Analisis Filogenetik dan Jarak Genetik Kopi Robusta (Coffea canephora) Berdasarkan Sekuen Internal Transcribed Spacer (ITS)
Phylogenetic and Genetic Distance Analysis of Robusta Coffee (Coffea canephora) Using Internal Transcribed Spacer (ITS) Sequences
Abstract
Kopi robusta (Coffea canephora) merupakan komoditas perkebunan penting yang memiliki nilai ekonomi tinggi dan berperan besar dalam produksi kopi dunia. Informasi mengenai keragaman genetik dan hubungan kekerabatan antar genotipe kopi robusta diperlukan untuk mendukung program pemuliaan tanaman, konservasi plasma nutfah, dan pengembangan varietas unggul. Penelitian ini bertujuan untuk menganalisis hubungan filogenetik dan jarak genetik C. canephora berdasarkan sekuens Internal Transcribed Spacer (ITS). Penelitian ini menggunakan data sekuens DNA dari database GenBank NCBI. Sampel yang digunakan terdiri atas 18 aksesi C. canephora dari Brazil, Uganda, Meksiko, Sierra Leone, Filipina, dan Inggris, serta satu spesies outgroup, yaitu Psilanthus ebracteolatus. Panjang awal sekuens berkisar antara 657 dan 842 bp. Rentang ini menunjukkan bahwa data yang dianalisis merupakan fragmen ITS lengkap. Analisis filogenetik dilakukan menggunakan MEGA 12 dengan metode Maximum Likelihood, model substitusi Tamura-Nei, dan uji bootstrap 1000 replikasi. Analisis pairwise genetic distance dilakukan untuk menghitung jarak genetik antar sekuens. Hasil analisis menunjukkan bahwa aksesi C. canephora membentuk satu kelompok utama yang terbagi menjadi beberapa subclade. Sebagian besar aksesi memiliki jarak genetik rendah, yang menunjukkan kemiripan genetik tinggi. Aksesi Uganda membentuk kelompok tersendiri dan memperlihatkan jarak yang tinggi terhadap aksesi non-Uganda. Nilai jarak yang tinggi tersebut perlu ditafsirkan secara hati-hati karena dapat dipengaruhi oleh diferensiasi genetik alami populasi Afrika dan oleh faktor teknis akibat perbandingan fragmen ITS yang belum sama. Temuan ini memberi dasar awal untuk pemilihan aksesi dalam konservasi plasma nutfah dan pemuliaan kopi robusta.
Kata kunci: analisis filogenetik, Coffea canephora, ITS, jarak genetik, MEGA 12
References
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Kairupan, C.F., Koneri, R. and Tallei, T.E., 2015. Variasi Genetik Troides helena (Lepidoptera: Papilionidae) Berdasarkan Gen COI (Cytochrome C Oxydase I). Jurnal MIPA, 4(2), p.141. https://doi.org/10.35799/jm.4.2.2015.9039.
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Maurin, O., Davis, A.P., Chester, M., Mvungi, E.F., Jaufeerally-Fakim, Y. and Fay, M.F., 2007. Towards a phylogeny for Coffea (Rubiaceae): identifying well-supported lineages based on nuclear and plastid DNA sequences. Annals of Botany, 100(7), pp.1565–1583. https://doi.org/10.1093/aob/mcm257.
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Subari, A., Razak, A. and Sumarmin, R., 2021. Phylogenetic Analysis of Rasbora spp. Based on the Mitochondrial DNA COI gene in Harapan Forest. Jurnal Biologi Tropis, 21(1), pp.89–94. https://doi.org/10.29303/jbt.v21i1.2351.
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Syahruddin, K.-, 2021. Keragaman genetik koleksi plasmanutfah jewawut (Setaria italica (L.) P. Beauv.) berkerabat dekat menggunakan markah SSR. Kultivasi, 20(3). https://doi.org/10.24198/kultivasi.v20i3.34843.
Yao, H., Song, J., Liu, C., Luo, K., Han, J., Li, Y., Pang, X., Xu, H., Zhu, Y., Xiao, P. and Chen, S., 2010. Use of ITS2 region as the universal DNA barcode for plants and animals. PLoS ONE, 5(10), p.e13102. https://doi.org/10.1371/journal.pone.0013102.
Yosilia, R., Afandi, A., Hoya, A.L., Cahyani, C.N. and Hieno, A., 2024. Phytophthora palmivora Relationship Analysis on ITS rDNA Primers Using MEGA11 Software (NCBI DNA Sequencing Library Study). Jurnal Agrotek Tropika, 12(4). https://doi.org/10.23960/jat.v12i4.9532.
Andani, T.R., Analianasari, A. and Agassi, T.N., 2025. Karakteristik Fisiko Kimia Dan Cita Rasa Kopi Robusta (Coffea canephora) Pengolahan Black Honey Pada Ketinggian Dan Tingkatan (Level) Penyangraian Berbeda. Jurnal Pengembangan Agroindustri Terapan, 3(2). https://doi.org/10.25181/jupiter.v3i2.3287.
