Phylogenetic analysis of wild bananas (Musa spp.) in West Kalimantan, Indonesia, based on maturase K (matK) genes

##plugins.themes.bootstrap3.article.sidebar##

PDF
DOI https://doi.org/10.13057/biodiv/d250833
Issue
Vol. 25 No. 8 (2024)
Section
Articles
Creative Commons License

This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

##plugins.themes.bootstrap3.article.main##

HAYATUL FAJRI ♥
Department of Biology Education, Faculty of Teachers Training and Education, Universitas Tanjungpura. Jl. Prof. Hadari Nawawi, Pontianak 78124, West Kalimantan, Indonesia
ARI SUNANDAR
Department of Biology Education, Faculty of Teachers Training and Education, Universitas Muhammadiyah Pontianak. Jl. Jend. A. Yani No. 111, Pontianak 78123, West Kalimantan, Indonesia
MAHWAR QURBANIAH
Department of Biology Education, Faculty of Teachers Training and Education, Universitas Muhammadiyah Pontianak. Jl. Jend. A. Yani No. 111, Pontianak 78123, West Kalimantan, Indonesia

Abstract

Abstract. 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: 2612-2618. West Kalimantan is home to wild bananas (Musa spp.). Genetic assessment of wild banana relatives is important for future breeding purposes. This study aims to analyze the phylogenetic relationship of wild banana species in West Kalimantan based on maturase K (matK) gene sequence data to understand better the relationship among wild banana species in West Kalimantan. A total of 30 samples, including 23 matK sequences from GenBank, were used. Species of Heliconia schiedeana were incorporated as an outgroup. The phylogenetic analysis was conducted using the Maximum Likelihood (ML) algorithm in MEGA 11 application. The size of PCR-amplified matK is estimated at 540-561 bp. It showed high variability with conservation level A+T, with an average value was 66.26%. Some unique nucleotides were found in Musa acuminata subsp. microcarpa, Musa campestris, and Musa borneensis. The matK sequences of Musa spp. have a polymorphic site on 23 nucleotide numbers. The phylogenetic analysis with ML algorithm of 30 Musa spp. from West Kalimantan and GenBank data was successfully divided into two main cladesbootstrap value. Our study showed that matK genes are able to describe the differences in M. acuminata, M. campestris, and M. borneensis in West Kalimantan. This study will benefit taxonomic, genetic conservation strategy, and banana breeding efforts. It will provide valuable insights and tools for these fields, thereby contributing to the conservation and breeding of bananas.

