Phenotypic characters and identification CYPs (Cyclophilin) gene in Cucumis melo L. cv. Gama Melon Parfum
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Abstract. Wibowo WA, Maryanto SD, Daryono BS. 2021. Phenotypic characters and identification CYPs (Cyclophilin) gene in Cucumis melo L. cv. Gama Melon Parfum. Biodiversitas 22: 3007-3014. Cucumis melo L. cv. Gama Melon Parfum is a new cultivar with a very strong fragrance as its main character. As a new cultivar with unique characters, it is necessary to characterize phenotype and molecular related to the fragrant aroma. The research aimed to study the phenotypic of the fruit of C. melo cv. Gama Melon Parfum (F3) and to identify the CYPs gene as one of the genes that act in encoding volatile compounds. Analysis of qualitative characters was based on International Plant Genetic Resources Institute (IPGRI) and Plant Variety Protection (PVP), phenotypic characters in melons observed by abiding the Rules for Registration of Varieties from the Indonesian Minister of Agriculture Decree No. 700/Kpts/OT.320/D/12/2011, while analysis of quantitative characters was using the ANOVA methods and software PKBT-STAT-2. The methods of molecular characterization included RNA isolation, cDNA synthesis used Reverse Transcriptase-PCR, amplification of DNA target used PCR, visualization of DNA target used electrophoresis, and DNA sequencing. Analysis of the in silico approach was carried out on the CuGenDB Melon database. Analysis of protein sequences and classification was obtained from InterPro. Phylogeny analysis using MEGA-X Software. The results were 18 qualitative characters and 11 quantitative characters were stable and uniform, whereas the molecular characterization of the genes was predicted Cyclophilin with peptidylprolyl isomerase (PPIase) activity and located in chromosome 1 (17059021-17058899).
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References
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Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol 16: 111-120. https://doi.org/10.1007/BF01731581.
Kumari S, Roy S, Singh P, Singla-Pareek S, Pareek A. 2013. Cyclophilins: Proteins in search of function. Journal Plant Signaling & Behavior 8: 25-32. https://doi.org/10.4161/psb.22734.
Latrasse D, Rodriguez-Granadoz NY, Veluchamy A, Mariappan KG, Bevilacqua C, Crapart N, Camps C, Sommard V, Raynaud C, Dogimont C, Boualem A, Benhamed M, Bendahmane A. 2017. The quest for epigenetic regulation underlying unisexual flower development in Cucumis melo. Epigenetics Chromatin. 10: 22. https://doi.org/10.1186/s13072-017-0132-6.
Lee J, Kim SS. 2010. An overview of cyclophilins in human cancers. J. Int. Med. Res 38: 1561-1574. https://doi.org/10.1177/147323001003800501.
Nagy PD, Wang RY, Pogany J, Harfen A, Makinen K. 2011. The dependence of viral RNA replication on co-opted host factors. Virology 411: 374-382. https://doi.org/ 10.1038/nrmicro2692.
Nutzmann HW, Huang A, Osbourn A. 2016. Plant metabolic clusters – from genetics to genomics. New Phytologist 211: 771–789. https://doi.org/10.1111/nph.13981.
Paris HS, Amar Z, Lev E. 2012. Medieval emergence of sweet melons, Cucumis melo (Cucurbitaceae). Ann. Bot. 110: 23 - 33. https://doi.org/10.1093/aob/mcs098.
Portnoy V, Benyamini Y, Bar E, Harel-Beja R, Gepstein S, Giovanni JJ, Schaffer AA, Burger J, Tadmor Y, Lewinsohn E, Katzir N. 2008. The molecular and biochemical basis for varietal variation in sesquiterpene content in melon (Cucumis melo L.) rinds. Plant Molecular Biology 66: 647–661. https://doi.org/10.1007/s11103-008-9296-6.
Ruggieri V, Alexiou KG, Morata J, Argyris J, Pujol M, Yano R, Nonaka S, Ezura H, Latrasse D, Boualem A, Benhamed M, Bendahmane A, Cigliano RA, Sanseverion W, Puigdomenech P, Casacuberta JM, Garcia-Mas J. 2018. An improved assembly and annotation of the melon (Cucumis melo L.) reference genome. Scientific Reports 8088: 1–9. https://doi.org/10.1038/s41598-018-26416-2.
