Assessing the Utility of Partial Chloroplast matK Sequences for DNA Barcoding of Indonesian Grapevine (Vitis vinifera L.) Cultivar from Magelang, Central Java
Keywords:
Automatic barcoding gap discovery, Grapevine, Indonesia, Magelang, Phylogenetic tree reconstruction
Abstract
Grapevine (Vitis vinifera) is an important fruit crop in Indonesia, but its local cultivars remain poorly characterized at the molecular level. This study evaluated the utility of a partial chloroplast maturase K (matK) gene for preliminary DNA barcoding of nine grapevine samples from Magelang, Indonesia. DNA was extracted and amplified using conventional PCR, but only five samples yielded usable matK sequences. Phylogenetic and Automatic Barcode Gap Discovery (ABGD) analyses showed that the 131 bp matK fragment was highly conserved, with no nucleotide variation among the Indonesian samples. The sequences formed a single clade, while ABGD detected no clear barcode gap or cultivar differentiation. These findings indicate that the short partial matK fragment has limited utility for discriminating Indonesian grapevine cultivars. Future studies should use longer or multiple barcode regions and higher-resolution molecular markers to improve cultivar identification and genetic characterization.
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References
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Pei, D., Song, S., Kang, J., Zhang, C., Wang, J., Dong, T., Ge, M., Pervaiz, T., Zhang, P., & Fang, J. (2023). Characterization of Simple Sequence Repeat (SSR) markers mined in whole grape genomes. Genes, 14(3), 663–663. https://doi.org/10.3390/genes14030663
Pentinsaari, M., Vos, R., & Mutanen, M. (2016). Algorithmic single-locus species delimitation: effects of sampling effort, variation and nonmonophyly in four methods and 1870 species of beetles. Molecular Ecology Resources, 17(3), 393–404. https://doi.org/10.1111/1755-0998.12557
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Puillandre, N., Fedosov, A. E., Zaharias, P., Aznar-Cormano, L., & Kantor, Y. I. (2017). A quest for the lost types of Lophiotoma (Gastropoda: Conoidea: Turridae): Integrative taxonomy in a nomenclatural mess. Zoological Journal of the Linnean Society. https://doi.org/10.1093/zoolinnean/zlx012
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Ranatunge, I., Adikary, S., Dasanayake, P., Fernando, C. D., & Soysa, P. (2017). Development of a rapid and simple method to remove polyphenols from plant extracts. International Journal of Analytical Chemistry, 2017, 7230145. https://doi.org/10.1155/2017/7230145
Sharko, F. S., Petrova, K. O., Molchanov, N. V., Patrushev, M. V., Fedosov, D. Yu., & Toshchakov, S. V. (2024). The complete chloroplast genome sequence of Vitis vinifera “Krasnostop Zolotovskiy”, an autochthonous variety of the Don Valley. Turczaninowia, 27(1), 124–129. https://doi.org/10.14258/turczaninowia.27.1.16
Tabidze, V., Baramidze, G., Pipia, I., Gogniashvili, M., Ujmajuridze, L., Beridze, T., Hernandez, A. G., & Schaal, B. (2014). The complete chloroplast DNA sequence of eleven grape cultivars. simultaneous resequencing methodology. OENO One, 48(2), 99–99. https://doi.org/10.20870/oeno-one.2014.48.2.1568
