Genetic variability and phylogenetic relationships of Begonia multangula based on atpB-rbcL non-coding spacer of cpDNA sequences
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TRI WARSENO
♥
https://orcid.org/0000-0002-8051-3740
MUHAMMAD EFENDI
https://orcid.org/0000-0002-9710-4775
ABDUL RAZAQ CHASANI
BUDI SETIADI DARYONO
https://orcid.org/0000-0002-0703-2123
Abstract
Abstract. Warseno T, Efendi M, Chasani AR, Daryono BS. 2022. Genetic variability and phylogenetic relationships of Begonia multangula based on atpB-rbcL non-coding spacer of cpDNA sequences. Biodiversitas 23: 5491-5501. Begonia (Begoniaceae) belongs to Section Platycentrum-Sphenanthera Group which has a wide distribution from Sumatra to the Lesser Sunda Islands and Sulawesi. Information on B. multangula genetic variability and intraspecies relationships based on molecular characters is critical for developing appropriate strategies in conservation biology, breeding activities, and many other applied fields. The genetic variability and interspecific relationships of B. multangula in Indonesia were investigated using sequence data from the atpB-rbcL intergenic spacer (IGS) cpDNA regions. The atpB-rbcL IGS fragment was amplified using atpB-1 as the forward primer and rbcL-1 as the reversed primer. Genetic variations were found in the length of the sequence and nucleotide divergences in the atpB-rbcL IGS region. The genetic distance between 822 fixed sites ranged from 0 to 0.61%. Eighteen of the 822 sites (99.27%) analyzed were invariable, six sites (0,73%) were variable consisting of 4 singleton variable sites and two parsimony informative sites, and twelve sites were gaps. The phylogenetic relationships generated by B. multangula based on the atpB-rbcL IGS sequence analysis indicated the genetic variation and divided it into two clades. However, the clustering pattern of B. multangula specimens resulting from molecular analysis based on atpB-rbcL IGS sequences did not show the geographic clustering grouping pattern.
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References
Alcántara-Ayala O, Oyama K, Ríos-Muñoz, Rivas G, Ramirez-Barahona S, Luna-Vega I. 2020. Morphological variation of leaf traits in the Ternstroemia lineata species complex (Ericales: Penthaphylacaceae) in response to geographic and climatic variation. PeerJ 8: e8307. DOI: 10.7717/peerj.8307.
Andrews JM. 2001. Determination of minimum inhibitory concentrations. Journal of Antimicrobial Chemotherapy, 48 (Suppl. 1), 5–16.
Ardi, WH, Chikmawati T, Witono, JR & Thomas, DC. 2018. A synopsis of Begonia (Begoniaceae) of Southeastern Sulawesi including four new species. Phytotaxa 381.1: 027-050.
Beaumont MA, Ibrahim KM, Boursot P, Bruford MW. 1998. Measuring genetic distance. In: Karp A, Isaac PG, Ingram DS. Molecular Tools for Screening Biodiversity. Chapman & Hall, London.
Cahyanto T, Efendi M, Shofara RM, Dzakiyyah M, Nurlaela, Prima G. Satria. 2019. Short Communication: Floristic survey of vascular plant in the submontane forest of Mt. Burangrang Nature Reserve, West Java, Indonesia. Biodiversitas, 20(8): 2197-2205.
Chen J, Xu, Y, Wei G, Liao S, Zhang Y, Huang W, Yuan L, Wang Y. 2015. Chemotypic and genetic diversity in Epimedium sagittatum from different geographical regions of China. Phytochemistry, 116:180–187.
Chen J M, Liu F, Wang Q F and Motley T J. 2008. Phylogeography of a Marsh Herb Sagittaria trifolia (Alismataceae) in China Inferred from cpDNA atpB – rbcL Intergenic Spacer. Mol. Phylogenet. Evol., 48:168 – 75.
Chiang, TY, Schaal, BA, Peng C. 1998. Universal primers for amplification and sequencing a noncoding spacer between the atpB and rbcL genes of chloroplast DNA. Botanical Bulletin of Academia Sinica, 39: 245 – 250.