##plugins.themes.bootstrap3.article.details##

References
Abbas B, Kabes R.J. MawikereNL, Ruimassa RMR, Maturbong RA. 2020. DNA barcode of Metroxylon sagu and others palm species using matK gene. Biodiversitas Journal of Biological Diversity 21(9):4047-4057. DOI:10.13057/biodiv/d210916.
Ardiyani M, Ermawar R, Yulita K, Dewi C, Ahmad A, Sulistyaningsih L, Sari F, Fatriasari F. 2023. Identification of genetic relationship between Indonesia banana cultivars and the wild relatives using DNA barcodes. Journal of Tropical Forest Science (JTFS) 35(1): 93-107. DOI: 10.26525/jtfs2023.35.1.93.
Arif MF, Aristya GR, Subositi D, Sari AN, Kasiamdari RS. 2019. Short Communication: rbcL and matK chloroplast DNA composition of green chireta (Andrographis paniculata) from Indonesia. Biodiversitas Journal of Biological Diversity 20(12): 3575-3583. DOI: 10.13057/biodiv/d201216.
Barthet MM, Moukarzel K, Smith KN, Patel J, Hilu K.W. 2015. Alternative translation initiation codons for the plastid maturase matK: Unraveling the pseudogene misconception in the Orchidaceae. BMC Evolutionary Biology 15(1): 210. DOI: 10.1186/s12862-015-0491-1.
Bieniek W, Mizianty M, Szklarczyk M. 2014. Sequence variation at the three chloroplast loci (matK, rbcL, trnH-psbA) in the Triticeae tribe (Poaceae): Comments on the relationships and utility in DNA barcoding of selected species. Plant Systematics and Evolution 301: 1275-1286. DOI: 10.1007/s00606-014-1138-1.
Costion C, Ford A, Cross H, Crayn D, Harrington M, Lowe A. 2011. Plant DNA barcodes can accurately estimate species richness in poorly known floras. PloS One 6(11): e26841. DOI: 10.1371/journal.pone.0026841.
Dharmayanti NLPI. 2011. Molecular phylogenetic: Organism taxonomy methods based on evolutionary history. Wartazoa 21(1): 1-10.
Du H, Yang J, Chen B, Zhang X, Zhang J, Yang K, Geng S, Wen C. 2019. Target sequencing reveals genetic diversity, population structure, core-SNP markers, and fruit shape-associated loci in pepper varieties. BMC Plant Biology 19(1): 578. DOI: 10.1186/s12870-019-2122-2.
Guo L, Wang X, Zhao M, Huang C, Li C, Li D, Yang CJ, York AM, Xue W, Xu G, Liang Y, Chen Q, Doebley JF, Tian F. 2018. Stepwise cis regulatory changes in ZCN8 contribute to maize flowering-time adaptation. Current Biology: CB 28(18): 3005-3015.e4. DOI: 10.1016/j.cub.2018.07.029.
Guo S, Zhao S, Sun H, Wang X, Wu S, Lin T, Ren Y, Gao L, Deng Y, Zhang J, Lu X, Zhang H, Shang J, Gong G, Wen C, He N, Tian S, Li M, Liu J, … Xu Y. 2019. Resequencing of 414 cultivated and wild watermelon accessions identifies selection for fruit quality traits. Nature Genetics 51: 1616-1623. DOI: 10.1038/s41588-019-0518-4.
Guo YY, Huang LQ, Liu ZJ, Wang XQ. 2016. Promise and challenge of DNA barcoding in Venus Slipper (Paphiopedilum). PLOS ONE 11(1): e0146880. DOI: 10.1371/journal.pone.0146880.
Hapsari L, Lestari AD, Probojati R. 2020. Haplotype network analysis of wild banana relatives Ensete glaucum, Musa acuminata and Musa balbisiana based on cpDNA rbcL sequences in ex-situ collection. Indian Journal of Genetics and Plant Breeding (The) 80(03): 301–307. DOI: 10.31742/IJGPB.80.3.9.
Hapsari L, Azrianingsih R, Arumingtyas EL. 2018. Genetic variability and relationship of banana cultivars (Musa L.) from East Java, Indonesia based on the Internal transcribed spacer region nrDNA sequences. Journal of Tropical Biology & Conservation (JTBC) 15: 101-120. DOI: 10.51200/jtbc.v15i0.1482
Hapsari L, Damaiyani J, Yulistyarini T, Auliya I, Gusmiati LH, Zaro RM. 2022. Characterization, potential and conservation of Pisang Kates (Musa cv. ABB), a unique local banana cultivar from Pasuruan, East Java, Indonesia. Biodiversitas Journal of Biological Diversity 23(7): 3521-3532. DOI: 10.13057/biodiv/d230727.