Tatarynova, V. I., Vlasenko, V. A., Burdulaniuk, A. O., Bakumenko, O. M., Demenko, V. M., Yemets, O. M., Rozhkova, T. O., & Sakhoshko, M. M. (2022). Influence of agroecological factors on the phytosanitary condition of grape agrocenoses in the conditions of the north-eastern forest steppe of Ukraine. Серія, 2(48). https://doi.org/10.32845/agrobio.2022
Tnah, L. H., Lee, S. L., Lee, C. T., Kit, K., Ng, C. H., & Zawiah, N. (2023). DNA barcode identification of cultivated and wild tropical fruit species. 3 Biotech, 14(1). https://doi.org/10.1007/s13205-023-03848-w
Torregrosa, L., Vialet, S., Adivèze, A., Iocco-Corena, P., & Thomas, M. R. (2015). Grapevine (Vitis vinifera L.). Methods in Molecular Biology (Clifton, N.J.), 1224, 177–194. https://doi.org/10.1007/978-1-4939-1658-0_15
Wen, J., Lu, L., Nie, Z., Liu, X., Zhang, N., Ickert‐Bond, S., Gerrath, J., Manchester, S. R., Boggan, J., & Chen, Z. (2018). A new phylogenetic tribal classification of the grape family (Vitaceae). Journal of Systematics and Evolution, 56(4), 262–272. https://doi.org/10.1111/jse.12427
Wu, Y., Li, M., Yang, Y., Jiang, L., Liu, M., Wang, B., & Wang, Y. (2018). Authentication of small berry fruit in fruit products by DNA barcoding method. Journal of Food Science, 83(6), 1494–1504. https://doi.org/10.1111/1750-3841.14177
Yeo, D., Srivathsan, A., & Meier, R. (2020). Longer is not always better: Optimizing barcode length for large-scale species discovery and identification. Systematic Biology, 69(5), 999–1015. https://doi.org/10.1093/sysbio/syaa014
Zhang, L., Song, Y., Li, J., Liu, J., Zhang, Z., Xu, Y., Fan, D., Liu, M., Ren, Y., He, J., Song, S., Xu, W., Liu, H., Xi, X., & Ma, C. (2024). Identification, comparative and phylogenetic analysis of eight Vitis species based on the chloroplast genome revealed their contribution to heat tolerance in grapevines. Scientia Horticulturae, 327, 112833–112833. https://doi.org/10.1016/j.scienta.2023.112833
Zhao, H., Sun, S., Ding, Y., Wang, Y., Yue, X., Du, X., Wei, Q., Fan, G., Sun, H., Lou, Y., Yang, H., Wang, J., Xu, X., Li, L., Yang, K., Xu, H., Wang, J., Zhu, C., Wang, S., & Shan, X. (2021). Analysis of 427 genomes reveals moso bamboo population structure and genetic basis of property traits. Nature Communications, 12(1). https://doi.org/10.1038/s41467-021-25795-x
Zhou, Y., Massonnet, M., Sanjak, J. S., Cantu, D., & Gaut, B. S. (2017). Evolutionary genomics of grape (Vitis vinifera ssp. vinifera) domestication. Proceedings of the National Academy of Sciences of the United States of America, 114(44), 11715–11720. https://doi.org/10.1073/pnas.1709257114
Ali, Q., Salisu, I. B., Raza, A., Shahid, A. A., Rao, A. Q., & Husnain, T. (2019). A modified protocol for rapid DNA isolation from cotton (Gossypium spp.). MethodsX, 6, 259–264. https://doi.org/10.1016/j.mex.2019.01.010
Damayanti, I. A. M., & Antari, N. W. S. (2025). Phytochemical screening of Balinese grape (Vitis vinifera L. var. alphonso lavallee) peel extract: Resources local plant-based lessons in biology. BIO-INOVED : Jurnal Biologi-Inovasi Pendidikan, 7(2), 228. https://doi.org/10.20527/bino.v7i2.22239
Doyle, J. J., & Doyle, J. L. (1987). A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin, 19(11-15).
