An In Silico Approach for Evaluation of ITS, rbcL, and psbA-trnH for DNA Barcoding of Eugenia spp.

Syifara Chika, Shofiyyatuz Zahro

Abstract


The genus Eugenia is known to be complex with intricate synonyms and taxonomy, and morphological identification is often unreliable due to overlapping characteristics and environmental influences, particularly in the flowers. DNA barcoding provides a way around this problem, as it can identify specimens using very short gene sequence fragments obtained from a small number of tissues.  The method used in this research is the in silico dengan menggunakan barcode DNA ITS, rbcL, dan psbA-trnH dari spesies Eugenia spp yang ditemukan di NCBI GenBank. The successful reconstruction of the phylogenetic tree from the three regions, including ITS, rbcL, and psbA-trnH shows that several species of Eugenia spp. are divided into 2 clades. Research successfully analyzed Eugenia plant relationship with using the ITS, rbcL, and psbA-trnH gene sequences in silico based shows that several species of Eugenia spp. are divided into 2 clades. In general, high bootstrap values are shown by phylogenetic trees based on the ITS region.

ABSTRAK: Genus Eugenia dikenal kompleks dengan sinonim dan taksonomi yang rumit, serta identifikasi morfologis yang sering tidak dapat diandalkan karena karakter yang tumpang tindih dan dipengaruhi oleh lingkungan, terutama pada bagian bunga. Barcoding DNA memberikan jalan keluar dari masalah ini, karena dapat mengidentifikasi spesimen menggunakan fragmen urutan gen yang sangat pendek yang diperoleh dari sejumlah kecil jaringan. Metode yang digunakan dalam penelitian ini adalah in silico dengan menggunakan barcode DNA ITS, rbcL, dan psbA-trnH dari spesies Eugenia spp yang ditemukan di NCBI GenBank. Keberhasilan rekonstruksi pohon filogenetik dari tiga wilayah antara lain ITS, rbcL, dan psbA-trnH menunjukkan bahwa beberapa spesies Eugenia spp. dibagi menjadi 2 clade. Penelitian yang berhasil menganalisis hubungan tanaman Eugenia dengan menggunakan rangkaian gen ITS, rbcL, dan psbA-trnH secara silico menunjukkan bahwa beberapa spesies Eugenia spp. dibagi menjadi 2 clade. Secara umum nilai bootstrap yang tinggi ditunjukkan oleh pohon filogenetik berdasarkan wilayah ITS.


Keywords


DNA barcode; Eugenia; ITS; psbA-trnh; rbcL.

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References


Araujo, N. M., Arruda, H. S., de Paulo Farias, D., Molina, G., Pereira, G. A., & Pastore, G. M. (2021). Plants from the genus Eugenia as promising therapeutic agents for the management of diabetes mellitus: A review. Food Research International, 142(February). https://doi.org/10.1016/j.foodres.2021.110182

Arita, M., Karsch-Mizrachi, I., & Cochrane, G. (2021). The international nucleotide sequence database collaboration. Nucleic Acids Research, 49(D1), D121–D124. https://doi.org/10.1093/nar/gkaa967

Aung, E. E., Kristanti, A. N., Aminah, N. S., Takaya, Y., & Ramadhan, R. (2020). Plant description, phytochemical constituents and bioactivities of Syzygium genus: A review. Open Chemistry, 18(1), 1256–1281. https://doi.org/10.1515/chem-2020-0175

Badou, R. B., Yedomonhan, H., Ewedje, E. E. B. K., Dassou, G. H., Adomou, A., Tossou, M., & Akoegninou, A. (2020). Floral morphology and pollination system of Syzygium guineense (Willd.) DC. subsp. macrocarpum (Engl.) F. White (Myrtaceae), a subspecies with high nectar production. South African Journal of Botany, 131, 462–467. https://doi.org/10.1016/j.sajb.2020.04.013

