Dergiler / Yüzüncü Yıl Üniversitesi Tarım Bilimleri Dergisi / 2026 / Issue: 1

Global Phylogenetic Insights into the Moth Orchid (Phalaenopsis amabilis) Population from the Meratus Mountains of South Kalimantan, Indonesia

Dindin Hidayatul Mursyidin(University of Lambung Mangkurat)0000-0002-1200-0927
Tanto Susilo(Lambung Mangkurat University)0009-0006-8245-7486
Yudhi Ahmad Nazari(Lambung Mangkurat University)0000-0002-9554-6887
Nove Arisandi(Ministry of Agriculture)0009-0002-2114-3361
Sayfa
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Yayın Tarihi
2026-10-16
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⚡ TL;DR(1 Cümlede Hızlı Çıkarım)

The findings are expected to provide critical insights to guide future conservation strategies and targeted breeding programs for these native orchids.

📌 3 Maddede Bu Makale

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Amaç & Hipotez:Phalaenopsis amabilis constitutes one of the most valuable and economically significant orchids (ornamental plants) worldwide.
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Temel Bulgular & Veri:Sixty-one samples of Phalaenopsis, comprising six of Phalaenopsis amabilis from the Meratus Mountains of South Kalimantan, Indonesia, and 55 of another Phalaenopsis species from GenBank, were molecularly characterized using the matK marker to assess genetic diversity and phylogenetic relationships.
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Sonuç & Katkı:The findings are expected to provide critical insights to guide future conservation strategies and targeted breeding programs for these native orchids.
🔬Tür:Research Article
📍Kapsam:Genişletilmiş Akademik Örneklem
⚙️Değişkenler:Ornamental crop · Orchidaceae · Plant breeding

Abstract

Phalaenopsis amabilis constitutes one of the most valuable and economically significant orchids (ornamental plants) worldwide. The present study aimed to investigate the genetic diversity and phylogenetic relationships of the moth orchid (Phalaenopsis amabilis) population native to the Meratus Mountains of South Kalimantan, Indonesia, using the matK marker. Sixty-one samples of Phalaenopsis, comprising six of Phalaenopsis amabilis from the Meratus Mountains of South Kalimantan, Indonesia, and 55 of another Phalaenopsis species from GenBank, were molecularly characterized using the matK marker to assess genetic diversity and phylogenetic relationships. Genetic diversity was determined using the Maximum Composite Likelihood method, and phylogenetic relationships were estimated using the Kimura 2-Parameter Maximum Likelihood method. In this study, moth orchid populations had lower levels of matK polymorphism at the intraspecific than at the interspecific level, with values of 10.07% and 47.91%, respectively. Similarly, this is directly proportional to the genetic diversity at both levels, which is lower (0.016) at the intraspecific level than at the interspecific level (0.062). However, this marker reveals unique phylogenetic relationships in Phalaenopsis, both locally and globally, with P. amabilis ‘Halong 2’ closely related to three similar species from Singapore, Japan, and the USA. At the same time, all samples of P. amabilis are closely related to two other Phalaenopsis species, i.e., P. sanderiana and P. aphrodite. The findings are expected to provide critical insights to guide future conservation strategies and targeted breeding programs for these native orchids.

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Bu Makaleye Atıf Yap

Mursyidin, D. H., Susilo, T., Nazari, Y. A., Arisandi, N. (2026). Global Phylogenetic Insights into the Moth Orchid (Phalaenopsis amabilis) Population from the Meratus Mountains of South Kalimantan, Indonesia. Yüzüncü Yıl Üniversitesi Tarım Bilimleri Dergisi, Issue: 1. https://doi.org/10.29133/yyutbd.1787201

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Kaynakça (55)

