GENETIC VARIATION OF WAX APPLE (Syzygium samarangense (Blume) Merr. & L.M. Perry) CULTIVAR USING INTERNAL TRANSCRIBED SPACER 2 (ITS2)
DOI:
https://doi.org/10.55981/floribunda.v7i4.2024.3910Abstract
Syifara Chika, Tiara Dwi Meilina, Muhammad Ramdhani Arfan, Asri Febriana & Arnia Sari Mukaromah 2024. Genetic variation of wax apple (Syzygium samarangense (Blume) Merr. & L.M. Perry) cultivar using internal transcribed spacer 2 (ITS2). Floribunda 7(4): 153–165 — Wax apple (Syzygium samarangense (Blume) Merr. & L.M. Perry) is a tropical fruit, has diverse cultivars and classified as a non-climacteric fruit. The study objectives were to identify the genetic variation of the S. samarangense cultivars in the ITS2 DNA barcode region, analyze the phylogenetic relationships among S. samarangense cultivars and determine successfulness of ITS2 barcode to describe genetic variation of the S. samarangense cultivars from Demak Regency, Central Java, Indonesia. Furthermore, the stages in this study consisted of sampling, environmental parameters analysis, DNA isolation, DNA amplification, electrophoresis, DNA sequencing in the First Base Malaysia, analysis of DNA sequencing data, secondary structure prediction of ITS2, and reconstruction a phylogenetic tree using MEGA 11 and ITS2 database. The result shown appearance of few nucleotide variation among S. samarangense cultivars and there were nucleotides variations between S. samarangense and Syzygium aqueum in the ITS2 region. S. samarangense cultivar Citra Wonosari and cultivar Delima Wonosari had the identical secondary structure of ITS2. However, this was slightly different between S. samarangense cultivar Citra Botorejo secondary structure of ITS2 which consisted of only two loops in helix I and cultivar Citra Tempuran second loop in helix I which bigger than all samples. The phylogenetic tree described the closely relationship between S. samarangense Citra cultivars, and had separated S. samarangense cultivar Delima in the different clade. The genetic relationship of S. samarangense cultivars were more influenced by cultivar type rather than cultivated location. Therefore, ITS2 could be utilized for genetic variation analysis of S. samarangense cultivars.
References
Ananto, A. D. 2022. Autentikasi Metabolit Ekstrak Buah Jambu Semarang (Syzygium samarangense (Blume) Merr. & L.M. Perry) ’Citra’ di Kabupaten Demak. Skripsi Universitas Islam Negeri Walisongo Semarang.
Buys, M. H., Flint, H. J., Miller, E. M., Yao, H., Caird, A. R., & Ganley, R. J. 2016. Preparing for the invasion: efficacy of DNA barcoding to discern the host range of myrtle rust (Puccinia psidii) among species of Myrtaceae. Forestry, 89(3), 263–270.
Chen, S., Yao, H., Han, J., Liu, C., Song, J., Shi, L., Zhu, Y., Ma, X., Gao, T., & Pang, X. 2010. Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PloS One, 5(1), e8613.
Cheng, T., Xu, C., Lei, L., Li, C., Zhang, Y., & Zhou, S. 2016. Barcoding the kingdom Plantae: new PCR primers for ITS regions of plants with improved universality and specificity. Molecular Ecology Resources, 16(1), 138–149.
Coker, O. M. 2017. Importance of genetics in conservation of biodiversity. J Wildl Manage, 1, 11–18.
Coleman, A. W. 2003. ITS2 is a double-edged tool for eukaryote evolutionary comparisons. 19(7), 370–375. https://doi.org/10.1016/S0168-9525(03)00118-5
Duan, H., Wang, W., Zeng, Y., Guo, M., & Zhou, Y. 2019. The screening and identification of DNA barcode sequences for Rehmannia. Scientific Reports, 9(1), 1–12.
Felsenstein J. (1985). Confidence limits on phylogenies: An approach using the bootstrap. Evolution. 39:783-791.
Feng, S., Jiang, Y., Wang, S., Jiang, M., Chen, Z., Ying, Q., & Wang, H. 2015. Molecular identification of Dendrobium species (Orchidaceae) based on the DNA barcode ITS2 region and its application for phylogenetic study. International Journal of Molecular Sciences, 16(9), 21975–21988.
Hall, T. A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41(41), 95–98.
Ilmi, Z. L. 2021. Keragaman kultivar Pisang Kepok (Musa acuminata x Musa balbisiana (ABB) cv. Kepok) di Kabupaten Malang berdasarkan karakter morfologi dan molekuler RAPD (Random Amplified Polymorphic DNA). Universitas Islam Negeri Maulana Malik Ibrahim.
Irawan, P. D., Tallei, T. E., & Kolondam, B. J. 2016. Analisis Sekuens dan Filogenetik Beberapa Tumbuhan Syzygium (Myrtaceae) di Sulawesi Utara Berdasarkan Gen matK. Jurnal Ilmiah Sains, 16(2), 43. https://doi.org/10.35799/jis.16.2.2016.14022
Joko. 2014. Sukses Bertanam Jambu Biji Dan Jambu Air Di Pekarangan Rumah Dan Kebun. Pustaka Baru Press.