Bare, Y., Sari, D. R. T., Nita, A. D., & Taek, M. M. (2022). Berberine: A Potential Inhibitor of Dihydrofolate Reductase- Thymidylate Synthase (DHFR-TS) for Malaria. Biosfer: Jurnal Tadris Biologi, 13(1), 93–99. https://doi.org/10.24042/biosfer.v13i1.11145

Batiha, G. E. S., Akhtar, N., Alsayegh, A. A., Abusudah, W. F., Almohmadi, N. H., Shaheen, H. M., Singh, T. G., & De Waard, M. (2022). Bioactive Compounds, Pharmacological Actions, and Pharmacokinetics of Genus Acacia. Molecules, 27(21), 1–22. https://doi.org/10.3390/molecules27217340

Canay, I. A., Santos, A., & Shaikh, A. M. (2021). The wild bootstrap with a “small” number of “large” clusters. Review of Economics and Statistics, 103(2), 346–363. https://doi.org/10.1162/rest_a_00887

Cardoso, C. M. V., & Sajo, M. das G. (2004). Vascularização foliar e a identificação de espécies de Eugenia L. (Myrtaceae) da bacia hidrográfica do Rio Tibagi, PR. Revista Brasileira de Botânica, 27(1), 47–54. https://doi.org/10.1590/s0100-84042004000100006

da Costa, J. S., da Cruz, E. de N. S., Setzer, W. N., da Silva, J. K. D. R., Maia, J. G. S., & Figueiredo, P. L. B. (2020). Essentials oils from Brazilian eugenia and syzygium species and their biological activities. Biomolecules, 10(8), 1–36. https://doi.org/10.3390/biom10081155

de Paulo Farias, D., Neri-Numa, I. A., de Araújo, F. F., & Pastore, G. M. (2020). A critical review of some fruit trees from the Myrtaceae family as promising sources for food applications with functional claims. Food Chemistry, 306(October 2019), 125630. https://doi.org/10.1016/j.foodchem.2019.125630

Defaveri, A. C. A., Arruda, R. C. O., & Sato, A. (2011). Leaf anatomy and morphology of eugenia rotundifolia applied to the authentication of the “abajurú” commercially sold. Revista Brasileira de Farmacognosia, 21(3), 373–381. https://doi.org/10.1590/S0102-695X2011005000029

Enagbonma, B. J., Aremu, B. R., & Babalola, O. O. (2019). Profiling the functional diversity of termite mound soil bacteria as revealed by shotgun sequencing. Genes, 10(9). https://doi.org/10.3390/genes10090637

Foresti, A. C., Reis, L. C., Paula, S., Scalon, Q., Dresch, D. M., Santos, C. C., & Jesus, M. V. (2024). Salicylic acid mitigating damage to the photosynthetic apparatus and quality of Eugenia myrcianthes seedlings under water deficit. Rodriguésia, 73, e00872021.

Giaretta, A., Murphy, B., Maurin, O., Mazine, F. F., Sano, P., & Lucas, E. (2022). Phylogenetic Relationships Within the Hyper-Diverse Genus Eugenia (Myrtaceae: Myrteae) Based on Target Enrichment Sequencing. Frontiers in Plant Science, 12(February), 1–20. https://doi.org/10.3389/fpls.2021.759460

Guollo, K., Neto, C. K., da Rosa, V., Garay, I. A., Wagner, A., & Rocha, M. A. M. (2024). Floral, reproductive, and pollination biology of Eugenia myrcianthes Nied. Comunicata Scientiae, 15(August). https://doi.org/10.14295/CS.v15.3504

Hu, D., Liu, B., Wang, L., & Reeves, P. R. (2020). Living Trees: High-Quality Reproducible and Reusable Construction of Bacterial Phylogenetic Trees. Molecular Biology and Evolution, 37(2), 563–575. https://doi.org/10.1093/molbev/msz241

