Isolation and characterization of chalcone synthase (CHS) gene from Phalaenopsis and Doritaenopsis orchids
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http://orcid.org/0000-0003-3026-8182
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Abstract. Sukma D, Handini AS, Sudarsono. 2020. Isolation and characterization of chalcone synthase (CHS) gene from Phalaenopsis and Doritaenopsis orchids. Biodiversitas 21: 5054-5064. Chalcone synthase (CHS) is a key enzyme in flavonoid biosynthesis. The research aims to isolate and characterize the CHS gene nucleotide sequence diversity of nine Phalaenopsis and one Doritaenopsis genotypes. Genomic DNA was isolated from young leaves and used to PCR amplify the gene using CHS specific degenerate primers. Results of PCR amplification yielded DNA fragments of 700 bp. Upon sequencing and nucleotide sequence analysis, we found that the genomic fragments were partial CHS gene from Phalaenopsis and Doritaenopsis genotypes and deposited the sequences in the NCBI Genebank Database accession numbers of KR184089-KR184098. More analysis of the sequences confirmed they shared ranged from 81-99% sequence identities to known CHS genes from Phalaenopsis deposited in the NCBI Database. They also shared 84-100% amino acid residues identity to CHS polypeptides. Multiple sequence alignment (MSA) and phylogenetic analysis further revealed the determined CHS nucleotide sequences from Phalaenopsis and Doritaenopsis genotypes were closely related to CHS genes from other orchid species.
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References
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Chao YT, Yen SH, Yeh JH, Chen WC, Shih MC. 2017. Orchidstra 2.0 A transcriptomics resource for the orchid family. Plant and Cell Physiol 58 (1): e9. doi: 10.1093/pcp/pcw220.
Christenson EA. 2001. Phalaenopsis. Timber Press, Portland, Oregon.330 pp.
Dao T, Linthorst H, Verpoorte R. 2011. Chalcone synthase and its functions in plant resistance. Phytochem Rev. 10(3): 397. https://doi.org/10.1007/s11101-011-9211-7 P
Doyle JJ, Doyle JL. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19: 11-15.
Conrad AC, Mathabatha MF. 2016. Characterization and expression analyses of chalcone synthase (CHS) and anthocyanidin synthase (ANS) genes in Clivia miniata. Transcriptomics 4: 136. doi:10.4172/2329-8936.1000136
Ferrer JL, Jez JM, Bowman ME, Dixon RA, Noel JP. 1999. Structure of chalcone synthase and the molecular basis of plant polyketide biosynthesis. Nat Struct Biol 6:775–784. doi: 10.1038/11553.
Garces-Claver A, Fellman SM, Gil-Ortega R, Jahn M, Arnedo-Andres MS. 2007. Identification, validation and survey of a single nucleotide polymorphism (SNP) associated with pungency in Capsicum spp, Theor Appl Genet 115:907-916. doi: 10.1007/s00122-007-0617-y
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Sommer H, Bonas U, Saedler H. 1988. Transposon-induced alterations in the promoter region affect transcription of the chalcone synthase gene of Antirrhinum majus. Mol Gen Genet 211: 49-55. 24. doi: 10.1007/BF00338392.
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Sukma D, Elina J, Giyanto, Sudarsono. 2017. Disease resistance breeding of Phalaenopsis spp. for tropical environment and molecular marker development for plant selection. Acta Hort 1167:237-244. doi:10.17660/ActaHortic.2017.1167.36
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Tamura K, Stecher G, Peterson D, Filipski V, Kumar S. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30(12): 2725–2729. https://doi.org/10.1093/molbev/mst197 PMID: 24132122
Tanaka Y, Sasaki N, Ohmiya A. 2008. Biosynthesis of plant pigments: anthocyanins, betalains and carotenoids. Plant J 54(4): 733-749. doi: 10.1111/j.1365-313X.2008.03447.
Tang CY, Chen WH. 2007. Breeding and development of new varieties in Phalaenopsis. pp 1-22. In: W.H. Chen and H.H. Chen HH (eds.). Orchid Biotechnology. World Scientific, Singapore.
Tsai CC. 2011. Molecular phylogeny and biogeography of Phalaenopsis species. pp 1-24. In: W.H. Chen and H.H. Chen (eds.). Orchid Biotechnology II. Word Scientific. Singapore.