Budiasih, R.B., Mustopa, A.S. and Julianti, A., 2025. Identifikasi dan Karakterisasi Morfologi Tanaman Kopi (Coffea Sp.) Beserta Kekerabatannya di Kawasan Gunung Manglayang Timur Petak 9b Kab. Sumedang Jawa Barat. Jurnal Greenation Pertanian Dan Perkebunan, 2(3), pp.55–71. https://doi.org/10.38035/jgpp.v2i3.184.
Fajarningsih, N.D., 2016. Internal Transcribed Spacer (ITS) as Dna Barcoding to Identify Fungal Species: a Review. SQUALEN Bulletin of Marine and Fisheries Postharvest and Biotechnology, 11(2), p.37. https://doi.org/10.15578/squalen.v11i2.213.
Ferreira, T., Shuler, J., Guimarães, R. and Farah, A., 2019. CHAPTER 1. Introduction to Coffee Plant and Genetics. In: Coffee: Production, Quality and Chemistry. pp.1–25. https://doi.org/10.1039/9781782622437-00001.
Firly, F.R.R., 2024. Pengaruh Modal, Luas Lahan, Pupuk, dan Tenaga Kerja terhadap Produksi Kopi Robusta BSIP-TRI. Jurnal Agribisnis Dan Pembangunan Pertanian (JAPP), 2(1), pp.48–56. https://doi.org/10.37150/japp.v2i1.2536.
Gomez, C., Dussert, S., Hamon, P., Hamon, S., De Kochko, A. and Poncet, V., 2009. Current genetic differentiation of Coffea canephoraPierre ex A. Froehn in the Guineo-Congolian African zone: cumulative impact of ancient climatic changes and recent human activities. BMC Evolutionary Biology, 9(1), p.167. https://doi.org/10.1186/1471-2148-9-167.
Hermawan, C., 2023. Analisis Filogeni Kura-Kura Batok (Cuora amboinensis) Wilayah Indonesia Timur (Ambon, Luwu, Dan Gorontalo) Berbasis Sekuen Gen Cytochrome B. Jurnal Biosense, 6(01), pp.26–46. https://doi.org/10.36526/biosense.v6i01.2602.
Hillis, D.M. and Bull, J.J., 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systematic Biology, 42(2), pp.182–192. https://doi.org/10.1093/sysbio/42.2.182.
Huang, J., Liu, Y., Zhu, T. and Yang, Z., 2020. The asymptotic behavior of bootstrap support values in molecular phylogenetics. Systematic Biology, 70(4), pp.774–785. https://doi.org/10.1093/sysbio/syaa100.
Kairupan, C.F., Koneri, R. and Tallei, T.E., 2015. Variasi Genetik Troides helena (Lepidoptera: Papilionidae) Berdasarkan Gen COI (Cytochrome C Oxydase I). Jurnal MIPA, 4(2), p.141. https://doi.org/10.35799/jm.4.2.2015.9039.
Katsura, Y., Stanley, C.E., Kumar, S. and Nei, M., 2016. The Reliability and Stability of an Inferred Phylogenetic Tree from Empirical Data. Molecular Biology and Evolution, 34(3), p.msw272. https://doi.org/10.1093/molbev/msw272.
Keller, A., Schleicher, T., Schultz, J., Müller, T., Dandekar, T. and Wolf, M., 2008. 5.8S-28S rRNA interaction and HMM-based ITS2 annotation. Gene, 430(1–2), pp.50–57. https://doi.org/10.1016/j.gene.2008.10.012.
Kholqiyah, S.F., Wahyudi, D. and Hapsari, L., 2022. Kekerabatan Fenetik Heliconia spp. Koleksi Kebun Raya Purwodadi Berdasarkan Deskriptor Kualitatif. Buletin Plasma Nutfah, 28(1), p.45. https://doi.org/10.21082/blpn.v28n1.2022.p45-56.
Kiwuka, C., Goudsmit, E., Tournebize, R., De Aquino, S. O., Douma, J. C., Bellanger, L., Crouzillat, D., Stoffelen, P., Sumirat, U., Legnaté, H., Marraccini, P., De Kochko, A., Andrade, A. C., Mulumba, J. W., Musoli, P., Anten, N. P. R., & Poncet, V. (2021). Genetic diversity of native and cultivated Ugandan Robusta coffee (Coffea canephora Pierre ex A. Froehner): Climate influences, breeding potential and diversity conservation. PLoS ONE, 16(2), e0245965. https://doi.org/10.1371/journal.pone.0245965
Kumar, S., Stecher, G., Suleski, M., Sanderford, M., Sharma, S. and Tamura, K., 2024. MEGA12: Molecular Evolutionary Genetic Analysis Version 12 for Adaptive and Green Computing. bioRxiv. https://doi.org/10.1101/2024.12.10.627672.