Guo, D., Li, D., Li, H., Wang, S., Wang, L., Niu, J., & Ma, C. (2019). The complete chloroplast genome sequence of Vitis vinifera Muscat Hamburg. Mitochondrial DNA Part B, 5(1), 117–118. https://doi.org/10.1080/23802359.2019.1698333
Heikrujam, J., Kishor, R., & Mazumder, P. B. (2020). The chemistry behind plant DNA isolation protocols. Biochemical Analysis Tools - Methods for Bio-Molecules Studies. https://doi.org/10.5772/intechopen.92206
Ho, V. T., & Nguyen, M. P. (2020). An in silico approach for evaluation of rbcL and matK loci for DNA barcoding of Cucurbitaceae family. Biodiversitas Journal of Biological Diversity, 21(8). https://doi.org/10.13057/biodiv/d210858
Hu, T., Chitnis, N., Monos, D., & Dinh, A. (2021). Next-generation sequencing technologies: An overview. Human Immunology, 82(11). https://doi.org/10.1016/j.humimm.2021.02.012
Hubert, N., & Hanner, R. (2015). DNA Barcoding, species delineation and taxonomy: a historical perspective. DNA Barcodes, 3(1). https://doi.org/10.1515/dna-2015-0006
Jansen, R. K., Kaittanis, C., Saski, C., Lee, S.-B., Tomkins, J., Alverson, A. J., & Daniell, H. (2006). Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids. BMC Evolutionary Biology, 6(1). https://doi.org/10.1186/1471-2148-6-32
Ji, F., Ma, Q., Zhang, W., Liu, J., Feng, Y., Zhao, P., Song, X., Chen, J., Zhang, J., Wei, X., Zhou, Y., Chang, Y., Zhang, P., Huang, X., Qiu, J., & Pei, D. (2021). A genome variation map provides insights into the genetics of walnut adaptation and agronomic traits. Genome Biology, 22(1). https://doi.org/10.1186/s13059-021-02517-6
Kamila, S., Widodo, W. D., Santosa, E., & Suhartanto, M. R. (2024). Flowering and fruiting phenology in two varieties of grapes (Vitis vinifera) in tropical regions, Indonesia. Biodiversitas, 25(11). https://doi.org/10.13057/biodiv/d251158
Li, P., Xiao, L., Du, Q., Quan, M., Song, Y., He, Y., Huang, W., Xie, J., Lv, C., Wang, D., Zhou, J., Li, L., Liu, Q., El‐Kassaby, Y. A., & Zhang, D. (2023). Genomic insights into selection for heterozygous alleles and woody traits in Populus tomentosa. Plant Biotechnology Journal, 21(10), 2002–2018. https://doi.org/10.1111/pbi.14108
Liang, Y., Gao, Y., Fontana, A., Abt, M. R., Gicgier, A. P., Liu, C., Sharma, M., Zoschke, R., Zeeman, S. C., & Pfister, B. (2025). Maturase K forms a plastidial splicing complex with a neofunctionalized branching enzyme. BioRxiv (Cold Spring Harbor Laboratory). https://doi.org/10.1101/2025.01.08.628318
Liu, B., Ma, Z., Ren, C., Richard, Sun, M., Liu, X., Liu, G., De‐Yuan, H., Zimmer, E. A., & Wen, J. (2021). Capturing single‐copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae. Journal of Systematics and Evolution, 59(5), 1124–1138. https://doi.org/10.1111/jse.12806
Liu, D., Li, N., Song, D., & Lv, Z. (2025). Structural bioinformatics and gene expression analysis of maturase K from Lavandula angustifolia (lavender). Frontiers in Molecular Biosciences, 12. https://doi.org/10.3389/fmolb.2025.1628118
Liu, Z., Wang, N., Su, Y., Long, Q., Peng, Y., Shangguan, L., Zhang, F., Cao, S., Wang, X., Ge, M., Xue, H., Ma, Z., Liu, W., Xu, X., Li, C., Cao, X., Ahmad, B., Su, X., Liu, Y., & Huang, G. (2024). Grapevine pangenome facilitates trait genetics and genomic breeding. Nature Genetics. https://doi.org/10.1038/s41588-024-01967-5
