Genetic Diversity and Relationships of Dendrobium Based on TrnL-F Markers: An Approach In-silico
Keywords:
genetic diversity, dendrobium, in-silico, phylogenetic, trnl-f
Abstract
The development of DNA sequencing technologies has deepened our understanding of genetic variation within Dendrobium species and revealed evolutionary relationships among them. in-silico methods facilitate efficient phylogenetic determination, leveraging computational advantages to process sequence data with high accuracy. This study aims to significantly contribute to the understanding of genetic diversity within the genus Dendrobium based on the TrnL-F marker, with potential implications for the conservation and management of these plant genetic resourcesThis paper presents nucleotide diversity analysis and phylogenetic analysis to determine the kinship relationships among Dendrobium species. The analysis revealed a high degree of relatedness among the Dendrobium species, with kinship relationships dividing them into three distinct groups.
References
Cahyaningsih R, Compton LJ, Rahayu S, Brehm JM, and Maxted N, 2022. DNA barcoding medicinal plant species from Indonesia. Plants. 10 (2022): pp. 1375.
Chase MW, Cameron KM, Freudenstein JV, Pridgeon AM, Salazar G, Berg CVD, and Schuiteman, 2015. An updated classification of Orchidaceae. Botanical Journal of the Linnean Society, 177(2), pp. 151–174. https://doi.org/10.1111/boj.12234
Chatterjee N and Walker C, 2017. Mechanisms of DNA damage, repair, and mutagenesis. Environmental and Molecular Mutagenesis. 58(5), pp. 235–263.
Chen S, Yao H, Han J, Liu C, Song J, Shi L, Zhu Y, Ma X, Gao T, Pang X, Luo K, Li Y, Li X, Jia X, Lin Y, and Leon C, 2015. Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLoS One. 5(1):e8613. 10.1371/journal.pone.0008613.
Choate LA, Koleilat A, Harris K, Vidal-Folch N, Guenzel A, Newman J, Peterson BJ, Peterson SE, Rice CS, Train LJ, Hasadsri L, Marcou CA, Moyer AM, and Baudhuin LM, 2023. Confirmation of Insertion, Deletion, and Deletion-Insertion Variants Detected by Next-Generation Sequencing. Clinical chemistry, 69(10), pp. 1155–1162. 10.1093/clinchem/hvad110.
Dressler RL, 1993. Phylogeny and classification of the orchid family. New York, NY, USA: Cambridge University Press.
Feng, S. G., Lu, J. J., Gao, L., Liu, J. J., and Wang, H. Z. (2014). Molecular phylogeny analysis and species identification of Dendrobium (Orchidaceae) in China. Biochemical genetics, 52, pp. 127–136.
Givnish TJ, Spalink D, Ames M, Lyon SP, Hunter SJ, Zuluaga A, Iles WJ, Clements MA, Arroyo MT, Leebens-Mack J, Endara L, Kriebel R, Neubig KM, Whitten WM, Williams NH, and Cameron KM, 2015. Orchid phylogenomics and multiple drivers of their extraordinary diversification. Proceedings of the Royal Society B, 282(1814), 20151553. 10.1098/rspb.2015.1553.
Haldar S, 2019. Bioinformatics methods: Application toward analyses and interpretation of experimental data. In Advances in biological science research. pp. 1–19. Academic Press.
Hollingsworth PM, Forrest LL, Spouge JL, Hajibabaei M, Ratnasingham S, Bank M van der, Chase MW, Cowan RS, Erickson DL, Fazekas AJ, Graham SW, James KE, Kim KJ, Kress WJ, Schneider H, AlphenStahl J van, Barrett SCH, Berg C van den, Bogarin Chaves DG, Burgess KS, Cameron KM, Carine M, Chacon J, Clark A, Clarkson JJ, Conrad F, Devey DS, Ford CS, Hedderson TAJ, Hollingsworth ML, Husband BC, Kelly LJ, Kesanakurti PR, Kim JS, Kim YD, Lahaye R, Lee HL, Long DG, Madrinan S, Maurin O, Meusnier I, Newmaster SG, Park CW, Percy DM, Petersen G, Richardson JE, Salazar Gerardo A, Savolainen V, Seberg O, Wilkinson MJ, Yi DK, and Little DP, 2011. A DNA barcode for land plants. Proceedings of the National Academy of Sciences, 106(31), pp. 12794–12797.
Kallner A, 2017. Laboratory statistics: methods in chemistry and health sciences. Elsevier.op.
Liu Y, Liang N, Xian Q, and Zhang W, 2023. GC heterogeneity reveals sequence-structures evolution of angiosperm ITS2. BMC Plant Biology, 23(1), pp. 608.
Mahfut, Handayani TT, Wahyuningsih S, and Sukimin, 2021. Identification of Dendrobium (Orchidaceae) in Liwa Botanical Garden Based on Leaf Morphological Characters. Journal of Tropical Biodiversity and Biotechnology. 6(1).