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Sarabia LE, Lopez MF, Obregon-Molina G, Cano-Ramirez C, Sanchez-Martinez G, Zuniga G. 2019. The differential expression of mevalonate pathway genes in the gut of the bark beetle Dendroctonus rhizophagus (Curculionidae?: Scolytinae) is unrelated to the de novo synthesis of terpenoid pheromones. International Journal of Molecular Sciences 20: 4011. https://doi.org/10.3390/ijms20164011
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Shaw PE. 2002. Peptidyl?prolyl isomerases: a new twist to transcription. EMBO Rep. 3: 521-526. https://doi.org/10.1093/embo-reports/kvf118
Srivathsan A, Meier R. 2012. On the inappropriate use of Kimura-2-Parameter (K2P) divergences in the DNA – barcoding literature. Cladistics 28: 190-194. https://doi.org/10.1111/j.1096-0031.2011.00370.x.
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Van Pelt-Verkuil E, Van Belkum A, Hays JP. 2008. Principles and technical aspect of PCR amplification. Springer Science + Business Media, Dordrecht, Netherland.
Wang P, Heitman J. 2005. The cyclophilins. Genome Biology 6: 226. https://doi.org/10.1186/gb-2005-6-7-226.
Wang Q, Hillwig HL, Wu Y, Peters RJ. 2012. CYP701A8: A rice ent-kaurene oxidase paralog diverted to more specialized diterpenoid metabolism. Plant Physiology 158: 1418-1425. https://doi.org/10.1104/pp.111.187518
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Zheng Y, Wu S, Bai Y, Sun H, Jiao C, Guo S, Zhao K, Blanca J, Zhang Z, Huang S, Xu Y, Weng Y, Mazourek M, Reddy UK, Ando K, McCreight JD, Schaffer AA, Burger J, Tadmor Y, Katzir N, Tang X, Liu Y, Giovannoni JJ, Ling KS, Wechter WP, Levi A, Garcia-Mas J, Grumet R, Fei Z. 2019. Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops. Nucleic Acids Research 47: D1128-D1136. https://doi.org/10.1093/nar/gky944
Zwenger S, Basu C. 2008. Plant Terpenoids: applications and future potentials. Biotechnology and Molecular Biology Reviews 3: 001-007.
Aubourg S, Lecharny A, Bohlmann J. 2002. Genomic analysis of the terpenoid synthase (AtTPS) gene family of Arabidopsis thaliana. J. Mol. Gen. Genomics 267: 730-745. https://doi.org/10.1007/s00438-002-0709-y.
Avalos AA, Zini LM, Ferrucci MS, Lattar EC. 2019. Anther and gynoecium structure and development of male and female gametophytes of Koelreuteraia elegans subsp. formosana (Sapindaceae): Phylogenetic implications. Flora: Morphology, Distribution, Functional Ecology of Plants 255: 98–109. https://doi.org/10.1016/j.flora.2019.04.003.
Bagheriyan S, Karimi HR, Esmaelizadeh M. 2015. Evaluation of Genetic Relationships Among Melon Genotypes Based on Morphological Markers. International Journal of Vegetable Science 21: 36-52. https://doi.org/10.1080/19315260.2013.818608.
Bohlmann J, Meyer-Gauen G, Croteau R. 1998. Plant terpenoid synthases: Molecular biology and phylogenetic analysis. Proceedings of the National Academy of Sciences of the United States of America 95: 4126–4133. https://doi.org/ 10.1073/pnas.95.8.4126.
Croteau R, Kutchan TM, Lewis NG. 2000. Natural Products (Secondary Metabolites). In: Buchanan B, Gruissem W, Jones R (eds) Biochemistry & Molecular Biology of Plants. American Society of Plant Physiologist., Rockville.
Daryono BS, Maryanto SD. 2017. Keanekaragaman dan Potensi Sumber Daya Genetik Melon. Gadjah Mada University Press, Yogyakarta.
Daryono BS, Nofriarno N. 2018. Pewarisan Karakter Fenotip Melon (Cucumis melo L. ‘Hikapel Aromatis’) Hasil Persilangan ? ‘Hikapel’ dengan ? ‘Hikadi Aromatik’. Biosfera 35: 44-48. https://doi.org/10.20884/1.mib.2018.35.1.586.
Daryono BS, Subiastuti AS, Fatmadanni A, Sartika D. 2019. Phenotypic and genetic stability of new indonesian melon cultivar (Cucumis melo L. “Melonia”) based on ISSR markers. Biodiversitas 20: 1069–1075. https://doi.org/10.13057/biodiv/d200419.
Dewick PM. 2002. Medicinal Natural Product: A Biosynthetic Approach, second ed. John Wiley & Sons, Inc, Chicester.
Dos Santos IB, Park SW. 2019. Versatility of cyclophilins in plant growth and survival: A case study in arabidopsis. Biomolecules 9: 20. https://doi.org/10.3390/biom9010020.
