Phylogenetic analysis of local Papuan (Indonesia) sweet potato genotypes using the maturase K (matK) molecular marker
Article Sidebar
Abstract Views: 286
File Views: 123
Main Article Content
Abstract
Abstract. Mawikere NL, Prabawardani S, Suparno A, Taberima S, Olludium N, Warbaal A, Wibawati Z, Sulistyaningsih LD. 2025. Phylogenetic analysis of local Papuan (Indonesia) sweet potato genotypes using the maturase K (matK) molecular marker. Biodiversitas 26: 1367-1375. This study aimed to investigate the genetic relationship among 12 local Papuan sweet potato genotypes using the maturase K (matK) molecular marker. DNA was extracted from fresh leaf samples and amplified using the matK primer, with sequencing conducted through the Sanger method. Sequence analysis was performed using MEGA11 software, employing BLAST for alignment with GenBank data. Clustering analysis was performed using the neighbor-joining method. While, the phylogenetic tree was constructed using Maximum Likelihood analysis with 1,000 bootstrap replications. The study showed extensive morphological diversity among the sweet potato genotypes, except for L-MKW and Biak-1 genotypes. Nucleotide variation ranges from 858 bp to 867 bp, with polymorphic sites identified at key nucleotide positions. Sweet potato genotype with the largest number of nucleotides was Numfor (867 bp). There were 12 polymorphic sites in nucleotide sequences 1-8, 837, 838, 864, and 865. The average nucleotide composition of twelve sweet potato genotypes was T/U (28.34%), C (15.76%), A (38.01%), and G (17.89%). The number of amino acids formed varied from 265 (Nabire) to 271 (Prafi-1, Mokwam), with an average number of 267.58. The highest amino acid composition was Lysine (Lys/K) 11.87%. Only four sites had polymorphic amino acids in the amino acid sequences 1, 2, 3, and 280. The grouping pattern of Papuan sweet potato genotypes based on nucleotide similarities amplified by the matK primer formed three groups based on their nucleotide similarities, namely i) Mokwam, Numfor, L-MKW; ii) Airani Serui, Prafi, Nabire; and iii) Ungu MKW, L-Sorong, Koya-4, Tinta-1, Biak-1, Amban Pantai-2. This cluster highlights the genetic diversity within Papuan sweet potato populations. Phylogenetic analysis revealed a close relationship between the studied genotypes and other species of the Ipomoea genus. These findings provide valuable insights into the genetic diversity of Papuan sweet potatoes, offering potential applications for conservation and local crop improvement efforts.
Article Details
Issue
Section
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
References
Barthet MM, Hilu KW. 2007. Expression of matK: Functional and evolutionary implications. Am J Bot 94 (8): 1402-1412. DOI: 10.3732/ajb.94.8.1402.
BPS [Bapan Pusat Statistik]. 2020. Central Bureau of Statistics of West Papua Province. West Papua Province in Figures. https://www. papuabarat.bps.go.id. [Indonesian]
Dharmayanti NLPI. 2011. Molecular phylogenetic: Organism taxonomy methods based on evolutionary history. Wartazoa 21 (1): 1-10.
Dong B-C, Yang Q, Kinlock NL, Pouteau R, Pyšek P, Weigelt P, Yu F-H, van Kleunen M. 2024. Naturalization of introduced plants is driven by life-form-dependent cultivation biases. Divers Distrib 30 (1): 55-70. DOI: 10.1111/ddi.13788.
Fajri H, Sunandar A, Qurbaniah M. 2024. Phylogenetic analysis of wild bananas (Musa spp.) in West Kalimantan, Indonesia, based on maturase K (matK) genes. Biodiversitas 25 (8): 2612-2618. DOI: 10.13057/biodiv/d250833.
Gomes-Pereira M, Monckton DG. 2017. Ethidium bromide modifies the agarose electrophoretic mobility of CAG•CTG alternative DNA structures generated by PCR. Front Cell Neurosci 11: 153. DOI: 10.3389/fncel.2017.00153.