Hariyanto S, Ainiyah R, Utami E, Hapsari L. 2021. Genetic diversity and network within dessert bananas (Musa acuminata cv. AA and AAA) inferred by newly designed matK marker. International Journal of Conservation Science 12(2): 585–598.
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 Journal of Biological Diversity 19(3): 1074-1080. DOI: 10.13057/biodiv/d190340.
Hastuti H, Purnomo P, Sumardi I, Daryono BS. 2019. Diversity wild banana species (Musa spp.) in Sulawesi, Indonesia. Biodiversitas Journal of Biological Diversity 20(3): 824-832. DOI: 10.13057/biodiv/d200328.
Heckenhauer J, Barfuss MHJ, Samuel R. 2016. Universal multiplexable matK primers for DNA barcoding of angiosperms. Applications in Plant Sciences 4(6): apps.1500137. DOI: 10.3732/apps.1500137.
Heslop-Harrison P. 2011. Genomics, Banana Breeding and Superdomestication. Acta Horticulturae 897: 55-62. DOI: 10.17660/ActaHortic.2011.897.4.
Janssens SB, Vandelook F, De Langhe E, Verstraete B, Smets E, Vandenhouwe I, Swennen R. 2016. Evolutionary dynamics and biogeography of Musaceae reveal a correlation between the diversification of the banana family and the geological and climatic history of Southeast Asia. New Phytologist 210(4): 1453–1465. DOI: 10.1111/nph.13856.
Kolondam BJ. 2015. Applying matK gene for identification of liliopsida plant species from North Sulawesi through bold systems. International Journal of Applied Biology and Pharmaceutical Technology 6(2): 242–245.
Kress J, Specht C. 2006. The evolutionary and biogeographic origin and diversification of the tropical monocot order Zingiberales. Aliso 22(1): 621–632. DOI: 10.5642/aliso.20062201.49.
Li LF, Wang HY, Zhang C, Wang XF, Shi FX, Chen WN, Ge XJ. 2013. Origins and domestication of cultivated banana inferred from chloroplast and nuclear genes. PloS One 8(11): e80502. DOI: 10.1371/journal.pone.0080502.
Liu G, Zhao T, You X, Jiang J, Li J, Xu X. 2019. Molecular mapping of the Cf-10 gene by combining SNP/InDel-index and linkage analysis in tomato (Solanum lycopersicum). BMC Plant Biology 19(1): 15. DOI: 10.1186/s12870-018-1616-7.
Mustilli AC, Fenzi F, Ciliento R, Alfano F, Bowler C. 1999. Phenotype of the tomato high pigment-2 Mutant Is caused by a mutation in the tomato homolog of DEETIOLATED1. The Plant Cell 11(2): 145–157. DOI: 10.1105/tpc.11.2.145.
Nikmah IA, Azrianingsih R, Wahyudi D. 2016. Genetic diversity of porang populations (Amorphophallus muelleri Blume) In Central Java and West Java based on LEAFY second Intron Marker. Journal of Tropical Life Science 6(1): 23-27. DOI: 10.11594/jtls.06.01.05.
Nyine M, Uwimana B, Akech V, Brown A, Ortiz R, Doležel J, Lorenzen J, Swennen R. 2019. Association genetics of bunch weight and its component traits in East African highland banana (Musa spp. AAA group). Theoretical and Applied Genetics 132(12): 3295–3308. DOI: 10.1007/s00122-019-03425-x.
Osman SA, Ramadan WA. 2019. DNA barcoding of different Triticum species. Bulletin of the National Research Centre 43(1): 174. DOI: 10.1186/s42269-019-0192-9.
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. Bulletin of the National Research Centre 45(1): 33. DOI: 10.1186/s42269-021-00492-3.
Rav I, Uma S, Vaganan M, Mustaffa M. 2013. Phenotyping bananas for drought resistance. Frontiers in Physiology 4(9): 1–15. DOI: 10.3389/fphys.2013.00009.
Roslim DI, Khumairoh S, Herman H. 2016. Confirmation of Tuntun Angin (Elaeocarpus floribundus) Taxonomic Status Using matK and ITS Sequences. Biosaintifika: Journal of Biology & Biology Education 8(3): 393-400. DOI: 10.15294/biosaintifika.v8i3.7406.
Shekhar R, Bhavya G, Prakash HS, Geetha N. 2019. DNA barcoding based authentication of Musa acuminata var. nanjangud rasabale. Jetir 6(3): 62–65.
Sil S, De K, Ghosh A. 2021. Phylogenetic analysis of six different species of Saraca L. (Fabaceae, Caesalpinioideae) based on chloroplast matK gene. Biodiversitas Journal of Biological Diversity 22(9): 3880-3889. DOI: 10.13057/biodiv/d220934.
