Phylogenetic Analysis of Baccaurea Spp. in West Sumatra Using MatK Molecular Markers
(1) Department of Biology, Faculty of Mathematics and Natural Sciences, Andalas University, Limau Manis Campus, Padang 25163, West Sumatra, Indonesia
(2) Department of Biology, Faculty of Mathematics and Natural Sciences, Andalas University, Limau Manis Campus, Padang 25163, West Sumatra, Indonesia
(3) Department of Biology, Faculty of Mathematics and Natural Sciences, Andalas University, Limau Manis Campus, Padang 25163, West Sumatra, Indonesia
(4) Department of Biology Education, Faculty of Teacher Training and Education, Samudra University, Langsa, Aceh, Indonesia
(5) School of Science Department of Biological Sciences Tokyo Metropolitan University, Japan
Abstract
Baccaurea is a group of fruit-producing plants found in wild forests. Many of these plant species have not yet explored their potential. The high rate of deforestation in West Sumatra poses a threat of extinction to the genetic resources of the genus Baccaurea before being explored and identified. The research aims to analyze the sequence characters and phylogenetic of Baccaurea found in West Sumatra using the MatK molecular marker. Phylogenetic analysis using the Maximum Likelihood (ML) method in MEGA X application. The results of the analysis of the six species of Baccaurea found that the sequence length ranged from 854-1019bp, the percentage of G+C base composition is 33.4%, the percentage of A+T base composition is 66.6%, the genetic distance range is 0-4% with a conservative character of 484bp and informative characters of 4bp. While the phylogenetic analysis using the ML method grouping the six species of Baccaurea to form a monophyletic clade with a bootstrap value of 100%, all species collected were in the same clade. These results reveal the first time that the MatK sequences from six species Baccaurea native to West Sumatra will be included in NCBI for use by other studies in conducting broader phylogenetic research.
Keywords
Full Text:
PDFReferences
Amanda K, Sari R, and Apridamayanti P. 2019. Optimization of the Annealing Temperature of the PCR Amplification Process of the shv Gene for Eschericia coli Bacteria in Diabetic Ulcer Patients. Journal of Pharmacy Students, Faculty of Medicine, UNTAN. 4(1): 1-6.
Amandita, FY., Rembold, K., Vornam, B., Rahayu, S., Siregar, IZ., Kreft, H. and Finkeldey, R. 2019. DNA barcoding of flowering plants in Sumatra, Indonesia. Ecol Evol. press.
Anzani, AN., Martiansyah I., and Yuliani, N. 2021. In Silico DNA barcoding studies on softwoods (Ixora). Proceedings of Biology Achieving the Sustainable Development Goals with Biodiversity in Confronting Climate Change Gowa. http://journal.uin-alauddin.ac.id/index.php/psb.
Aulia, A. 2022. In silico study of the potential of DNA barcoding based on chloroplast DNA (cpDNA) for the identification of genetic variations of Opuntis sp. Syntac Admiration Journal. Vol. 3(11): 1383–1394.
Barthet, MM., Pierpont, CL., and Tavernier, E.K. 2020. Unraveling the role of the enigmatic MatK maturase in chloroplast group IIA intron excision. Plant Direct. Vol. 4(3). Beentje, Henk. 2016. The Kew Plant Glossary second edition. Royal Botanic Gardens Kew. In North America by the University of Chicago Press.
Candramila, W., Fajri, H., Mardiyyaningsih, AN., Firmansyah, R., and Akbar, D. 2023. Taxonomic Confirmation of Rare Fruits in West Kalimantan Using rbcl and matK Sequences. Bioscience. Vol. 15(1): 20-25.
GBIF Backbone Taxonomy. Baccaurea Lour. in GBIF Secretariat. 2022.https://doi.org/10.15468/39omeiaccessed via GBIF.org on 2023-07-09
Gunawan., Chikmawati T., Sobir., and Sulistijorini. 2016. Reviews: Phytochemicals of the Marga Baccaurea sp. Bioexperiment. Vol. 2(2): 96-107. Doi: 10.23917/ Bio Experiment.V2i2.2488.