Mursyidin D H, Ahyar G M Z, Saputra A W, and Hidayat A, 2021. Genetic diversity and relationships of Phalaenopsis based on the rbcL and TrnL-F markers: In-silico approach. Biosaintifika: Journal of Biology & Biology Education. 13(2): pp. 212–221.
Morihito R V, Chungdinata S E, Nazareth T A, Pulukadang M I, Makalew R A, and Pinontoan B, 2017. Identifikasi perubahan struktur dna terhadap pembentukan sel kanker menggunakan dekomposisi graf. Jurnal Ilmiah Sains. pp. 153–160.
Nagar A and Hahsler M 2013. Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment. BMC bioinformatics. 14, pp. 1–12.
Ng, T.B., et al. (2012). Dendrobium orchids: A review of their traditional uses, phytochemistry and pharmacology. Chinese Medicine, 7, 16.
Ponnikas S, Sigeman H, Lundberg M, and Hansson B, 2022. Extreme variation in recombination rate and genetic diversity along the Sylvioidea neo‐sex chromosome. Molecular Ecology. 31(13), pp.3566–3583.
Seidenfaden G, 1985. Orchid genera in Thailand XIV. Dendrobium Sw. Opera Botanica, 83, pp. 1–295.
Sharma R, Surveswaran S, Gowda V, Sun M, 2018. Molecular systematics and phylogenetic analyses in Orchidaceae: A review. PhytoKeys, 113, pp. 39–59.
Stoltzfus A and McCandlish DM, 2017. Mutational biases influence parallel adaptation. Molecular Biology and Evolution. 34(9), pp. 2163–2172.
Taberlet P, Gielly L, and Pautou G, 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol. Biol. 17: pp. 1105–1109. https://doi.org/10.1007/BF00037152.
Teixeira da Silva JA, Jin X, Dobránszki J, Lu J, Wang H, Zotz G, Cardoso JC, and Zeng S, 2016. Advances in Dendrobium breeding. Plant Cell Reports. 35(7): pp. 1581–1600.
Teoh ES, 2020. Medicinal orchids of Asia. Springer Nature.
Wang Y, Wang H, Ye C, Wang Z, Ma C, Lin D, and Jin X, 2009. Phylogenetic analysis of Dendrobium species based on nuclear ITS and plastid trnL-F sequences. Plant Systematics and Evolution. 283: pp. 165–177.
Xu X, Zhang C, Wang N, Xu Y, Tang G, Xu L, and Feng Y, 2015. Phylogenetic relationships and species delimitation in Dendrobium using DNA barcoding. Molecular Phylogenetics and Evolution. 85: pp. 30–37.
Yukawa T and Stern WL, 2002. Comparative vegetative anatomy and systematics of Dendrobium, Epidendrum, and Cattleya. Botanical Journal of the Linnean Society, 138(4), pp. 383–394.
Chase MW, Cameron KM, Freudenstein JV, Pridgeon AM, Salazar G, Berg CVD, and Schuiteman, 2015. An updated classification of Orchidaceae. Botanical Journal of the Linnean Society, 177(2), pp. 151–174. https://doi.org/10.1111/boj.12234
Chatterjee N and Walker C, 2017. Mechanisms of DNA damage, repair, and mutagenesis. Environmental and Molecular Mutagenesis. 58(5), pp. 235–263.
Chen S, Yao H, Han J, Liu C, Song J, Shi L, Zhu Y, Ma X, Gao T, Pang X, Luo K, Li Y, Li X, Jia X, Lin Y, and Leon C, 2015. Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLoS One. 5(1):e8613. 10.1371/journal.pone.0008613.
Choate LA, Koleilat A, Harris K, Vidal-Folch N, Guenzel A, Newman J, Peterson BJ, Peterson SE, Rice CS, Train LJ, Hasadsri L, Marcou CA, Moyer AM, and Baudhuin LM, 2023. Confirmation of Insertion, Deletion, and Deletion-Insertion Variants Detected by Next-Generation Sequencing. Clinical chemistry, 69(10), pp. 1155–1162. 10.1093/clinchem/hvad110.
Dressler RL, 1993. Phylogeny and classification of the orchid family. New York, NY, USA: Cambridge University Press.
Feng, S. G., Lu, J. J., Gao, L., Liu, J. J., and Wang, H. Z. (2014). Molecular phylogeny analysis and species identification of Dendrobium (Orchidaceae) in China. Biochemical genetics, 52, pp. 127–136.
Givnish TJ, Spalink D, Ames M, Lyon SP, Hunter SJ, Zuluaga A, Iles WJ, Clements MA, Arroyo MT, Leebens-Mack J, Endara L, Kriebel R, Neubig KM, Whitten WM, Williams NH, and Cameron KM, 2015. Orchid phylogenomics and multiple drivers of their extraordinary diversification. Proceedings of the Royal Society B, 282(1814), 20151553. 10.1098/rspb.2015.1553.