Song B, Marco-Sola S, Moreto M, Johnson L, Buckler ES, Stitzer, MC. 2022. AnchorWave: Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication. Proceedings of the National Academy of Sciences of the United States of America 119(1): e2113075119. DOI: 10.1073/pnas.2113075119.
Sulistyaningsih LD. 2016. The diversity of wild banana species (Genus Musa) in Java. Makara Journal of Science 20(1): 40–48. DOI: 10.7454/mss.v20i1.5660.
Sulistyaningsih LD. 2017. Newly described and newly recorded of infraspecific taxa of Musa borneensis Becc. (Musaceae) from Sulawesi, Indonesia. Reinwardtia 16(1): 19-24. DOI: 10.14203/reinwardtia.v16i1.2744.
Sulistyaningsih LD, Irawanto R. 2011. Penyebaran Musa campestris Becc. var. sarawakensis Häkkinen. Berk. Penel. Hayati Edisi Khusus 5A: 121–124.
Sulistyaningsih LD, Megia R, Widjaja EA. 2014. Two new records of wild bananas (Musa balbisiana and Musa itinerans) from Sulawesi. Makara Journal of Science 18(1): 1–6. DOI: 10.7454/mss.v18i1.3043.
Sunandar A. 2017. Short Communication: New record of wild banana (Musa balbisiana Colla) in West Kalimantan, Indonesia. Biodiversitas Journal of Biological Diversity 18(4): 1324–1330. DOI: 10.13057/biodiv/d180406.
Sunandar A, Kurniawan AD. 2020. Distribution record of Musa borneensis var. sarawakensis Becc. and Musa campestris var. sarawakensis Becc. In West Kalimantan, Indonesia. Journal of Tropical Biodiversity and Biotechnology 5(3): 172–177. DOI: 10.22146/jtbb.57681.
Sunaryo W, Wahida, Idris SD, Pratama AN, Ratanasut K, Nurhasanah. 2020. Genetic relationships among cultivated and wild bananas from East Kalimantan, Indonesia based on ISSR markers. Biodiversitas Journal of Biological Diversity 21(2): 824-832. DOI: 10.13057/biodiv/d210250.
Udensi OU, Ita EE, Ikpeme EV, Ubi G, Emeagi LI. 2017. Sequence analysis of Maturase K (matK): A chloroplast-encoding gene in some selected pulses. Global Journal of Pure and Applied Sciences 23(2): 213-230. DOI: 10.4314/gjpas.v23i2.2.
Wahyudi D, Azrianingsih R, Mastuti R. 2013. Genetic variability of porang populations (Amorphophallus muelleri) in West Java and Central Java based on trnL intron sequences. Journal of Biodiversity and Environmental Sciences (JBES) 3(9): 31-41.
Wang JF, Gong X, Chiang YC, Kuroda C. 2013. Phylogenetic patterns and disjunct distribution in Ligularia hodgsonii Hook (Asteraceae). J Biogeogr 40: 1741–175. DOI: 10.1111/jbi.12114.
Wang S, Yang X, Xu M, Lin X, Lin T, Qi J, Shao G, Tian N, Yang Q, Zhang Z, Huang S. 2015. A Rare SNP Identified a TCP transcription factor essential for tendril development in Cucumber. Molecular Plant 8(12): 1795–1808. DOI: 10.1016/j.molp.2015.10.005.
Wang XL, Chiang TY, Roux N, Hao G, Ge XJ. 2007. Genetic diversity of wild banana (Musa balbisiana Colla) in China as revealed by AFLP markers. Genetic Resources and Crop Evolution 54(5): 1125–1132. DOI: 10.1007/s10722-006-9004-9.
Wattoo JI, Saleem MZ, Shahzad MS, Arif A, Hameed A, Saleem MA. 2016. DNA barcoding: amplification and sequence analysis of rbcL and matK genome regions in three divergent plant species. Advancements in Life Sciences 4(1): 03-07.
Yuan QJ, Zhang B, Jiang D, Zhang WJ, Lin TY, Wang NH, Chiou SJ, Huang LQ. 2015. Identification of species and materia medica within Angelica L. (Umbelliferae) based on phylogeny inferred from DNA barcodes. Molecular Ecology Resources 15(2): 358–371. DOI: 10.1111/1755-0998.12296.
Zhou H, Liu Q, Li J, Jiang D, Zhou L, Wu P, Lu S, Li F, Zhu L, Liu Z, Chen L, Liu YG, Zhuang C. 2012. Photoperiod- and thermo-sensitive genic male sterility in rice are caused by a point mutation in a novel noncoding RNA that produces a small RNA. Cell Research 22(4): 649-660. DOI: 10.1038/cr.2012.28.