  1. Aboul-Maaty, N. A.-F., & Oraby, H. A. (2019). Extraction of high quality genomic DNA from different plant orders applying a modified CTAB based method. Bulletin of the National Research Centre, 43, 25. https://doi.org/10.1186/s42269-019-0066-1
  2. Allendorf, F. W., Luikart, G., & Aitken, S. N. (2013). Conservation and the genetics of populations (2nd ed.). Wiley Blackwell. https://doi.org/10.1002/9781118409250
  3. Barthet, M. M., Pierpont, C. L., & Tavernier, E. K. (2020). Unraveling the role of the enigmatic matK maturase in chloroplast group IIA intron excision. Plant Direct, 4(3), e00208. https://doi.org/10.1002/pld3.208
  4. Bentkowski, P., & Radwan, J. (2019). Evolution of major histocompatibility complex gene copy number. PLoS Computational Biology, 15, e1007015. https://doi.org/10.1371/journal.pcbi.1007015
  5. Besi, E. E., Mustafa, M., Yong, C. S. Y., & Go, R. (2023). Habitat ecology, structure influence diversity, and host species associations of wild orchids in undisturbed and disturbed forests in Peninsular Malaysia. Forests, 14, 544. https://doi.org/10.3390/f14030544
  6. Bossu, C. M., Rodriguez, M., Rayne, C., Chromczak, D. A., Higgins, P. G., Trulio, L. A., & Ruegg, K. C. (2023). Genomic approaches to mitigating genetic diversity loss in declining populations. Molecular Ecology, 32(19), 5228–5240. https://doi.org/10.1111/mec.17109
  7. Cardillo, M. (2023). Phylogenetic diversity in conservation: A brief history, critical overview, and challenges to progress. Cambridge Prisms: Extinction, 1, e11. https://doi.org/10.1017/ext.2023.8
  8. Carvalho, S. B., Velo Antón, G., Tarroso, P., Portela, A. P., Barata, M., Carranza, S., Moritz, C., & Possingham, H. P. (2017). Spatial conservation prioritization of biodiversity spanning the evolutionary continuum. Nature Ecology & Evolution, 1, 0151. https://doi.org/10.1038/s41559-017-0151
  9. Chen, W., Xing, R., Xia, P., Yang, Y., Ma, C., & Xia, L. (2025). Whole genome sequencing informs SNP based breeding strategies to safeguard genetic diversity in captive African lions. Frontiers in Veterinary Science, 12, 1577726. https://doi.org/10.3389/fvets.2025.1577726
  10. Davidescu, M. A., Pânzaru, C., Mădescu, B. M., Radu Rusu, R. M., Doliș, M. G., Simeanu, C., Usturoi, A., Ciobanu, A., & Creangă, Ș. (2024). Genetic diversity and phylogenetic analysis of the endangered Transylvanian Pinzgau cattle: A key resource for biodiversity conservation and the sustainability of livestock production. Agriculture, 14, 2234. https://doi.org/10.3390/agriculture14122234
  11. De, L. C. (2021). Studies on seventy five morphological characters in orchids. International Journal of Botany Studies, 6(6), 557–568.
  12. Dwivedi, S. L., Upadhyaya, H. D., Stalker, H. T., Blair, M. W., Bertioli, D. J., Nielen, S., & Ortiz, R. (2007). Enhancing crop gene pools with beneficial traits using wild relatives. In J. Janick (Ed.), Plant breeding reviews (pp. 179–230). John Wiley & Sons.
  13. Ellegren, H., & Galtier, N. (2016). Determinants of genetic diversity. Nature Reviews Genetics, 17, 422–433. https://doi.org/10.1038/nrg.2016.58
  14. Fatimah, & Sukma, D. (2011). Development of sequence based microsatellite marker for Phalaenopsis orchid. Hayati Journal of Biosciences, 18, 71–76. https://doi.org/10.4308/hjb.18.2.71
  15. Frankham, R., Ballou, J. D., & Briscoe, D. A. (2010). Introduction to conservation genetics (2nd ed.). Cambridge University Press. https://doi.org/10.1017/CBO9780511809002
  16. Frankham, R., Ballou, J. D., Ralls, K., Eldridge, M. D. B., Dudash, M. R., Fenster, C. B., Lacy, R. C., & Sunnucks, P. (2019). Inbreeding and loss of genetic diversity increase extinction risk. In R. Frankham et al. (Eds.), A practical guide for genetic management of fragmented animal and plant populations (pp. 31–48). Oxford University Press. https://doi.org/10.1093/oso/9780198783411.003.0003
  17. Freudenstein, J. V. (2025). Orchid phylogenetics and evolution: History, current status and prospects. Annals of Botany, 135, 805–822. https://doi.org/10.1093/aob/mcae202
  18. Futuyma, D. J., & Kirkpatrick, M. (2017). Evolution (4th ed.). Sinauer Associates.
  19. González-Orozco, C. E., Sosa, C. C., Thornhill, A. H., & Laffan, S. W. (2021). Phylogenetic diversity and conservation of crop wild relatives in Colombia. Evolutionary Applications, 14, 2603–2617. https://doi.org/10.1111/eva.13295