Esteras C, Rambla JL, Sanchez G, Lopez-Gresa MP, Gonzalez-Mas MC, Fernandez-Trujillo JP, Belles JM, Granell A, Pico MB. 2018. Fruit flesh volatile and carotenoid profile analysis within the Cucumis melo L. species reveals unexploited variability for future genetic breeding. Journal of the Science of Food and Agriculture 98: 3915–3925. https://doi.org/10.1002/jsfa.8909.
Fischer G, Schmidt FX. 1990. The mechanism of protein folding. Implications of in vitro refolding models for de novo protein folding and translocation in the cell. Biochemistry 29: 2205-2212. https://doi.org/10.1021/bi00461a001.
Fradj N, Goncalves dos Santos KC, Montigny N, Awwad F, Boumghar Y, Germain H, Desgagne-Penix I. 2019. RNA-seq de novo assembly and differential transcriptome analysis of chaga (Inonotus obliquus) cultured with different betulin sources and the regulation of genes involved in terpenoid biosynthesis. International Journal of Molecular Sciences 20: 1–27. https://doi.org/10.3390/ijms20184334.
Garcia-mas J, Benjak A, Sanseverino W, Bourgeois M, Mir G, Gonzalez VM, Henaff E, Camara F, Cozzuto L, Lowy E, Alioto T, Capella-Guitierrez S, Blanca J, Canizares J, Ziarsolo P, Gonzalez-Ibeas D, Rodriguez-Moreno L, Droege M, Du L, Alvarez-Tejado M, Lorente-Galdos B, Mele M, Yang L, Weng Y, Navarro A, Marques-Bonet T, Aranda MA, Nuez F, Pico B, Gabaldon T, Roma G, Guigo R, Casacuberta JM, Arus P, Puigdomenech P. 2012. The genome of melon (Cucumis melo L.). PNAS Early Edition 109: 11872-11877. https://doi.org/10.1073/pnas.1205415109.
Gomez KA, Gomez AA. 2007. Prosedur statistik untuk penelitian pertanian. I-Press, Jakarta.
Hasbullah UHA, Supriyadi, Daryono BS. 2019. Aroma volatile compounds profile of melon (Cucumis melo L .) cv . Gama Melon Parfum. IOP Conference Series: Earth and Environmental Science 292: 012027. https://doi.org/10.1088/1755-1315/292/1/012027.
International Plant Genetic Resources Institute. 2003. Descriptor for melon (Cucumis melo L.). International Plant Genetic Resources Institute, Rome, Italy
Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol 16: 111-120. https://doi.org/10.1007/BF01731581.
Kumari S, Roy S, Singh P, Singla-Pareek S, Pareek A. 2013. Cyclophilins: Proteins in search of function. Journal Plant Signaling & Behavior 8: 25-32. https://doi.org/10.4161/psb.22734.
Latrasse D, Rodriguez-Granadoz NY, Veluchamy A, Mariappan KG, Bevilacqua C, Crapart N, Camps C, Sommard V, Raynaud C, Dogimont C, Boualem A, Benhamed M, Bendahmane A. 2017. The quest for epigenetic regulation underlying unisexual flower development in Cucumis melo. Epigenetics Chromatin. 10: 22. https://doi.org/10.1186/s13072-017-0132-6.
Lee J, Kim SS. 2010. An overview of cyclophilins in human cancers. J. Int. Med. Res 38: 1561-1574. https://doi.org/10.1177/147323001003800501.
Nagy PD, Wang RY, Pogany J, Harfen A, Makinen K. 2011. The dependence of viral RNA replication on co-opted host factors. Virology 411: 374-382. https://doi.org/ 10.1038/nrmicro2692.
Nutzmann HW, Huang A, Osbourn A. 2016. Plant metabolic clusters – from genetics to genomics. New Phytologist 211: 771–789. https://doi.org/10.1111/nph.13981.
Paris HS, Amar Z, Lev E. 2012. Medieval emergence of sweet melons, Cucumis melo (Cucurbitaceae). Ann. Bot. 110: 23 - 33. https://doi.org/10.1093/aob/mcs098.
Portnoy V, Benyamini Y, Bar E, Harel-Beja R, Gepstein S, Giovanni JJ, Schaffer AA, Burger J, Tadmor Y, Lewinsohn E, Katzir N. 2008. The molecular and biochemical basis for varietal variation in sesquiterpene content in melon (Cucumis melo L.) rinds. Plant Molecular Biology 66: 647–661. https://doi.org/10.1007/s11103-008-9296-6.
