Transcriptome profiling of Cucumis melo fruit development and ripening

Abstract

Hami melon (Cucumis melo) is the most important melon crop grown in the north-western provinces of China. In order to elucidate the genetic and molecular basis of developmental changes related to size, flesh, sugar and sour content, we performed a transcriptome profiling of its fruit development. Over 155 000 000 clean reads were mapped to MELONOMICS genome, yielding a total of 23 299 expressed genes. Of these, 554 genes were specifically expressed in flowers, and 3260 genes in fruit flesh tissues. The 7892 differentially expressed genes (DEGs) were related to fruit development and mediated diverse metabolic processes and pathways; 83 DEGs and 13 DEGs were possibly associated with sucrose and citric acid accumulation, respectively. The quantitative real-time PCR results showed that six out of eight selected candidate genes displayed expression trends similar to our DEGs. This study profiled the gene expression related to different growing stages of flower and fruit at the whole transcriptome level to provide an insight into the regulatory mechanism underlying Hami melon fruit development.

References

[1] Erickson DL, Smith BD, Clarke AC, Sandweiss DH, Tuross N . An Asian origin for a 10,000-year-old domesticated plant in the Americas. Proc Natl Acad Sci USA 2005; 102: 18315-18320.

[2] Pech J-C, Bouzayen M, Latché A . Climacteric fruit ripening: ethylene-dependent and independent regulation of ripening pathways in melon fruit. Plant Sci 2008; 175: 114-120.

[3] Boualem A, Fergany M, Fernandez R, Troadec C, Martin A, Morin H et al. A conserved mutation in an ethylene biosynthesis enzyme leads to andromonoecy in melons. Science 2008; 321: 836-838.

[4] Martin A, Troadec C, Boualem A, Rajab M, Fernandez R, Morin H et al. A transposon-induced epigenetic change leads to sex determination in melon. Nature 2009; 461: 1135-1138.

[5] Zhang B, Tolstikov V, Turnbull C, Hicks LM, Fiehn O . Divergent metabolome and proteome suggest functional independence of dual phloem transport systems in cucurbits. Proc Natl Acad Sci USA 2010; 107: 13532-13537.

[6] Dahmani-Mardas F, Troadec C, Boualem A, Lévêque S, Alsadon AA, Aldoss AA et al. Engineering melon plants with improved fruit shelf life using the TILLING approach. PLoS One 2010; 5: e15776.

[7] Garcia-Mas J, Benjak A, Sanseverino W, Bourgeois M, Mir G, González VM et al. The genome of melon (Cucumis melo L.) . Proc Natl Acad Sci USA 2012; 109: 11872-11877.

[8] Corbacho J, Romojaro F, Pech J-C, Latché A, Gomez-Jimenez MC . 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 2013; 8: e58363.

[9] Blanca J, Cañizares J, Ziarsolo P, Nuez F, Picó B . Melon transcriptome characterization. SSRs and SNPs discovery for high throughput genotyping across the species. Plant Genome 2011; 4: 118-131.

[10] Obando-Ulloa JM, Eduardo I, Monforte AJ, Fernández-Trujillo JP . Identification of QTLs related to sugar and organic acid composition in melon using near-isogenic lines. Sci Hortic 2009; 121: 425-433.

[11] Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL . TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 2013; 14: R36.

[12] Robinson MD, McCarthy DJ, Smyth GK . edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010; 26: 139-140.

[13] Götz S, Garcia-Gómez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ et al. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 2008; 36: 3420-3435.

[14] Livak KJ, Schmittgen TD . Analysis of relative gene expression data using real-time quantitative PCR and the 2^−ΔΔCT method . Methods 2001; 25: 402-408.

[15] Dai N, Cohen S, Portnoy V, Tzuri G, Harel-Beja R, Pompan-Lotan M et al. Metabolism of soluble sugars in developing melon fruit: a global transcriptional view of the metabolic transition to sucrose accumulation. Plant Mol Biol 2011; 76: 1-18.

[16] Vendrell M, Palomer X . Hormonal control of fruit ripening in climacteric fruits. Acta Hortic 1998; 463: 325-334.

[17] Zhong S, Fei Z, Chen Y-R et al. Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nat Biotechnol 2013; 31: 154-159.

[18] Yamaguchi M, Hughes D, Yabumoto K, Jennings W . Quality of cantaloupe muskmelons: variability and attributes. Sci Hortic 1977; 6: 59-70.

[19] Burger Y, Schaffer AA . The contribution of sucrose metabolism enzymes to sucrose accumulation in Cucumis melo . J Am Soc Hortic Sci 2007; 132: 704-712.

[20] Hubbard NL, Huber SC, Pharr DM . Sucrose phosphate synthase and acid invertase as determinants of sucrose concentration in developing muskmelon (Cucumis melo L.) fruits . Plant Physiol 1989; 91: 1527-1534.

[21] Rosa JT . Changes in composition during ripening and storage of melons: University of California 1928.

[22] Schaffer AA, Aloni B, Fogelman E . Sucrose metabolism and accumulation in developing fruit of Cucumis . Phytochemistry 1987; 26: 1883-1887.

[23] Schaffer AA, Pharr DM, Madore MA. Cucurbits. In: Zamski E, Schaffer AA (eds.). Photoassimilate distribution in plants and crops. New York: CRC Press, 1996; 729-757.

[24] Lester GE, Arias LS, Gomez-Lim M . Muskmelon fruit soluble acid invertase and sucrose phosphate synthase activity and polypeptide profiles during growth and maturation. J Am Soc Hortic Sci 2001; 126: 33-36.