Luh, N., & Sustia, E. (2023). Productivity and brix value of green grapes (Vitis vinifera L var. muscat saint vallier) at different location and pruning time in Buleleng Bali. SEAS (Sustainable Environment Agricultural Science), 7(2), 139–144. https://doi.org/10.22225/seas.7.2.8222.139-144
Martínez, M. C., Boso, S., Gago, P., Muñoz-Organero, G., De Andrés, M. T., Gaforio, L., Cabello, F., & Santiago, J. L. (2018). Value of two Spanish live grapevine collections in the resolution of synonyms, homonyms and naming errors. Australian Journal of Grape and Wine Research, 24(4), 430–438. https://doi.org/10.1111/ajgw.12348
Oner, T. O., Temel, M., Pamay, S., Abaci, A. K., & Kaya, H. B. (2023). An improved method for efficient DNA extraction from grapevine. International Journal of Life Sciences and Biotechnology, 6(1), 21–36. https://doi.org/10.38001/ijlsb.1150387
Pei, D., Song, S., Kang, J., Zhang, C., Wang, J., Dong, T., Ge, M., Pervaiz, T., Zhang, P., & Fang, J. (2023). Characterization of Simple Sequence Repeat (SSR) markers mined in whole grape genomes. Genes, 14(3), 663–663. https://doi.org/10.3390/genes14030663
Pentinsaari, M., Vos, R., & Mutanen, M. (2016). Algorithmic single-locus species delimitation: effects of sampling effort, variation and nonmonophyly in four methods and 1870 species of beetles. Molecular Ecology Resources, 17(3), 393–404. https://doi.org/10.1111/1755-0998.12557
Pipia, I., Ujmajuridze, L., Mamasakhlisashvili, L., Hernández, Á., & Tabidze, V. (2024). Plastid genomics of wild grapevines (Vitis vinifera subsp. sylvestris) of Georgia the cradle of viticulture. OENO One, 58(4). https://doi.org/10.20870/oeno-one.2024.58.4.8087
Probojati, R. T., Listyorini, D., Sulisetijono, S., & Wahyudi, D. (2021). Phylogeny and estimated genetic divergence times of banana cultivars (Musa spp.) from Java Island by maturase K (matK) genes. Bulletin of the National Research Centre, 45(1). https://doi.org/10.1186/s42269-021-00492-3
Puillandre, N., Fedosov, A. E., Zaharias, P., Aznar-Cormano, L., & Kantor, Y. I. (2017). A quest for the lost types of Lophiotoma (Gastropoda: Conoidea: Turridae): Integrative taxonomy in a nomenclatural mess. Zoological Journal of the Linnean Society. https://doi.org/10.1093/zoolinnean/zlx012
Rajaei, S., Farshi, R. S., Jazi, M. M., & Seyedi, S. M. (2017). Efficient strategies for elimination of phenolic compounds during DNA extraction from roots of Pistacia vera L. AGRIVITA Journal of Agricultural Science, 39(3). https://doi.org/10.17503/agrivita.v39i3.734
Ranatunge, I., Adikary, S., Dasanayake, P., Fernando, C. D., & Soysa, P. (2017). Development of a rapid and simple method to remove polyphenols from plant extracts. International Journal of Analytical Chemistry, 2017, 7230145. https://doi.org/10.1155/2017/7230145
Sharko, F. S., Petrova, K. O., Molchanov, N. V., Patrushev, M. V., Fedosov, D. Yu., & Toshchakov, S. V. (2024). The complete chloroplast genome sequence of Vitis vinifera “Krasnostop Zolotovskiy”, an autochthonous variety of the Don Valley. Turczaninowia, 27(1), 124–129. https://doi.org/10.14258/turczaninowia.27.1.16