Gunawan., Chikmawati, T., Sobir., Sulistijorini. 2018. Distribution, Morphological Variations and New Varieties of Baccaurea Angulata (Phyllanthaceae). Florida. Vol. 6(1):1-11. Doi: 10.32556/ Floribunda.V6i1.2018.226.
Gunawan. 2020. Biosystematics of Red Starfruit in Kalimantan and Natuna Island. [Dissertation]. Bogor: Bogor Agricultural Institute.
Hidayat T., and Pancoro A. 2016. Review of molecular phylogenetic studies and their role in providing basic information to improve the quality of orchid genetic resources. Journal of AgroBiogen. Vol. 4(1): 35-40.
Manurung, J., Prakasa, H., Tanjung, UJ., and Harsono, T. 2018. Species Relationships in the Genus Zanthoxylum using the Maturase K (MatK) gene sequence of Chloroplast DNA. Journal of Biosciences. Vol. 4. No. 2. Pg. 69-77.
Muzzazinah. 2017. Phylogenetic Methods on Indigofera. Proceedings of the National Seminar on Biology and Biology Education. Yogyakarta State University
Okuno, S., Yin, T., Nanami, S., Matsuyama, S., Kamiya, K., Tan, S., Davies, SJ, Mohamad, M., Yamakura, T. and Itoh,A. 2022. Community phylogeny and spatial scale affect phylogenetic diversity metrics in a species-rich rainforest in Borneo. Ecol Evol. Vol. 12, e9536. DOI:10.1002/ece3.9536.
Ramayani and Fitmawati. 2020. Rambai Diversity (Baccaurea Motleyana (Müll.Arg.) Müll.Arg.) on Bengkalis Island Based on Morphological Characters. Botanical Gardens Bulletin. Vol. 23(1): 46–58.
Ratnaningati, Dewi. 2017. Intraspecies Phylogenetic Relations of Cucumis melo L. based on MatK Gene Barcode DNA. Biota Journal. Vol. 2(2): 62-67.
Roslim, DI., Khumairoh, S., dan Herman. 2016. Confirmation of Tuntun Angin (Elaeocarpus floribundus) Taxonomic Status Using matK and ITS Sequences. Biosaintifika Journal. Vol. 8(3): 392-399. DOI: 10.15294/biosaintifika.v8i3.7406
Samuel, R., Kathriarachchi, H., Hoffmann, P., Barfuss, MH., Wurdack, KJ., Davis, CC. and Chase, MW .2016. Molecular phylogenetics of Phyllanthaceae: evidence from plastid MATK and nuclear PHYC sequences. Am. J.Bot. Vol. 92(1), 132-141.
Syamsuardi, S., Chairul, C., and Murni, P. 2018. Analysis of Genetic Impurity of An Original Cultivar Duku (Lansium parasiticum (Osbeck.) KC Sahni Bennet.) from Jambi, Indonesia Using ITS and MatK Gene. International Journal of Environment, Agriculture and Biotechnology. Vol. 3 (2): 239084.
Turhadi, LH. 2023. In-Silico Evaluation of Chloroplast Loci for DNA Barcoding in the Genus Stelechocarpus (Annonaceae). Agricultural Journal. Vol. 6(1): 56-64.
Vinitha, MR., Kumar, US., Aishwarya, K., Sabu, M., and Thomas, G. 2014. Prospects for discriminating Zingiberaceae species in India using DNA barcodes. Journal of integrative plant biology. Vol. 56(8): 760-773.
Vinolia. 2017. Notes from West Sumatra: from deforestation to people's management rights.https://www.mongabay.co.id/2017/12/31/catatan-dari-sumbardarisoal-deforestasbesar-hak-kelolarakyat/. Retrieved June 14, 2019.
Wang,JF., Gong, X., Chiang, YC., and Kuroda, C. 2013. Phylogenetic patterns and disjunct distribution in Ligularia hodgsonii Hook (Asteraceae). J Biogeogr. Vol. 40:1741–175
Refbacks
- There are currently no refbacks.
This work is licensed under a Creative Commons Attribution 4.0 International License.