Hall BG. 2013. Building phylogenetic trees from molecular data with MEGA. Mol Biol Evol 30: 1229-1235. DOI: 10.1093/molbev/mst012.
Harnelly E, Thomy Z, Fathiya N. 2018. Phylogenetic analysis of Dipterocarpaceae in Ketambe Research Station, Gunung Leuser National Park (Sumatra, Indonesia) based on rbcL and matK genes. Biodiversitas 19 (3): 1074-1080. DOI: 10.13057/biodiv/d190340.
Herman, Al-Khairi H, Wansyah AR, Asmania, Utami RI, Anzaelina DN, Oktaviano Z, Lestari W, Adiwirman, Roslim DI. 2023. The ability of matK and trnL-trnL-trnF intergenic spacer to discern certain species accessions of the families Solanaceae and Fabaceae. Sabrao J Breed Genet 55 (1): 97-106. DOI: 10.54910/sabrao2023.55.1.9.
Immanissa S, Faizal I, Salamah A, Sari IA, Susilo AW. 2020. Genetic variation in Maturase K (matK) from cacao (Theobroma cacao L.) varieties in Indonesia. IOP Conf Ser: Earth Environ Sci 481: 012026. DOI: 10.1088/1755-1315/481/1/012026.
Indow L, Maturbongs RA, Prabawardani S, Hendri, Lyons G. 2021. Implementation of the remote indigenous community empowerment program on the sustainability of the local food crops in West Papua, Indonesia. Biodiversitas 22: 5247-5254. DOI: 10.13057/biodiv/d221202.
Jayaraj G. 2024. The role of matK gene in Eucalyptus species identification and its importance in phylogenetics. BioMed Res J 8 (2): 753-762.
Kalangi C, Kamu VS, Kumaunang M. 2024. Barcode DNA tanaman Leilem (Clerodendrum minahassae L.) berdasarkan gen matK. Jurnal Mipa Unsrat Online 3: 108-112. DOI: 10.35799/jm.3.2.2014.5861. [Indonesian]
Karudapuram S, Padilla R, Chen S, Koepf S, Hauser J, Wang Y, Jacobson K, White M, Bordoni R, Wenz M, Shah A, Joe L. 2007. P48-T a new high-density size standard for sizing large fragments across multiple fragment analysis capillary electrophoresis applications. J Biomol Tech 18 (1): 17.
Karuwal RL, Kasiamdari R, Daryono BS. 2024. Genetic variation of Fei banana (Musa troglodytarum L.) in Maluku Islands using RAPD markers. Sabrao J Breed Genet 56 (1): 101-111. DOI: 10.54910/sabrao2024.56.1.9.
Kiran U, Moahnty SK, Roy PS, Behera L, Chand PK. 2015. Genetic diversity among banana cultivars from Odisha using RAPD markers. Sci Res Rep 5 (2): 118-124.
Mims MC, Hauser L, Goldberg CS, Olden JD. 2016. Genetic differentiation, isolation-by-distance, and metapopulation dynamics of the Arizona Treefrog (Hyla wrightorum) in an isolated portion of its range. PLoS One 11: e0160655. DOI: 10.1371/journal.pone.0160655.
Motohashi K. 2019. Development of highly sensitive and low-cost DNA agarose gel electrophoresis detection systems, and evaluation of non-mutagenic and loading dye-type DNA-staining reagents. PLoS One 14 (9): e0222209. DOI: 10.1371/journal.pone.0222209.
Nater A, Burri R, Kawakami T, Smeds L, Ellegren H. 2015. Resolving evolutionary relationships in closely related species with whole-genome sequencing data. Syst Biol 64 (6): 1000-1017. DOI: 10.1093/sysbio/syv045.
Probojati RT, 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. Bull Natl Res Cent 45: 33. DOI: 10.1186/s42269-021- 00492-3.
