Abstract
In the past years, there has been a great effort to obtain genomic tools in melon (Cucumis melo L.). Advances in next-generation sequencing technologies have made possible to obtain de novo draft genome sequences for many plant species, including melon and other cucurbits. Since the publication of the cucumber, melon and watermelon genomes, the cucurbit scientific community has a collection of powerful tools that can be used to help understand important biological processes that are unique to these species. At the same time, genome sequences can be used to assist in breeding programs for the development of improved varieties. This chapter describes the collection of genetic and genomic tools that have been developed in melon until the publication of the melon genome, some of which have been centralized at the ICuGI webpage. The main features of the published melon genome, some data about comparative genomic studies among cucurbit species and some possible applications of the melon genome sequence are also discussed.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Al-Faifi S, Meyer J, Garcia-Mas J, Monforte A, Havey M (2008) Exploiting synteny in Cucumis for mapping of Psm: a unique locus controlling paternal mitochondrial sorting. Theor Appl Genet 117:523–529
Argyris JM, Ruiz-Herrera A, Madriz-Masis P, Sanseverino W, Morata J, Pujol M, Ramos-Onsins SE, Garcia-Mas J (2015) Use of targeted SNP selection for an improved anchoring of the melon (Cucumis melo L.) scaffold genome assembly. BMC Genomics 16:4
Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Report 9:208–218
Blanca J, Cañizares J, Roig C, Ziarsolo P, Nuez F, Pico B (2011a) Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae). BMC Genomics 12:104
Blanca JM, Cañizares J, Ziarsolo P, Esteras C, Mir G, Nuez F, Garcia-Mas J, Picó M (2011b) Melon transcriptome characterization: simple sequence repeats and single nucleotide polymorphisms discovery for high throughput genotyping across the species. Plant Genome 4:118–131
Blanca J, Esteras C, Ziarsolo P, Perez D, Fernandez-Pedrosa V, Collado C, Rodriguez de Pablos R, Ballester A, Roig C, Cañizares J, Picó B (2012) Transcriptome sequencing for SNP discovery across Cucumis melo. BMC Genomics 13:280
Blanca JM, Cañizares J, Ziarsolo P, Esteras C, Mir G, Nuez F, Garcia-Mas J, Picó M (2011c) Melon transcriptome characterization: simple sequence repeats and single nucleotide polymorphisms discovery for high throughput genotyping across the species. Plant Genome 4:118–131
Boualem A, Fergany M, Fernandez R, Troadec C, Martin A, Morin H, Sari M-A, Collin F, Flowers J, Pitrat M, Purugganan M, Dogimont C, Bendahmane A (2008) A conserved mutation in an ethylene biosynthesis enzyme leads to andromonoecy in melons. Science 321:836–838
Brotman Y, Normantovich M, Goldenberg Z, Zvirin Z, Kovalski I et al (2013) Dual resistance of melon to Fusarium oxysporum races 0 and 2 and to Papaya ring-spot virus is controlled by a pair of head-to-head-oriented NB-LRR genes of unusual architecture. Mol Plant 6:235–238
Clepet C, Joobeur T, Zheng Y, Jublot D, Huang M et al (2011) Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon. BMC Genomics 12:252
Corbacho J, Romojaro F, Pech J-C, Latche A, Gomez-Jimenez M (2013) Transcriptomic events involved in melon mature-fruit abscission comprise the sequential induction of cell-wall degrading genes coupled to a stimulation of endo and exocytosis. PLoS One 8:e58363
Dahmani-Mardas F, Troadec C, Boualem A, LĂ©vĂŞque S, Alsadon A, Aldoss A, Dogimont C, Bendahmane A (2010) Engineering melon plants with improved fruit shelf life using the TILLING approach. PLoS One 5:e15776