Ruggieri V, Alexiou KG, Morata J, Argyris J, Pujol M, Yano R, Nonaka S, Ezura H, Latrasse D, Boualem A, Benhamed M, Bendahmane A, Cigliano RA, Sanseverion W, Puigdomenech P, Casacuberta JM, Garcia-Mas J. 2018. An improved assembly and annotation of the melon (Cucumis melo L.) reference genome. Scientific Reports 8088: 1–9. https://doi.org/10.1038/s41598-018-26416-2.
Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425. https://doi.org/10.1093/oxfordjournals.molbev.a040454.
Sarabia LE, Lopez MF, Obregon-Molina G, Cano-Ramirez C, Sanchez-Martinez G, Zuniga G. 2019. The differential expression of mevalonate pathway genes in the gut of the bark beetle Dendroctonus rhizophagus (Curculionidae?: Scolytinae) is unrelated to the de novo synthesis of terpenoid pheromones. International Journal of Molecular Sciences 20: 4011. https://doi.org/10.3390/ijms20164011
Schiestl FP, Johnson SD. 2013. Pollinator-mediated evolution of floral signals. Trends in Ecology & Evolution. 28: 307-315. https://doi.org/10.1016/j.tree.2013.01.019.
Schwab W, Davidovich-Rikanati R, Lewinsohn E. 2008. Biosynthesis of plant-derived flavor compounds. the plant journal 54: 712–732. https://doi.org/10.1111/j.1365-313X.2008.03446.x.
Shalit M, Katzir N, Tadmor Y, Larkov O, Burger Y, Shalekhet F, Lastochkin E, Ravid U, Amar O, Edelstein M, Karchi Z, Lewinsohn E. 2001. Acetyl-CoA?: alcohol acetyltransferase activity and aroma formation in ripening melon fruits. J. Agric. Food. Chem. 49: 794-799. https://doi.org/10.1021/jf001075p
Shaw PE. 2002. Peptidyl?prolyl isomerases: a new twist to transcription. EMBO Rep. 3: 521-526. https://doi.org/10.1093/embo-reports/kvf118
Srivathsan A, Meier R. 2012. On the inappropriate use of Kimura-2-Parameter (K2P) divergences in the DNA – barcoding literature. Cladistics 28: 190-194. https://doi.org/10.1111/j.1096-0031.2011.00370.x.
Stamnes MA, Rutherford SL, Zuker CS. 1992. Cyclophilins: a new family of proteins involved in intracellular folding. Trends in Cell Biology 2: 272-276. https://doi.org/10.1016/0962-8924(92)90200-7.
Van Pelt-Verkuil E, Van Belkum A, Hays JP. 2008. Principles and technical aspect of PCR amplification. Springer Science + Business Media, Dordrecht, Netherland.
Wang P, Heitman J. 2005. The cyclophilins. Genome Biology 6: 226. https://doi.org/10.1186/gb-2005-6-7-226.
Wang Q, Hillwig HL, Wu Y, Peters RJ. 2012. CYP701A8: A rice ent-kaurene oxidase paralog diverted to more specialized diterpenoid metabolism. Plant Physiology 158: 1418-1425. https://doi.org/10.1104/pp.111.187518
Yang L, Cai K, Huang H, Zhang Y, Zong Y, Wang S, Shi J, Li X, Liao F, Lu M, Guo W. 2019. Comparative analysis of anatomy, gene expression of Vaccinium corymbosum cyclins and cyclin dependent kinases during the flower bud and fruit ontogeny. Scientia Horticulturae 251:252–259. https://doi.org/10.1016/j.scienta.2019.03.028.
Yu XZ, Lu CJ, Tang S, Zhang Q. 2019. Transcriptomic analysis of cytochrome P450 genes and pathways involved in chromium toxicity in Oryza sativa. Ecotoxicology. 29: 503-513. https://doi.org/10.1007/s10646-019-02046-w.
Zheng Y, Wu S, Bai Y, Sun H, Jiao C, Guo S, Zhao K, Blanca J, Zhang Z, Huang S, Xu Y, Weng Y, Mazourek M, Reddy UK, Ando K, McCreight JD, Schaffer AA, Burger J, Tadmor Y, Katzir N, Tang X, Liu Y, Giovannoni JJ, Ling KS, Wechter WP, Levi A, Garcia-Mas J, Grumet R, Fei Z. 2019. Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops. Nucleic Acids Research 47: D1128-D1136. https://doi.org/10.1093/nar/gky944
Zwenger S, Basu C. 2008. Plant Terpenoids: applications and future potentials. Biotechnology and Molecular Biology Reviews 3: 001-007.
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