Jukes T.H. and Cantor C.R. (1969). Evolution of protein molecules. In Munro HN, editor, Mammalian Protein Metabolism, pp. 21-132, Academic Press, New York.
Meitha, K., Fatmawati, I., Dwivany, F. M., Sutanto, A., Pratama, S. N., Nugrahapraja, H., & Wikantika, K. 2020. Phylogenetic analysis of 23 accessions of Indonesian banana cultivars based on internal transcribed spacer 2 (ITS2) region. Indonesian Journal of Biotechnology, 25(1), 1–11.
Merget, B., Koetschan, C., Hackl, T., Förster, F., Dandekar, T., Müller, T., Schultz, J., Wolf, M. 2012. The ITS2 database. Journal of Visualized Experiments. 12(61). doi:10.3791/3806" target="_blank"
Mukaromah, A. S. 2020. Wax Apple (Syzygium samarangense (Blume) Merr. & L.M. Perry): A Comprehensive Review in Phytochemical and Physiological Perspectives. Al-Hayat: Journal of Biology and Applied Biology, 3(1), 40. https://doi.org/10.21580/ah.v3i1.6070
Mukaromah, A.S., Ulfah, M. 2021. Autentikasi Tanaman Jambu Semarang (Syzygium samarangense (Blume) Merr. & L.M. Perry) Kultivar Delima dan Citra di Kabupaten Demak Menggunakan DNA Barcoding. Laporan Penelitian Litapdimas Kemenag Tahun 2021.
Mukaromah, A. S., Ulfah, M., Rachmah, A. N., Arfan, M. R., Kusumarini, N., & Febriana, A. 2023. Authentication of Wax Apple (Syzygium samarangense (Blume) Merr . & L . M Perry) Delima and Citra Cultivars by Morphological and Molecular Approach. Al-Hayat: Journal of Biology and Applied Biology, 6(1). https://doi.org/10.21580/ah.v6i1.18713
Octavia, D., Mukaromah, A. S., Martiansyah, I., Mimin, M., Ma’mun, S., & Rukmanto, H. 2021. Isolasi DNA tumbuhan hasil eksplorasi di Nusakambangan dengan metode kit di Laboratorium Treub, Kebun Raya Bogor. Prosiding Seminar Nasional Biologi, 7(1), 291–299.
Peltier, S. K., Brown, J. D., Ternent, M., Niedringhaus, K. D., Schuler, K., Bunting, E. M., Kirchgessner, M., & Yabsley, M. J. 2017. Genetic characterization of Sarcoptes scabiei from black bears (Ursus americanus) and other hosts in the eastern United States. Journal of Parasitology, 103(5), 593–597.
Rachmah, A. N., Febriana, A., Kusumarini, N., Oktaviani, E., & Mukaromah, A. S. 2023. Authentication of Three Wax Apples Cultivars (Syzygium samarangense (Blume) Merr. & LM Perry) Based on Morphological Character and Fruit Metabolite Profile. Floribunda, 7(2), 64–74.
Roslim, D. I., & Fitriani, A. 2021. Barkoding DNA pada Tumbuhan Durik-Durik (Syzygium sp.) Asal Riau Menggunakan Daerah Gen ndhF. Jurnal Bios Logos, 11(1), 41–46.
Schultz, J., Maisel, S., Gerlach, D., Müller, T., & Wolf, M. 2005. A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota. RNA, 11(4), 361–364. https://doi.org/10.1261/rna.7204505
Sinay, H., Arumingtyas, E. L., Harijati, N., & Indriyani, S. 2016. Keragaman dan kekerabatan kultivar jagung (Zea mays L.) lokal asal Pulau Kisar Kabupaten Maluku berdasarkan karakter fenotip. BIOPENDIX: Jurnal Biologi, Pendidikan Dan Terapan, 3(1), 18–27.
Tamura, K., Stecher, G., & Kumar, S. 2021. MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Molecular Biology and Evolution, 38(7), 3022–3027. https://doi.org/10.1093/molbev/msab120
Ubaidillah, R. & S. 2009. Pengantar Biosistemik: Teori dan Praktik. LIPI Press.
Widodo, P. 2015. Jambu semarang dan jambu air. Purwokerto: Universitas Jenderal Soedirman.
Widyatmoko, D. 2019. Strategi dan Inovasi Konservasi Tumbuhan Indonesia Untuk Pemanfaatan Secara Berkelanjutan. Seminar Nasional Pendidikan Biologi Dan Saintek (SNPBS) Ke-IV, 2527-533X(Tabel 2), 1–22.
Wilkerson, R. C., Reinert, J. F., & Li, C. 2014. Ribosomal DNA ITS2 sequences differentiate six species in the Anopheles crucians complex (Diptera: Culicidae). Journal of Medical Entomology, 41(3), 392–401.
Downloads
Published
Issue
Section
License
Copyright (c) 2024 Floribunda
This work is licensed under a Creative Commons Attribution 4.0 International License.
Authors who publish with this journal agree to the following terms:
- Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
- Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (SeeThe Effect of Open Access).