Jamdade, R., Mosa, K. A., El-Keblawy, A., Al Shaer, K., Al Harthi, E., Al Sallani, M., Al Jasmi, M., Gairola, S., Shabana, H., & Mahmoud, T. (2022). DNA Barcodes for Accurate Identification of Selected Medicinal Plants (Caryophyllales): Toward Barcoding Flowering Plants of the United Arab Emirates. Diversity, 14(4). https://doi.org/10.3390/d14040262

Kamelia, M., Ulmillah, A., & Pawhestri, S. W. (2024). Potential of Methane (CH4), Nitrogen (N2), and Carbon Dioxide (CO2) from Eco-Enzyme with the Addition of Cow Feces Starter. Biology, Medicine, & Natural Product Chemistry, 13(1), 35–42. https://doi.org/10.14421/biomedich.2024.131.35-42

Kapli, P., Flouri, T., & Telford, M. J. (2021). Systematic errors in phylogenetic trees. Current Biology, 31(2), R59–R64. https://doi.org/10.1016/j.cub.2020.11.043

Kapli, P., Yang, Z., & Telford, M. J. (2020). Phylogenetic tree building in the genomic age. Nature Reviews Genetics, 21(7), 428–444. https://doi.org/10.1038/s41576-020-0233-0

Kostikova, V. A., & Petrova, N. V. (2021). Phytoconstituents and bioactivity of plants of the genus spiraea l. (rosaceae): A review. International Journal of Molecular Sciences, 22(20). https://doi.org/10.3390/ijms222011163

Laha, S., Chatterjee, S., Das, A., Smith, B., & Basu, P. (2020). Exploring the importance of floral resources and functional trait compatibility for maintaining bee fauna in tropical agricultural landscapes. Journal of Insect Conservation, 24(3), 431–443. https://doi.org/10.1007/s10841-020-00225-3

Letunic, I., & Bork, P. (2021). Interactive tree of life (iTOL) v5: An online tool for phylogenetic tree display and annotation. Nucleic Acids Research, 49(W1), W293–W296. https://doi.org/10.1093/nar/gkab301

Low, Y. W., Rajaraman, S., Tomlin, C. M., Ahmad, J. A., Ardi, W. H., Armstrong, K., Athen, P., Berhaman, A., Bone, R. E., Cheek, M., Cho, N. R. W., Choo, L. M., Cowie, I. D., Crayn, D., Fleck, S. J., Ford, A. J., Forster, P. I., Girmansyah, D., Goyder, D. J., Albert, V. A. (2022). Genomic insights into rapid speciation within the world’s largest tree genus Syzygium. Nature Communications, 13(1), 1–15. https://doi.org/10.1038/s41467-022-32637-x

Madduppa, H., Sani, L. M. I., Nugroho, K. C., Bengen, D. G., Muchlisin, Z. A., Fadli, N., Subhan, B., Arafat, D., Zamani, N. P., Sunuddin, A., Ismet, M. S., Srimariana, E. S., Cakasana, N., Lestari, D. F., Santoso, P., Setyaningsih, W. A., Baksir, A., Manurung, V. R., Damora, A., Moore, A. M. (2022). eDNA metabarcoding of decapod crustaceans across Indonesian seas has implications for biodiversity conservation and fisheries sustainability. Frontiers in Marine Science, 9(September), 1–23. https://doi.org/10.3389/fmars.2022.918295

Mahmoud, M. F., Nabil, M., Abdo, W., Abdelfattah, M. A. O., El-Shazly, A. M., El Kharrassi, Y., & Sobeh, M. (2021). Syzygium samarangense leaf extract mitigates indomethacin-induced gastropathy via the NF-κB signaling pathway in rats. Biomedicine and Pharmacotherapy, 139(March), 111675. https://doi.org/10.1016/j.biopha.2021.111675