Dai N, Cohen S, Portnoy V, Tzuri G, Harel-Beja R et al (2011) Metabolism of soluble sugars in developing melon fruit: a global transcriptional view of the metabolic transition to sucrose accumulation. Plant Mol Biol 76:1–18
Danin-Poleg Y, Reis N, Tzuri G, Katzir N (2001) Development and characterization of microsatellite markers in Cucumis. Theor Appl Genet 102
Diaz A, Fergany M, Formisano G, Ziarsolo P, Blanca J et al (2011) A consensus linkage map for molecular markers and quantitative trait loci associated with economically important traits in melon (Cucumis melo L.). BMC Plant Biol 11:111
Dogimont C, Chovelon V, Tual S, Boissot N, Rittener V, Giovinazzo V, Bendahmane A (2008) Molecular diversity at the Vat/Pm-W resistance locus in melon. In: Pitat M (ed) IXth EUCARPIA meeting on genetics and breeding of Cucurbitaceae. Avignon, Institut National de la Recherche Agronomique
Ellis J, Dodds P, Pryor T (2000) Structure, function and evolution of plant disease resistance genes. Curr Opin Plant Biol 3:278–284
Esteras C, Gomez P, Monforte A, Blanca J, Vicente-Dolera N, Roig C, Nuez F, Pico B (2012) High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping. BMC Genomics 13:80
Esteras C, Formisano G, Roig C, Diaz A, Blanca J, Garcia-Mas J, Gomez-Guillamon M, Lopez-Sese A, Lazaro A, Monforte A, Pico B (2013) SNP genotyping in melons: genetic variation, population structure, and linkage disequilibrium. Theor Appl Genet 126:1285–1303
Garcia-Mas J, Benjak A, Sanseverino W, Bourgeois M, Mir G et al (2012) The genome of melon (Cucumis melo L.). Proc Natl Acad Sci U S A 109:11872–11877
Gonda I, Lev S, Bar E, Sikron N, Portnoy V, Davidovich-Rikanati R, Burger J, Schaffer A, Tadmor Y, Giovannonni J, Huang M, Fei Z, Katzir N, Fait A, Lewinsohn E (2013) Catabolism of l-methionine in the formation of sulfur and other volatiles in melon (Cucumis melo L.) fruit. Plant J 74:458–472
Gonzalez V, Benjak A, Henaff E, Mir G, Casacuberta J, Garcia-Mas J, Puigdomenech P (2010a) Sequencing of 6.7 Mb of the melon genome using a BAC pooling strategy. BMC Plant Biol 10:246
Gonzalez V, Rodriguez-Moreno L, Centeno E, Benjak A, Garcia-Mas J, Puigdomenech P, Aranda M (2010b) Genome-wide BAC-end sequencing of Cucumis melo using two BAC libraries. BMC Genomics 11:618
Gonzalez M, Xu M, Esteras C, Roig C, Monforte A, Troadec C, Pujol M, Nuez F, Bendahmane A, Garcia-Mas J, Pico B (2011) Towards a TILLING platform for functional genomics in Piel de Sapo melons. BMC Res Notes 4:289
Gonzalez-Ibeas D, Blanca J, Donaire L, Saladié M, Mascarell-Creus A, Cano-Delgado A, Garcia-Mas J, Llave C, Aranda M (2011) Analysis of the melon (Cucumis melo) small RNAome by high-throughput pyrosequencing. BMC Genomics 12:393
Gonzalez-Ibeas D, Cañizares J, Aranda M (2012) Microarray analysis shows that recessive resistance to Watermelon mosaic virus in melon is associated with the induction of defense response genes. Mol Plant Microbe Interact 25:107–118
Gonzalo M, Oliver M, Garcia-Mas J, Monfort A, Dolcet-Sanjuan R, Katzir N, Arus P, Monforte A (2005) Simple-sequence repeat markers used in merging linkage maps of melon (Cucumis melo L.). Theor Appl Genet 110:802–811
Guo S, Zhang J, Sun H, Salse J, Lucas W et al (2012) The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat Genet 45:51–58
Huang S, Li R, Zhang Z, Li L, Gu X et al (2009) The genome of the cucumber, Cucumis sativus L. Nat Genet 41:1275–1281
Hufford MB, Xu X, vanHeerwaarden J, Pyhäjärvi T, Chia J-M et al (2012) Comparative population genomics of maize domestication and improvement. Nat Genet 44:808–811