  20. Gunundu, R., Shimelis, H., & Tesfamariam, S. A. (2025). Genetic diversity and population structure analyses of tropical maize inbred lines using single nucleotide polymorphism markers. PLoS ONE, 20, e0315463. https://doi.org/10.1371/journal.pone.0315463
  21. Hsu, C.-C., Chen, H.-H., & Chen, W.-H. (2018). Phalaenopsis. In J. Van Huylenbroeck (Ed.), Ornamental crops (pp. 567–625). Springer International Publishing. https://doi.org/10.1007/978-3-319-90698-0_23
  22. Immanissa, S., Faizal, I., Salamah, A., Sari, I. A., & Susilo, A. W. (2020). Genetic variation in Maturase K (matK) from cacao (Theobroma cacao L.) varieties in Indonesia. IOP Conference Series: Earth and Environmental Science, 481, 012026. https://doi.org/10.1088/1755-1315/481/1/012026
  23. Jin, X. L., Tsai, C. C., Ko, Y. Z., & Chiang, Y. C. (2021). Phylogeny, polymorphism, and SSR markers of Phalaenopsis. In The orchid genome (pp. 145–162). Springer.
  24. Kardos, M., Taylor, H. R., Ellegren, H., Luikart, G., & Allendorf, F. W. (2021). Genomics advances the study of inbreeding depression in the wild. Evolutionary Applications, 14, 429–449. https://doi.org/10.1111/eva.13144
  25. Kumar, S., Stecher, G., Suleski, M., Sanderford, M., Sharma, S., & Tamura, K. (2024). MEGA12: Molecular evolutionary genetics analysis version 12 for adaptive and green computing. Molecular Biology and Evolution, 41, msae263. https://doi.org/10.1093/molbev/msae263
  26. Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J., & Higgins, D. G. (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947–2948. https://doi.org/10.1093/bioinformatics/btm404
  27. Le, D. T., Zhang, Y. Q., Xu, Y., Guo, L. X., Ruan, Z. P., Burgess, K. S., & Ge, X. J. (2020). The utility of DNA barcodes to confirm the identification of palm collections in botanical gardens. PLoS ONE, 15(1), e0227515. https://doi.org/10.1371/journal.pone.0235569
  28. Manly, B. F. J., & Navarro Alberto, J. A. (2020). Randomization, bootstrap and Monte Carlo methods in biology (4th ed.). Chapman and Hall/CRC. https://doi.org/10.1201/9780429329203
  29. MacKinnon, K., Hatta, G., Halim, H., & Mangalir, A. (1996). The ecology of Kalimantan (The Ecology of Indonesia Series, Vol. 3). Periplus Editions.
  30. Miller, S. M., Behrendorff, L., Allen, B. L., Andrew, R. L., Ballard, G., Ballard, J. W. O., Cairns, K. M., Conroy, G. C., Fleming, P. J. S., Grueber, C. E., Oakey, J., Smith, D. A., Stephens, D., Wade, C., & Bishop, J. M. (2024). Isolation, small population size, and management influence inbreeding and reduced genetic variation in K’gari dingoes. Conservation Genetics, 25, 955–971. https://doi.org/10.1007/s10592-024-01616-8
  31. Mursyidin, D. H., Ahyar, G. M. Z., Saputra, A. W., & 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, 178–186. https://doi.org/10.15294/biosaintifika.v13i2.29904
  32. Mursyidin, D. H., & Firnanda, M. R. (2024). Genetic diversity and relationship of native Phalaenopsis orchids: A case study of Indonesian Archipelago. Tekirdağ Journal of Agricultural Faculty, 21, 451–463. https://doi.org/10.33462/jotaf.1247037
  33. Mursyidin, D. H., & Hidayat, M. A. (2025). Genetic relationships of native Phalaenopsis orchids from the South Kalimantan (Borneo), Indonesia: A morphological and molecular approaches. Yuzuncu Yil University Journal of Agricultural Sciences, 35(2), 219–230. https://doi.org/10.29133/yyutbd.1577319
  34. Mursyidin, D. H., Rubiansyah, M., & Badruzsaufari. (2022). Genetic relationship of several morphological and molecular characteristics of Phalaenopsis amabilis (L.) Blume orchids from the Meratus Mountains of South Kalimantan, Indonesia. Indonesian Journal of Forestry Research, 9, 63–72. https://doi.org/10.20886/ijfr.2022.9.1.63-72
  35. Niknejad, A., Kadir, M. A., Kadzimin, S. B., Abdullah, N. A. P., & Sorkheh, K. (2009). Molecular characterization and phylogenetic relationships among and within species of Phalaenopsis (Epidendroideae: Orchidaceae) based on RAPD analysis. African Journal of Biotechnology, 8, 5225–5240. https://doi.org/10.5897/AJB09.703
  36. Nishimaki, T., & Sato, K. (2019). An extension of the Kimura two parameter model to the natural evolutionary process. Journal of Molecular Evolution, 87, 60–67. https://doi.org/10.1007/s00239-018-9885-1