Wani TA, Pandith SA, Gupta AP, Chandra S, Sharma N, Lattoo SK. 2017. Molecular and functional characterization of two isoforms of chalcone synthase and their expression analysis in relation to flavonoid constituents in Grewia asiatica L. PLoS ONE 12(6):e0179155. https://doi.org/10.1371/journal.pone.0179155
Zhao D, Tao J. 2015. Recent advances on the development and regulation of flower color in ornamental plants. Front Plant Sci 6:261. doi: 10.3389/fpls.2015.00261
Ye Y, Cai M, Ju Y, Jiao Y, Feng L, Pan H, Cheng T, Zhang Q. 2016. Identification and validation of SNP markers linked to dwarf traits using SLAF-Seq technology in Lagerstroemia. PLoS ONE 11(7): e0158970. http://doi.org/10.1371/journal.pone.0158970
Zhang W, Mirlohi S, Li X, He Y. 2018. Identification of functional single-nucleotide polymorphisms affecting leaf hair number in Brassica rapa. Plant Physiol 177:491-503. doi: 10.1104/pp.18.00025. Epub 2018 Apr 23.
Bast F. 2015. Sequence similarity search, multiple sequence alignment, model selection, distance matrix and phylogeny reconstruction. Nature Protocols · July 2013. doi: 10.1038/protex.2013.065
Chang YK, Veilleux RE, Iqbal MJ. 2009. Analysis of genetic variability among Phalaenopsis species and hybrids using Amplified Fragment Length Polymorphism. J Amer Soc Hort Sci 134(1):58–66. 2009
Chao YT, Yen SH, Yeh JH, Chen WC, Shih MC. 2017. Orchidstra 2.0 A transcriptomics resource for the orchid family. Plant and Cell Physiol 58 (1): e9. doi: 10.1093/pcp/pcw220.
Christenson EA. 2001. Phalaenopsis. Timber Press, Portland, Oregon.330 pp.
Dao T, Linthorst H, Verpoorte R. 2011. Chalcone synthase and its functions in plant resistance. Phytochem Rev. 10(3): 397. https://doi.org/10.1007/s11101-011-9211-7 P
Doyle JJ, Doyle JL. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19: 11-15.
Conrad AC, Mathabatha MF. 2016. Characterization and expression analyses of chalcone synthase (CHS) and anthocyanidin synthase (ANS) genes in Clivia miniata. Transcriptomics 4: 136. doi:10.4172/2329-8936.1000136
Ferrer JL, Jez JM, Bowman ME, Dixon RA, Noel JP. 1999. Structure of chalcone synthase and the molecular basis of plant polyketide biosynthesis. Nat Struct Biol 6:775–784. doi: 10.1038/11553.
Garces-Claver A, Fellman SM, Gil-Ortega R, Jahn M, Arnedo-Andres MS. 2007. Identification, validation and survey of a single nucleotide polymorphism (SNP) associated with pungency in Capsicum spp, Theor Appl Genet 115:907-916. doi: 10.1007/s00122-007-0617-y
Han Y, Ding T, Su B, Jiang H. 2016. Genome-wide identification, characterization and expression analysis of the chalcone synthase family in maize. Int J Mol Sci. 17(2): 161. https://doi.org/10.3390/ ijms17020161 PMID: 26828478
Han YY, Ming F, Wang W, Wang JW, Ye MM, Shen DL. 2006. Molecular evolution and functional specialization of chalcone synthase superfamily from Phalaenopsis orchid. Genetica 128: 429–438. doi: 10.1007/s10709-006-7668-x [PubMed]
Handini AS. 2014. Morphological and biochemical analysis on Phalaenopsis and genetic diversity by SNAP marker. MSc.Thesis. Bogor Agricultural University. Bogor. [Indonesian]
Handini AS, Sukma D, Sudarsono. 2016. Analisis keragaman morfologi dan biokimia pada anggrek Phalaenopsis (Orchidaceae) J. Agron Indonesia 44 (1) : 62 – 67. doi: 10.24831/jai.v44i1.12502
Hsiao HI, Chang CC, Wu CH. 2015. Decision-making factors for country-of-origin agriculture branding in international markets: the case of orchids in Taiwan. J Horticulture 2: 134. doi:10.4172/2376-0354.1000134
Humaira M, Purwito A, Sudarsono, Sukma D. 2020. Multiplikasi tunas in vitro anggrek Phalaenopsis dan analisis keragaman Genetik dengan marka SNAP. J Agronomi Indonesia 48 (1):59-67. doi: https://doi.org/10.24831/jai.v48i1.29149
Kuo YT, Chao YT, Chen WC, Shih MC, Chang SB. 2019. Segmental and tandem chromosome duplications led to divergent evolution of the chalcone synthase gene family in Phalaenopsis orchids. Annals of Botany 123: 69–77. doi: 10.1093/aob/mcy136
Mammadov J, Aggarwal R, Buyyarapu R, Kumpatla S. 2012. SNP markers and their impact on plant breeding. Int J Plant Genomics 2012:728398. doi: 10.1155/2012/728398. Epub 2012 Dec 18.