Kang H, Weng Y, Yang Y, Zhang Z, Zhang S, Mao Z, Cheng G, Gu X, Huang S, Xie B (2011) Fine genetic mapping localizes cucumber scab resistance gene Ccu into an R gene cluster. Theor Appl Genet 122:795–803
Li D, Cuevas H, Yang L, Li Y, Garcia-Mas J, Zalapa J, Staub J, Luan F, Reddy U, He X, Gong Z, Weng Y (2011a) Syntenic relationships between cucumber (Cucumis sativus L.) and melon (C. melo L.) chromosomes as revealed by comparative genetic mapping. BMC Genomics 12:396
Li Z, Zhang Z, Yan P, Huang S, Fei Z, Lin K (2011b) RNA-Seq improves annotation of protein-coding genes in the cucumber genome. BMC Genomics 12:540
Lin X, Zhang Y, Kuang H, Chen J (2013) Frequent loss of lineages and deficient duplications accounted for low copy number of disease resistance genes in Cucurbitaceae. BMC Genomics 14:335
Luo M, Wang Y, Frisch D, Joobeur T, Wing R, Dean R (2001) Melon bacterial artificial chromosome (BAC) library construction using improved methods and identification of clones linked to the locus conferring resistance to melon Fusarium wilt (Fom-2). Genome 44:154–162
Martin A, Troadec C, Boualem A, Rajab M, Fernandez R, Morin H, Pitrat M, Dogimont C, Bendahmane A (2009) A transposon-induced epigenetic change leads to sex determination in melon. Nature 461:1135–1138
Mascarell-Creus A, Cañizares J, Vilarrasa-Blasi J, Mora-Garcia S, Blanca J et al (2009) An oligo-based microarray offers novel transcriptomic approaches for the analysis of pathogen resistance and fruit quality traits in melon (Cucumis melo L.). BMC Genomics 10:467
Meyer J, Deleu W, Garcia-Mas J, Havey M (2008) Construction of a fosmid library of cucumber (Cucumis sativus) and comparative analyses of the eIF4E and eIF(iso)4E regions from cucumber and melon (Cucumis melo). Mol Genet Genomics 279:473–480
Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A et al (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452:991–996
Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin Y-C et al (2013) The Norway spruce genome sequence and conifer genome evolution. Nature 497:579–584
Paterson A, Freeling M, Tang H, Wang X (2010) Insights from the comparison of plant genome sequences. Annu Rev Plant Biol 61:349–372
Pech JC, Bouzayen M, Latche A (2008) Climacteric fruit ripening: ethylene-dependent and independent regulation of ripening pathways in melon fruit. Plant Sci 175:114–120
Pitrat M (2008) Melon (Cucumis melo L.). In: Prohens J, Nuez F (eds) Handbook of crop breeding vol I: vegetables. Springer, New York, pp 283–315
Portnoy V, Diber A, Pollock S, Karchi H, Lev S, Tzuri G, Harel-Beja R, Forer R, Portnoy V, Lewinsohn E, Tadmor Y, Burger J, Schaffer A, Katzir N (2011) Use of non-normalized, non-amplified cDNA for 454-based RNA sequencing of fleshy melon fruit. Plant Genome 4:36–46
Rodriguez-Moreno L, Gonzalez V, Benjak A, Marti M, Puigdomenech P, Aranda M, Garcia-Mas J (2011) 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 12:424
Roig C, Fita A, Rios G, Hammond J, Nuez F, Pico B (2012) Root transcriptional responses of two melon genotypes with contrasting resistance to Monosporascus cannonballus (Pollack et Uecker) infection. BMC Genomics 13:601
Sanseverino W, HĂ©naff E, Vives C, Pinosio S, Burgos-Paz W, Morgante M, Ramos-Onsins SE, Garcia-Mas J, Casacuberta JM (2015) Transposon insertion, structural variations and SNPs contribute to the evolution of the melon genome. Mol Biol Evol (in press)
Schnable P, Ware D, Fulton R, Stein J, Wei F et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115
Sebastian P, Schaefer H, Telford I, Renner S (2010) 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 107:14269–14273
Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26:1135–1145
Tadmor Y, Katzir N, Meir A, Yaniv-Yaakov A, Sa’ar U, Baumkoler F, Lavee T, Lewinsohn E, Schaffer A, Burger J (2007) Induced mutagenesis to augment the natural genetic variability of melon (Cucumis melo L.). Isr J Plant Sci 55:159–169
Tadmor Y, Burger J, Yaakov I, Feder A, Libhaber S, Portnoy V, Meir A, Tzuri G, Sa’ar U, Rogachev I, Aharoni A, Abeliovich H, Schaffer A, Lewinsohn E, Katzir N (2010) Genetics of flavonoid, carotenoid, and chlorophyll pigments in melon fruit rinds. J Agric Food Chem 58:10722–10728
Tanaka K, Akashi Y, Fukunaga K, Yamamoto T, Aierken Y, Nishida H, Long CL, Yoshino H, Sato Y-I, Kato K (2013) Diversification and genetic differentiation of cultivated melon inferred from sequence polymorphism in the chloroplast genome. Breed Sci 63:183–196
The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815
The French-Italian Public Consortium for Grapevine Genome Characterization (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463–467
The International Barley Genome Sequencing Consortium (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature 491:711–716
The International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793–800
Till B, Reynolds S, Greene E, Codomo C, Enns L, Johnson J, Burtner C, Odden A, Young K, Taylor N, Henikoff J, Comai L, Henikoff S (2003) Large-scale discovery of induced point mutations with high-throughput TILLING. Genome Res 13:524–530
Turnbull C, Lopez-Cobollo R (2013) Heavy traffic in the fast lane: long-distance signalling by macromolecules. New Phytol 198:33–51
Tuskan G, Difazio S, Jansson S, Bohlmann J, Grigoriev I et al (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313:1596–1604
van Leeuwen H, Monfort A, Zhang H-B, Puigdomenech P (2003) Identification and characterisation of a melon genomic region containing a resistance gene cluster from a constructed BAC library. Microcolinearity between Cucumis melo and Arabidopsis thaliana. Plant Mol Biol 51:703–718
Vegas J, Garcia-Mas J, Monforte A (2013) Interaction between QTLs induces an advance in ethylene biosynthesis during melon fruit ripening. Theor Appl Genet 126:1531–1544
Wan H, Yuan W, Bo K, Shen J, Pang X, Chen J (2013) Genome-wide analysis of NBS-encoding disease resistance genes in Cucumis sativus and phylogenetic study of NBS-encoding genes in Cucurbitaceae crops. BMC Genomics 14:109
WĂłycicki R, Witkowicz J, Gawronski P, Dabrowska J, Lomsadze A et al (2011) The genome sequence of the North-European cucumber (Cucumis sativus L.) unravels evolutionary adaptation mechanisms in plants. PLoS One 6(7):e22728
Yang L, Li D, Li Y, Gu X, Huang S, Garcia-Mas J, Weng Y (2013) A 1,681-locus consensus genetic map of cultivated cucumber including 67 NB-LRR resistance gene homolog and ten gene loci. BMC Plant Biol 13:53
Zhang B, Tolstikov V, Turnbull C, Hicks L, Fiehn O (2010) Divergent metabolome and proteome suggest functional independence of dual phloem transport systems in cucurbits. Proc Natl Acad Sci U S A 107:13532–13537
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Garcia-Mas, J., Puigdomènech, P. (2016). Melon Genome Sequence. In: Ezura, H., Ariizumi, T., Garcia-Mas, J., Rose, J. (eds) Functional Genomics and Biotechnology in Solanaceae and Cucurbitaceae Crops. Biotechnology in Agriculture and Forestry, vol 70. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-48535-4_2
Download citation
DOI: https://doi.org/10.1007/978-3-662-48535-4_2
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-662-48533-0
Online ISBN: 978-3-662-48535-4
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)