Qiu X, Zhang H, Wang Q, Jian H, Yan H, Zhang T, Wang J, Tang K. 2012. Phylogenetic relationships of wild roses in China based on nrDNA and matK data. Sci Hortic 140: 45-51. DOI: 10.1016/j.scienta.2012.03.014.
Qu Y, Legen J, Arndt J, Henkel S, Hoppe G, Thieme C, Ranzini G, Muino JM, Weihe A, Ohler U, Weber G, Ostersetzer O, Schmitz-Linneweber C. 2018. Ectopic transplastomic expression of a synthetic MatK gene leads to cotyledon-specific leaf variegation. Front Plant Sci 9: 1453. DOI: 10.3389/fpls.2018.01453.
Raza S, Farooqi S, Mubeen H. 2015. Role of molecular markers and their significance. Am J Pharm Health Res 3 (12): 1-8.
Rumere J. 2021. Karakter morfo-agronomi dan molekuler beberapa aksesi ubijalar (Ipomoea batatas (L.) Lam.) asal Biak Numfor. [Thesis]. Universitas Papua, Manokwari. [Indonesian]
Saraswati P, Soplanit A, Syahputra AT, Kossay L, Muid N, Ginting E, Lyons G. 2013. Yield trial and sensory evaluation of sweet potato cultivars in Highland Papua and West Papua Indonesia. J Trop Agric 51 (1): 74-83.
Scorsim B, da Silva AC, Ramos LI, Passere MD, Thomaz SM, de Oliveira AV. 2024. Molecular markers in genetic studies of aquatic macrophytes: A systematic review. Hydrobiologia 851: 3809-3820. DOI: 10.1007/s10750-024-05556-9.
Sevindik E, Korkom Y, Murathan ZT. 2024. Evaluating DNA barcoding using cpDNA matK and rbcL for species identification and phylogenetic analysis of Prunus armeniaca L. (Rosaceae) genotypes. Genet Resour Crop Evol 71: 1825-1835. DOI: 10.1007/s10722-023-01748-9.
Singhal H, Ren YR, Kern SE. 2010. Improved DNA electrophoresis in conditions favoring polyborates and lewis acid complexation. PLoS One 5 (6): e11318. DOI: 10.1371/journal.pone.0011318.
Thi NPA, Tam TT, Khang DT. 2023. Genetic diversity in the matK gene of Dimocarpus longan varieties in the Mekong Delta. Asian J Plant Sci 22 (3): 444-451. DOI: 10.3923/ajps.2023.444.451.
Utama MN, Etikawati N, Sugiyarto, Susilowati A. 2024. New specific primer matK and rbcL region for DNA barcode pitcher plant Nepenthes spathulate. Biodiversitas 25 (6): 2515-2523. DOI: 10.13057/biodiv/d250621.
Vlijm R, Torre JVD, Dekker C. 2015. Counterintuitive DNA sequence dependence in supercoiling-induced DNA melting. PLoS One 10 (10): e0141576. DOI: 10.1371/journal.pone.0141576.
Wang J-F, Gong X, Chiang Y-C, Kuroda C. 2013. Phylogenetic patterns and disjunct distribution in Ligularia hodgsonii Hook. (Asteraceae). J Biogeogr 40 (9): 1741-1754. DOI: 10.1111/jbi.12114.
Wanke S, Wicke S. 2023. Editorial: Phylogenomic discordance in plant systematics. Front Plant Sci 14: 1308126. DOI: 10.3389/fpls.2023.1308126.
Wibawati Z, Abbas B, Mustamu YA, Mawikere NL, Noya AI. 2024. Filogenetik 5 kultivar sagu dan spesies palmae lainnya berdasarkan penanda molekuler matK. Cassowary 7 (1): 47-55. DOI: 10.30862/casssowary.cs.v7.i1.202. [Indonesian]