Panche AN, Diwan AD, Chandra SR. 2016. Flavonoids: an overview. J Nutr Sci 2016;5:e47. doi:10.1017/jns.2016.41
Raynalta E, Elina J, Sudarsono, Sukma D. 2018. Clonal fidelity of micro-propagated Phalaenopsis plantlets based on assessment using eighteen Ph-Pto SNAP marker loci. Agrivita J Agric Sci 40:390–402. http://doi.org/10.17503/agrivita.v40i3.1493
Simko I, Eujayl IA, van Hintum T. 2012. Empirical evaluation of DArT, SNP, and SSR marker-systems for genotyping, clustering, and assigning sugar beet hybrid varieties into populations. Plant Science:154-162. doi: 10.1016/j.plantsci.2011.12.009. Epub 2011 Dec 19.
Schroder J. 1997. A family of plant-specific polyketide synthases: facts and predictions. Trends in Plant Science 2 (10):373-378. https://doi.org/10.1016/S1360-1385(97)87121-X
Sommer H, Bonas U, Saedler H. 1988. Transposon-induced alterations in the promoter region affect transcription of the chalcone synthase gene of Antirrhinum majus. Mol Gen Genet 211: 49-55. 24. doi: 10.1007/BF00338392.
Sudarsono, Haristianita MD, Sukma D. 2017. Molecular marker development based on diversity of genes associated with pigment biosynthetic pathways to support breeding for novel colors in Phalaenopsis. Acta Hort 1167:237-244 doi: 10.17660/ActaHortic.2017.1167.44
Sukma D, Elina J, Giyanto, Sudarsono. 2017. Disease resistance breeding of Phalaenopsis spp. for tropical environment and molecular marker development for plant selection. Acta Hort 1167:237-244. doi:10.17660/ActaHortic.2017.1167.36
Sun W, Meng X, Liang L, Jiang W, Huang Y, He J, Hu H, Almqvist J, Gao X, Wang L. 2015. Molecular and biochemical analysis of chalcone synthase from Freesia hybrid in flavonoid biosynthetic pathway. PLoS ONE 10(3): e0119054. doi:10.1371/journal.pone.0119054
Sweet HR. 1980. The Genus Phalaenopsis. The Orchid Digest. Pomona.CA.
Tamura K, Stecher G, Peterson D, Filipski V, Kumar S. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30(12): 2725–2729. https://doi.org/10.1093/molbev/mst197 PMID: 24132122
Tanaka Y, Sasaki N, Ohmiya A. 2008. Biosynthesis of plant pigments: anthocyanins, betalains and carotenoids. Plant J 54(4): 733-749. doi: 10.1111/j.1365-313X.2008.03447.
Tang CY, Chen WH. 2007. Breeding and development of new varieties in Phalaenopsis. pp 1-22. In: W.H. Chen and H.H. Chen HH (eds.). Orchid Biotechnology. World Scientific, Singapore.
Tsai CC. 2011. Molecular phylogeny and biogeography of Phalaenopsis species. pp 1-24. In: W.H. Chen and H.H. Chen (eds.). Orchid Biotechnology II. Word Scientific. Singapore.
Wani TA, Pandith SA, Gupta AP, Chandra S, Sharma N, Lattoo SK. 2017. Molecular and functional characterization of two isoforms of chalcone synthase and their expression analysis in relation to flavonoid constituents in Grewia asiatica L. PLoS ONE 12(6):e0179155. https://doi.org/10.1371/journal.pone.0179155
Zhao D, Tao J. 2015. Recent advances on the development and regulation of flower color in ornamental plants. Front Plant Sci 6:261. doi: 10.3389/fpls.2015.00261
Ye Y, Cai M, Ju Y, Jiao Y, Feng L, Pan H, Cheng T, Zhang Q. 2016. Identification and validation of SNP markers linked to dwarf traits using SLAF-Seq technology in Lagerstroemia. PLoS ONE 11(7): e0158970. http://doi.org/10.1371/journal.pone.0158970
Zhang W, Mirlohi S, Li X, He Y. 2018. Identification of functional single-nucleotide polymorphisms affecting leaf hair number in Brassica rapa. Plant Physiol 177:491-503. doi: 10.1104/pp.18.00025. Epub 2018 Apr 23.
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