Martin, D. P., Varsani, A., Roumagnac, P., Botha, G., Maslamoney, S., Schwab, T., Kelz, Z., Kumar, V., & Murrell, B. (2021). RDP5: A computer program for analyzing recombination in, and removing signals of recombination from, nucleotide sequence datasets. Virus Evolution, 7(1), 5–7. https://doi.org/10.1093/ve/veaa087

Mbobo, T., Richardson, D. M., & Wilson, J. R. U. (2023). Syzygium australe (J.C.Wendl. ex Link) B. Hyland (Myrtaceae) in South Africa: Current distribution and invasion potential. BioInvasions Records, 12(3), 637–648. https://doi.org/10.3391/bir.2023.12.3.01

Medeiros, F. L. B., Santos, C. A. F., & Costa, A. E. S. (2021). In silico microsatellite transferability from Psidium guajava to Eucalyptus globulus validated by PCR. Genetics and Molecular Research, 20(4), 1–9. https://doi.org/10.4238/GMR18985

Ningrum, W. D. A., Atmaja, M. B., Daryono, B. S., & Purnomo. (2020). Genetic variability of begonia longifolia blume from indonesia based on nuclear dna internal transcribed spacer (Its) sequence data. Biodiversitas, 21(12), 5778–5785. https://doi.org/10.13057/biodiv/d211239

Pittarelli, B. F. d. S., Mourão, K. S. M., & Thadeo, M. (2021). Pericarp development in Campomanesia Ruiz & Pav. (Myrtaceae) species and systematic implications for the genus. Flora: Morphology, Distribution, Functional Ecology of Plants, 282(January). https://doi.org/10.1016/j.flora.2021.151885

Rachmah, A. N., Febriana, A., Kusumarini, N., Oktaviani, E., & Mukaromah, A. S. (2023). Authentication of Three Wax Apples Cultivars (Syzygium Samarangense (Blume) Merr. & L.M. Perry) Based on Morphological Character and Fruit Metabolite Profile. Floribunda, 7(2), 64–74. https://doi.org/10.32556/floribunda.v7i2.2023.409

Reis, A. S., Silva, L. de S., Martins, C. F., & Paula, J. R. de. (2021). Analysis of the volatile oils from three species of the gender Syzygium. Research, Society and Development, 10(7), e13510716375. https://doi.org/10.33448/rsd-v10i7.16375

Riaz, S., & Abid, R. (2021). Foliar characteristics as an aid for the specific delimitation of the genus cleome l. (cleomaceae) from pakistan. Pakistan Journal of Botany, 53(4), 1325–1330. https://doi.org/10.30848/PJB2021-4(17)

Salem, M. A., Mahdy, O. A., Shaalan, M., & Ramadan, R. M. (2023). The phylogenetic position and analysis of Renicola and Apharyngostrigea species isolated from Cattle Egret (Bubulcus ibis). Scientific Reports, 13(1), 1–10. https://doi.org/10.1038/s41598-023-43479-y

Salsabila, A. R., Rahmawati, Y. F., & Jamallika, N. (2023). Diversity and Functional Role of The Coleoptera Order in The Nglanggeran Ancient Volcano Area, Yogyakarta. Biosfer : Jurnal Tadris Biologi, 14(2), 227–236. https://doi.org/10.24042/b

Santos, C. C., Scalon, S. P. Q., Foresti, A. C., Reis, L. C., & Dresch, D. M. (2022). The role of silicon in the mitigation of water stress in Eugenia myrcianthes Nied. seedlings. Brazilian Journal of Biology, 82, 1–7. https://doi.org/10.1590/1519-6984.260420

Shulgina, Y., & Eddy, S. R. (2023). Codetta: predicting the genetic code from nucleotide sequence. Bioinformatics, 39(1), 1–3. https://doi.org/10.1093/bioinformatics/btac802