  37. Palmer, C., & Fischer, B. (2022). Should global conservation initiatives prioritize phylogenetic diversity? Philosophia, 50, 2283–2302. https://doi.org/10.1007/s11406-021-00422-7
  38. Penjor, T., Yamamoto, M., Uehara, M., Ide, M., Matsumoto, N., Matsumoto, R., & Nagano, Y. (2013). Phylogenetic relationships of Citrus and its relatives based on matK gene sequences. PLoS ONE, 8, e62574. https://doi.org/10.1371/journal.pone.0062574
  39. Pontarotti, P. (Ed.). (2008). Evolutionary biology from concept to application. Springer. https://doi.org/10.1007/978-3-540-78993-2
  40. Rotimi, E. A. (2024). Application of genomics in livestock production: A review. World Scientific News, 198, 110–119.
  41. Sameer, A. S., Banday, M. Z., & Nissar, S. (2021). Mutations and polymorphisms: What is the difference In Genetic polymorphism and cancer susceptibility (pp. 1–21). Springer. https://doi.org/10.1007/978-981-33-6699-2_1
  42. Sharma, S. P., Katdare, S., Zaidi, Z., Ghazi, M. G., Gupta, S. K., & Hussain, S. A. (2020). Mitochondrial DNA analysis reveals extremely low genetic diversity in a managed population of the Critically Endangered gharial (Gavialis gangeticus, Gmelin, 1789). Herpetological Journal, 30, 202–206. https://doi.org/10.33256/hj30.4.202206
  43. Singh, H. P., Raigar, O. P., & Chahota, R. K. (2022). Estimation of genetic diversity and its exploitation in plant breeding. Botanical Review, 88, 413–435. https://doi.org/10.1007/s12229-021-09274-y
  44. Tajima, F. (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585–595. https://doi.org/10.1093/genetics/123.3.585
  45. Takahashi, Y., Tanaka, R., Yamamoto, D., Noriyuki, S., & Kawata, M. (2018). Balanced genetic diversity improves population fitness. Proceedings of the Royal Society B, 285, 20172045. https://doi.org/10.1098/rspb.2017.2045
  46. Teoh, E. S. (2021). Phalaenopsis Bl. In Orchid species from Himalaya and Southeast Asia, Vol. 2 (G–P) (pp. 245–304). Springer. https://doi.org/10.1007/978-3-030-80428-2_33
  47. Tiwari, P., Sharma, A., Bose, S. K., & Park, K.-I. (2024). Advances in orchid biology: Biotechnological achievements, translational success, and commercial outcomes. Horticulturae, 10(2), 152. https://doi.org/10.3390/horticulturae10020152
  48. Tsai, C. C., Chiang, Y. C., Huang, S. C., Chen, C. H., & Chou, C. H. (2010). Molecular phylogeny of Phalaenopsis Blume (Orchidaceae) on the basis of plastid and nuclear DNA. Plant Systematics and Evolution, 288, 77–98. https://doi.org/10.1007/s00606-010-0314-1
  49. Tsai, C. C., Chou, C. H., Wang, H. V., Ko, Y. Z., Chiang, T. Y., & Chiang, Y. C. (2015). Biogeography of the Phalaenopsis amabilis species complex inferred from nuclear and plastid DNAs. BMC Plant Biology, 15, 202. https://doi.org/10.1186/s12870-015-0560-z
  50. van Tongerlo, E., van Ieperen, W., Dieleman, J. A., & Marcelis, L. F. M. (2021). Vegetative traits can predict flowering quality in Phalaenopsis orchids despite large genotypic variation in response to light and temperature. PLoS ONE, 16(5), e0251405. https://doi.org/10.1371/journal.pone.0251405
  51. Wartha, C. A., & Lorenz, A. J. (2024). Genomic predictions of genetic variances and correlations among traits for breeding crosses in soybean. Heredity, 133, 173–185. https://doi.org/10.1038/s41437-024-00703-3
  52. Wicke, K., & Fischer, M. (2018). Phylogenetic diversity and biodiversity indices on phylogenetic networks. Journal of Theoretical Biology, 439, 216–225. https://doi.org/10.1016/j.jtbi.2017.11.002
  53. Wicke, S., Schneeweiss, G. M., dePamphilis, C. W., Müller, K. F., & Quandt, D. (2011). The evolution of the plastid chromosome in land plants: Gene content, gene order, gene function. Plant Molecular Biology, 76, 273–297. https://doi.org/10.1007/s11103-011-9762-4
  54. Xie, Z., Fan, S., Xu, J., Xiao, H., Yang, J., Guo, M., & Cheng, C. (2025). Identification and classification of Aquilaria (Thymelaeaceae): Inferences from a phylogenetic study based on matK sequences. PeerJ, 13, e19752. https://doi.org/10.7717/peerj.19752
  55. Xu, X., & Reid, N. (2011). On the robustness of maximum composite likelihood estimate. Journal of Statistical Planning and Inference, 141(9), 3047–3054. https://doi.org/10.1016/j.jspi.2011.03.026