Tabidze, V., Baramidze, G., Pipia, I., Gogniashvili, M., Ujmajuridze, L., Beridze, T., Hernandez, A. G., & Schaal, B. (2014). The complete chloroplast DNA sequence of eleven grape cultivars. simultaneous resequencing methodology. OENO One, 48(2), 99–99. https://doi.org/10.20870/oeno-one.2014.48.2.1568
Tatarynova, V. I., Vlasenko, V. A., Burdulaniuk, A. O., Bakumenko, O. M., Demenko, V. M., Yemets, O. M., Rozhkova, T. O., & Sakhoshko, M. M. (2022). Influence of agroecological factors on the phytosanitary condition of grape agrocenoses in the conditions of the north-eastern forest steppe of Ukraine. Серія, 2(48). https://doi.org/10.32845/agrobio.2022
Tnah, L. H., Lee, S. L., Lee, C. T., Kit, K., Ng, C. H., & Zawiah, N. (2023). DNA barcode identification of cultivated and wild tropical fruit species. 3 Biotech, 14(1). https://doi.org/10.1007/s13205-023-03848-w
Torregrosa, L., Vialet, S., Adivèze, A., Iocco-Corena, P., & Thomas, M. R. (2015). Grapevine (Vitis vinifera L.). Methods in Molecular Biology (Clifton, N.J.), 1224, 177–194. https://doi.org/10.1007/978-1-4939-1658-0_15
Wen, J., Lu, L., Nie, Z., Liu, X., Zhang, N., Ickert‐Bond, S., Gerrath, J., Manchester, S. R., Boggan, J., & Chen, Z. (2018). A new phylogenetic tribal classification of the grape family (Vitaceae). Journal of Systematics and Evolution, 56(4), 262–272. https://doi.org/10.1111/jse.12427
Wu, Y., Li, M., Yang, Y., Jiang, L., Liu, M., Wang, B., & Wang, Y. (2018). Authentication of small berry fruit in fruit products by DNA barcoding method. Journal of Food Science, 83(6), 1494–1504. https://doi.org/10.1111/1750-3841.14177
Yeo, D., Srivathsan, A., & Meier, R. (2020). Longer is not always better: Optimizing barcode length for large-scale species discovery and identification. Systematic Biology, 69(5), 999–1015. https://doi.org/10.1093/sysbio/syaa014
Zhang, L., Song, Y., Li, J., Liu, J., Zhang, Z., Xu, Y., Fan, D., Liu, M., Ren, Y., He, J., Song, S., Xu, W., Liu, H., Xi, X., & Ma, C. (2024). Identification, comparative and phylogenetic analysis of eight Vitis species based on the chloroplast genome revealed their contribution to heat tolerance in grapevines. Scientia Horticulturae, 327, 112833–112833. https://doi.org/10.1016/j.scienta.2023.112833
Zhao, H., Sun, S., Ding, Y., Wang, Y., Yue, X., Du, X., Wei, Q., Fan, G., Sun, H., Lou, Y., Yang, H., Wang, J., Xu, X., Li, L., Yang, K., Xu, H., Wang, J., Zhu, C., Wang, S., & Shan, X. (2021). Analysis of 427 genomes reveals moso bamboo population structure and genetic basis of property traits. Nature Communications, 12(1). https://doi.org/10.1038/s41467-021-25795-x
Zhou, Y., Massonnet, M., Sanjak, J. S., Cantu, D., & Gaut, B. S. (2017). Evolutionary genomics of grape (Vitis vinifera ssp. vinifera) domestication. Proceedings of the National Academy of Sciences of the United States of America, 114(44), 11715–11720. https://doi.org/10.1073/pnas.1709257114
Published
2026-09-30
How to Cite
Halim, A., Probowati, W., & Santosa, A. I. (2026). Assessing the Utility of Partial Chloroplast matK Sequences for DNA Barcoding of Indonesian Grapevine (Vitis vinifera L.) Cultivar from Magelang, Central Java. Indonesian Journal of Life Sciences, 8(02), 90-105. https://doi.org/10.54250/ijls.v8i02.292
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Genetics
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