Kumar, S., Tamura, K. and Nei, M., 1994. MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers. Computer Applications in the Biosciences, 10(2), pp.189–191. https://doi.org/10.1093/bioinformatics/10.2.189.
Maurin, O., Davis, A.P., Chester, M., Mvungi, E.F., Jaufeerally-Fakim, Y. and Fay, M.F., 2007. Towards a phylogeny for Coffea (Rubiaceae): identifying well-supported lineages based on nuclear and plastid DNA sequences. Annals of Botany, 100(7), pp.1565–1583. https://doi.org/10.1093/aob/mcm257.
Ningsih, S., Idami, Z. and Manalu, K., 2024. Keragaman Genetik Ikan Glodok (Periophthalmus sp.) Di Sungai Padang Kabupaten Batu Bara Menggunakan Gen CO1. Eduproxima Jurnal Ilmiah Pendidikan IPA, 6(4), pp.1306–1317. https://doi.org/10.29100/.v6i4.5706.
Pertiwi, A., Putri, A.K., Zains, A.R., Pratiwi, F.P. and Sandi, R.B., 2025. Studi Deskriptif Variabilitas Genetik Tanaman Kedelai sebagai Strategi Pertanian Berkelanjutan. RIGGS Journal of Artificial Intelligence and Digital Business, 4(4), pp.2628–2636. https://doi.org/10.31004/riggs.v4i4.3951.
Putri, M., 2022. Pengaruh Daerah Tempat Tumbuh Terhadap Kadar Kafein Biji Kopi Robusta (Coffea canephora). Jurnal Ilmu Kesehatan Bhakti Setya Medika, 7(1), pp.33–42. https://doi.org/10.56727/bsm.v7i1.83.
Subari, A., Razak, A. and Sumarmin, R., 2021. Phylogenetic Analysis of Rasbora spp. Based on the Mitochondrial DNA COI gene in Harapan Forest. Jurnal Biologi Tropis, 21(1), pp.89–94. https://doi.org/10.29303/jbt.v21i1.2351.
Sudradjat, A. and Kusrini, E., 2016. Hubungan Kekerabatan Beberapa Populasi Kerang Hijau (Perna viridis) di Indonesia Berdasarkan Sekuen Cytrocrome B mtDNA. Jurnal Riset Akuakultur, 5(1), pp.155–164. https://doi.org/10.15578/jra.5.1.2010.155-164.
Su’udi, M., Ulum, F.B., Ardiyansah, M. and Fitri, N.E., 2024. Evaluasi Lokus Potensial matK dan ITS2 Untuk DNA Barcoding Anggrek Bulbophyllum lobbii Lindl. AL-Kauniyah Jurnal Biologi, 17(2), pp.406–418. https://doi.org/10.15408/kauniyah.v17i2.33897.
Syafaruddin, S., Dani, D. and Pabendon, M.B., 2017. Keragaman Genetik antar Klon Kopi Robusta Lokal Pagar Alam berdasarkan Analisis Marka SSR. Jurnal Tanaman Industri Dan Penyegar, 4(3), p.133. https://doi.org/10.21082/jtidp.v4n3.2017.p133-144.
Syahruddin, K.-, 2021. Keragaman genetik koleksi plasmanutfah jewawut (Setaria italica (L.) P. Beauv.) berkerabat dekat menggunakan markah SSR. Kultivasi, 20(3). https://doi.org/10.24198/kultivasi.v20i3.34843.
Yao, H., Song, J., Liu, C., Luo, K., Han, J., Li, Y., Pang, X., Xu, H., Zhu, Y., Xiao, P. and Chen, S., 2010. Use of ITS2 region as the universal DNA barcode for plants and animals. PLoS ONE, 5(10), p.e13102. https://doi.org/10.1371/journal.pone.0013102.
Yosilia, R., Afandi, A., Hoya, A.L., Cahyani, C.N. and Hieno, A., 2024. Phytophthora palmivora Relationship Analysis on ITS rDNA Primers Using MEGA11 Software (NCBI DNA Sequencing Library Study). Jurnal Agrotek Tropika, 12(4). https://doi.org/10.23960/jat.v12i4.9532.
Published
2026-06-30
How to Cite
YOSILIA, Rani; FII KARISMA JANNAH, Husna; ADAWIAH, Adawiah.
Analisis Filogenetik dan Jarak Genetik Kopi Robusta (Coffea canephora) Berdasarkan Sekuen Internal Transcribed Spacer (ITS).
BioEksakta : Jurnal Ilmiah Biologi Unsoed, [S.l.], v. 8, n. 2, p. 81-88, june 2026.
ISSN 2714-8564.
Available at: <https://jos.unsoed.ac.id/index.php/bioe/article/view/19948>. Date accessed: 15 july 2026.
doi: https://doi.org/10.20884/1.bioe.2026.8.2.19948.
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Articles
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