Silverio, J. M., Dos Santos, J. K. V., da Silva, M. S., de P. Q. Scalon, S., Santos, C. C., Reis, L. C., & Linné, J. A. (2024). Does hydrogel help in the mitigation and recovery of Eugenia myrcianthes Nied. under water stress? Revista Caatinga, 37(1), 1–9. https://doi.org/10.1590/1983-21252024v3712000rc

Smith, M. R. (2020). Information theoretic generalized Robinson-Foulds metrics for comparing phylogenetic trees. Bioinformatics, 36(20), 5007–5013. https://doi.org/10.1093/bioinformatics/btaa614

Tefu, M. O., R Sabat, D., Muki, S., & Taek, D. (2023). The Use Value of Medicinal Plant Species of Dawan (Amanatun) Community in Hoineno Village, South Central Timor District. Biosfer: Jurnal Tadris Biologi, 13(2), 149–162. https://doi.org/10.24042/biosfer.v13i2.13927

Villaverde, T., Jiménez-Mejías, P., Luceño, M., Waterway, M. J., Kim, S., Lee, B., Rincón-Barrado, M., Hahn, M., Maguilla, E., Roalson, E. H., Hipp, A. L., Wilson, K. L., Larridon, I., Gebauer, S., Hoffmann, M. H., Simpson, D. A., Naczi, R. F. C., Reznicek, A. A., Ford, B. A., Martín-Bravo, S. (2020). A new classification of Carex (Cyperaceae) subgenera supported by a HybSeq backbone phylogenetic tree. Botanical Journal of the Linnean Society, 194(2), 141–163. https://doi.org/10.1093/botlinnean/boaa042

Wang, L. G., Lam, T. T. Y., Xu, S., Dai, Z., Zhou, L., Feng, T., Guo, P., Dunn, C. W., Jones, B. R., Bradley, T., Zhu, H., Guan, Y., Jiang, Y., & Yu, G. (2020). Treeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data. Molecular Biology and Evolution, 37(2), 599–603. https://doi.org/10.1093/molbev/msz240

Wibberg, D., Stadler, M., Lambert, C., Bunk, B., Spröer, C., Rückert, C., Kalinowski, J., Cox, R. J., & Kuhnert, E. (2021). High quality genome sequences of thirteen Hypoxylaceae (Ascomycota) strengthen the phylogenetic family backbone and enable the discovery of new taxa. Fungal Diversity, 106(1), 7–28. https://doi.org/10.1007/s13225-020-00447-5

Widiani, N., Winandari, O. P., Kamelia, M., & Nurrohmah, P. (2021). Analisis in Silico Senyawa Hibiscetin Kombucha Rosella Sebagai Imunomodulator Sel Imunokompeten Pada Penyakit Malaria. BIOEDUKASI (Jurnal Pendidikan Biologi), 12(2), 229. https://doi.org/10.24127/bioedukasi.v12i2.4452

Winandari, O. P., Saputri, D. A., & Yuliani, D. R. (2024). Ethnobotany of Javanese Medicinal Plants in Batumarta VI, South Sumatra. E3S Web of Conferences, 482. https://doi.org/10.1051/e3sconf/202448201012

Zahro, S., Wahidah, B. F., & Hariri, M. R. (2023). Short Notes on the Leaf Architecture and Morphometry of Syzygium spp . Leaves from the Living Collections of Bogor Botanic Gardens. Biosfer: Jurnal Tadris Biologi, 14(2), 181–191. https://doi.org/10.24042/b

Zhang, Y., Deng, T., Sun, L., Landis, J. B., Moore, M. J., Wang, H., Wang, Y., Hao, X., Chen, J., Li, S., Xu, M., Puno, P. T., Raven, P. H., & Sun, H. (2021). Phylogenetic patterns suggest frequent multiple origins of secondary metabolites across the seed-plant “tree of life.” National Science Review, 8(4). https://doi.org/10.1093/nsr/nwaa105




DOI: http://dx.doi.org/10.24042/biosfer.v15i1.21064

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