubMedPubMedCentralGoogle Scholar
  21. Michael TP, Jackson S. The first 50 plant genomes. Plant Genome. 2013;6.Google Scholar
  22. Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, et al. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature. 2008;452:991–6.CrossRefPubMedPubMedCentralGoogle Scholar
  23. Pitrat M. Melon (Cucumis melo L.). In: Prohens J, Nuez F, editors. Handbook of crop breeding Vol I: vegetables. New York: Springer; 2008. p. 283–315.CrossRefGoogle Scholar
  24. Proost S, Van Bel M, Vaneechoutte D, Van de Peer Y, Inzé D, Mueller-Roeber B, et al. PLAZA 3.0: an access point for plant comparative genomics. Nucleic Acids Res. 2015;43:81.CrossRefGoogle Scholar
  25. Qi J, Liu X, Shen D, Miao H, Xie B, Li X, et al. A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nat Genet. 2013;45:1510–5.CrossRefPubMedGoogle Scholar
  26. Rodriguez-Moreno L, Gonzalez VM, Benjak A, Marti MC, Puigdomenech P, Aranda MA, et al. Determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of DNA having a nuclear origin. BMC Genomics. 2011;12:424.CrossRefPubMedPubMedCentralGoogle Scholar
  27. Sanseverino W, Hénaff E, Vives C, Pinosio S, Burgos-Paz W, Morgante M, et al. Transposon insertions, structural variations, and SNPs contribute to the evolution of the melon genome. Mol Biol Evol. 2015;32:2760–74.CrossRefPubMedGoogle Scholar
  28. Sebastian P, Schaefer H, Telford I, Renner SS. Cucumber (Cucumis sativus) and melon (C. melo) have numerous wild relatives in Asia and Australia, and the sister species of melon is from Australia. Proc Natl Acad Sci U S A. 2010;107:14269–73.CrossRefPubMedPubMedCentralGoogle Scholar
  29. Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science. 2006;313:1596–604.CrossRefPubMedGoogle Scholar
  30. Tzuri G, Zhou X, Chayut N, Yuan H, Portnoy V, Meir A, et al. A ‘golden’ SNP in CmOr governs the fruit flesh color of melon (Cucumis melo). Plant J. 2015;82:267–79.CrossRefPubMedGoogle Scholar
  31. Yang L, Koo DH, Li D, Zhang T, Jiang J, Luan F, et al. Next-generation sequencing, FISH mapping and synteny-based modeling reveal mechanisms of decreasing dysploidy in Cucumis. Plant J. 2014;77:16–30.CrossRefPubMedGoogle Scholar
  32. Zhou S, Kile A, Bechner M, Place M, Kvikstad E, Deng W, et al. Single-molecule approach to bacterial genomic comparisons via optical mapping. J Bacteriol. 2004;186:7773–82.CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Josep Casacuberta
    • 1
  • Pere Puigdomènech
    • 1
  • Jordi Garcia-Mas
    • 1
    • 2
    Email author
  1. 1.Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UBBarcelonaSpain
  2. 2.Institut de Recerca i Tecnologia Agroalimentàries (IRTA)BarcelonaSpain

Personalised recommendations