Haldar S, 2019. Bioinformatics methods: Application toward analyses and interpretation of experimental data. In Advances in biological science research. pp. 1–19. Academic Press.
Hollingsworth PM, Forrest LL, Spouge JL, Hajibabaei M, Ratnasingham S, Bank M van der, Chase MW, Cowan RS, Erickson DL, Fazekas AJ, Graham SW, James KE, Kim KJ, Kress WJ, Schneider H, AlphenStahl J van, Barrett SCH, Berg C van den, Bogarin Chaves DG, Burgess KS, Cameron KM, Carine M, Chacon J, Clark A, Clarkson JJ, Conrad F, Devey DS, Ford CS, Hedderson TAJ, Hollingsworth ML, Husband BC, Kelly LJ, Kesanakurti PR, Kim JS, Kim YD, Lahaye R, Lee HL, Long DG, Madrinan S, Maurin O, Meusnier I, Newmaster SG, Park CW, Percy DM, Petersen G, Richardson JE, Salazar Gerardo A, Savolainen V, Seberg O, Wilkinson MJ, Yi DK, and Little DP, 2011. A DNA barcode for land plants. Proceedings of the National Academy of Sciences, 106(31), pp. 12794–12797.
Kallner A, 2017. Laboratory statistics: methods in chemistry and health sciences. Elsevier.op.
Liu Y, Liang N, Xian Q, and Zhang W, 2023. GC heterogeneity reveals sequence-structures evolution of angiosperm ITS2. BMC Plant Biology, 23(1), pp. 608.
Mahfut, Handayani TT, Wahyuningsih S, and Sukimin, 2021. Identification of Dendrobium (Orchidaceae) in Liwa Botanical Garden Based on Leaf Morphological Characters. Journal of Tropical Biodiversity and Biotechnology. 6(1).
Mursyidin D H, Ahyar G M Z, Saputra A W, and Hidayat A, 2021. Genetic diversity and relationships of Phalaenopsis based on the rbcL and TrnL-F markers: In-silico approach. Biosaintifika: Journal of Biology & Biology Education. 13(2): pp. 212–221.
Morihito R V, Chungdinata S E, Nazareth T A, Pulukadang M I, Makalew R A, and Pinontoan B, 2017. Identifikasi perubahan struktur dna terhadap pembentukan sel kanker menggunakan dekomposisi graf. Jurnal Ilmiah Sains. pp. 153–160.
Nagar A and Hahsler M 2013. Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment. BMC bioinformatics. 14, pp. 1–12.
Ng, T.B., et al. (2012). Dendrobium orchids: A review of their traditional uses, phytochemistry and pharmacology. Chinese Medicine, 7, 16.
Ponnikas S, Sigeman H, Lundberg M, and Hansson B, 2022. Extreme variation in recombination rate and genetic diversity along the Sylvioidea neo‐sex chromosome. Molecular Ecology. 31(13), pp.3566–3583.
Seidenfaden G, 1985. Orchid genera in Thailand XIV. Dendrobium Sw. Opera Botanica, 83, pp. 1–295.
Sharma R, Surveswaran S, Gowda V, Sun M, 2018. Molecular systematics and phylogenetic analyses in Orchidaceae: A review. PhytoKeys, 113, pp. 39–59.
Stoltzfus A and McCandlish DM, 2017. Mutational biases influence parallel adaptation. Molecular Biology and Evolution. 34(9), pp. 2163–2172.
Taberlet P, Gielly L, and Pautou G, 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol. Biol. 17: pp. 1105–1109. https://doi.org/10.1007/BF00037152.
Teixeira da Silva JA, Jin X, Dobránszki J, Lu J, Wang H, Zotz G, Cardoso JC, and Zeng S, 2016. Advances in Dendrobium breeding. Plant Cell Reports. 35(7): pp. 1581–1600.
Teoh ES, 2020. Medicinal orchids of Asia. Springer Nature.
Wang Y, Wang H, Ye C, Wang Z, Ma C, Lin D, and Jin X, 2009. Phylogenetic analysis of Dendrobium species based on nuclear ITS and plastid trnL-F sequences. Plant Systematics and Evolution. 283: pp. 165–177.
Xu X, Zhang C, Wang N, Xu Y, Tang G, Xu L, and Feng Y, 2015. Phylogenetic relationships and species delimitation in Dendrobium using DNA barcoding. Molecular Phylogenetics and Evolution. 85: pp. 30–37.
Yukawa T and Stern WL, 2002. Comparative vegetative anatomy and systematics of Dendrobium, Epidendrum, and Cattleya. Botanical Journal of the Linnean Society, 138(4), pp. 383–394.
Published
2025-11-27
Section
Original Research
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