[25] Carmi N, Zhang G, Petreikov M, Gao Z, Eyal Y, Granot D et al. Cloning and functional expression of alkaline α-galactosidase from melon fruit: similarity to plant SIP proteins uncovers a novel family of plant glycosyl hydrolases. Plant J 2003; 33: 97-106.

[26] Dai N, Petreikov M, Portnoy V, Katzir N, Pharr DM, Schaffer AA . Cloning and expression analysis of a UDP-galactose/glucose pyrophosphorylase from melon fruit provides evidence for the major metabolic pathway of galactose metabolism in raffinose oligosaccharide metabolizing plants. Plant Physiol 2006; 142: 294-304.

[27] Gao Z, Schaffer AA . A novel alkaline α-galactosidase from melon fruit with a substrate preference for raffinose. Plant Physiol 1999; 119: 979-988.

[28] Gao Z, Petreikov M, Burger Y, Shen S, Schaffer AA . Stachyose to sucrose metabolism in sweet melon (Cucumis melo) fruit mesocarp during the sucrose accumulation stage . In: Lebeda Paris (ed). Progress in cucurbit genetics and breeding research. Olomouc: Palacký University, 2004; 471-475.

[29] Keller F, Pharr DM . Metabolism of carbohydrates in sinks and sources: galactosyl-sucrose oligosaccharides. In: Zamski E, Schaffer AA (eds.). Photoassimilate Distribution in Plants and Crops: Source-Sink Relationships. New York: CRC Press, 1996; 157-183.

[30] Chrost B, Schmitz K . Changes in soluble sugar and activity of α-galactosidases and acid invertase during muskmelon (Cucumis melo L.) fruit development . J Plant Physiol 1997; 151: 41-50.

[31] Mitchell DE, Gadus MV, Madore MA . Patterns of assimilate production and translocation in muskmelon (Cucumis melo L.) I. Diurnal patterns . Plant Physiol 1992; 99: 959-965.

[32] Cohen S, Tzuri G, Harel-Beja R, Itkin M, Portnoy V, Sa’ar U et al. Co-mapping studies of QTLs for fruit acidity and candidate genes of organic acid metabolism and proton transport in sweet melon (Cucumis melo L.) . Theor Appl Genet 2012; 125: 343-353.

[33] Burger Y, Paris HS, Cohen R et al. Genetic diversity of Cucumis melo . Hortic Rev 2009; 36: 165-198.

[34] Danin-Poleg Y, Tadmor Y, Tzuri G, Reis N, Hirschberg J, Katzir N . Construction of a genetic map of melon with molecular markers and horticultural traits, and localization of genes associated with ZYMV resistance. Euphytica 2002; 125: 373-384.

[35] Kubicki B. Inheritance of some characters in muskmelons (Cucumis melo) . Genet Polonica 1962; 3: 265-274.

[36] Burger Y, Sa'ar U, Distelfeld A, Katzir N, Tadmor Y, Lewinsohn E et al. Development of sweet melon (Cucumis melo) genotypes combining high sucrose and organic acid content . J Am Soc Hortic Sci 2003; 128: 537-540.

[37] Tang M, Bie Z-l, Wu M-z, Yi H-p, Feng J-x . Changes in organic acids and acid metabolism enzymes in melon fruit during development. Sci Hortic 2010; 123: 360-365.

[38] Moing A, Rothan C, Svanella L et al. Role of phosphoenolpyruvate carboxylase in organic acid accumulation during peach fruit development. Physiol Plantarum 2000; 108: 1-10.

[39] Saradhuldhat P, Paull RE . Pineapple organic acid metabolism and accumulation during fruit development. Sci Hortic 2007; 112: 297-303.

[40] Sadka A, Dahan E, Cohen L, Marsh KB . Aconitase activity and expression during the development of lemon fruit. Physiol Plantarum 2000; 108: 255-262.

[41] Sadka A, Dahan E, Or E, Cohen L . NADP⁺-isocitrate dehydrogenase gene expression and isozyme activity during citrus fruit development . Plant Sci 2000; 158: 173-181.

[42] Sadka A, Dahan E, Or E, Roose ML, Marsh KB, Cohen L . Comparative analysis of mitochondrial citrate synthase gene structure, transcript level and enzymatic activity in acidless and acid-containing Citrus varieties . Funct Plant Biol 2001; 28: 383-390.

[43] Taureilles-Saurel C, Romieu CG, Robin J-P, Flanzy C . Grape (Vitis vinifera L.) malate dehydrogenase. II. Characterization of the major mitochondrial and cytosolic isoforms and their role in ripening . Am J Enol Viticult 1995; 46: 29-36.

[44] Iannetta PP, Escobar NM, Ross HA, Souleyre EJ, Hancock RD, Witte CP et al. Identification, cloning and expression analysis of strawberry (Fragaria × ananassa) mitochondrial citrate synthase and mitochondrial malate dehydrogenase . Physiol Plantarum 2004; 121: 15-26.

[45] Wang X-Y, Wang P, Qi Y-P, Zhou CP, Yang LT, Liao XY et al. Effects of granulation on organic acid metabolism and its relation to mineral elements in Citrus grandis juice sacs . Food Chem 2014; 145: 984-990.

[46] Diakou P, Svanella L, Raymond P, Gaudillere JP, Moing A . Phosphoenolpyruvate carboxylase during grape berry development: protein level, enzyme activity and regulation. Australian Journal of Plant Physiology 2000; 27: 221-229.