Chiang TY, Chiang YC, Chen YJ, Chou CH, Havanond S, Hong TN, Huang S (2001) Phylogeography of Kandelia candel in East Asiatic mangroves based on nucleotide variation of chloroplast and mitochondrial DNAs. Mol Ecol 10:2697–2710.
Darmayanti NLPI. 2011. Molecular Phylogenetic: Organism Taxonomy Method Based on Evolution History. Wartazoa, 21(1) 1-10. [Indonesian]
Djarwaningsih T, Sulistiarini D, Sunarti S, Aerida IH, Dewi, Mahyuni R. 2010. Karakterisasi Tipe Vegetasi dan Keanekaragaman Jenis Flora/ Jamur di Cagar Alam Gunung Tukung Gede Serang Banten. Laporan Akhir Program Insentif Peneliti dan perekayasa, LIPI Tahun 2010. Departemen Pendidikan Nasional dan Lembaga Ilmu Pengetahuan Indonesia. [Indonesian].
Doorenbos, J., M.S.M. Sosef, J.J.F.E. de Wilde. 1998. The sections of Begonia, including descriptions, keys and species lists. Backhuys Publishers, Leiden.
Efendi M, Azizah N, Supriyatna A, Destri. 2017.The diversity and ecological preference of wild Begonia in remnant forest of Cibodas Botanic Gardens. Berita Biologi 16 (3): 233 – 241.
Efendi M. 2019. Native Begonia in Baturaden Botanic Gardens, Central Java. Proceeding of national seminary Volume 5 (1):13-17. [Indonesian].
Fitmawati, Hartana A. 2010. Phylogenetic study of Mangifera laurina and its related species using cpDNA trnL-F spacer markers. Hayati J Biosci 17 (1): 9-14.
Forrest LL, Hollingsworth PM. 2003. A recircumscription of Begonia based on nuclear ribosomal sequences. Plant systematic and evolution., 241 (3): 193- 211.
Forrest LL, Hughes M, Hollingsworth PM. 2005. A phylogeny of Begonia using nuclear ribosomal sequence data and morphological characters. Syst Bot 30 (3): 671-682. DOI: 10.1600/0363644054782297.
Gao YD, Zhang Y, GaoXF, Zhu ZM, 2015. Pleistocene glaciations, demographic expansion and subsequent isolation promoted morphological heterogeneity: a phylogeographic study of the alpine Rosa sericea complex (Rosaceae). Sci. Rep. 5, 11698.
Girmansyah D. 2008. Biodiversity of Wild Begonia in West Java. Berita Biologi 9(2): 195-203.
Girmansyah D. 2009. A taxonomic study of Bali and Lombok Begonia (Begoniaceae). Reinwardtia 12 (5): 419-434.
Girmansyah D. 2017. Sinopsis Begonia liar di Sumatera Barat. Berita Biologi 16 (3) 2017: 219-231.
Ghorbani A, Saeedi Y, de Boer HJ. 2017. Unidentifiable by morphology: DNA barcoding of plant material in local markets in Iran. PLoS ONE 12(4): e0175722. https://doi.org/10.1371/journal.pone.0175722.
Hamzah H, Siregar KAAK, Suffiana Y, Yudhawan I, Nurwijayanto A. 2022. Antibacterial and antibiofilm activity of Begonia multangula Blume. leaf extract against Candida albicans. Food Research 6(1): 260-268.
Hartutiningsih. 2005. Begonia Kebun Raya Bali, Candikuning: UPT BalaiKonservasi TumbuhanKebun Raya Bali, LIPI. ISBN: LIPI PRESS. 797-26-2410-4 [Indonesian].
Hancock JF. 2003. Plant Evolution and the Origin of Crop Species. 2nd ed. CABI Publishing, Wallingford.UK.
Hidayat S. 2014. Spatial Distribution for Dominant Species of Wornojiwo Remnant Forest, Cibodas Botanic Garden. Media Konservasi 19(2): 88 – 94. [Indonesian].
Hoot SB, Douglas AW. 1998. Phylogeny of the Proteaceae Based on atpB and atpB–rbcL Intergenic Spacer Region Sequences. Australian Systematic Botany, 11, 301–320.
Huang S, Chiang YC, Schaal BA, Chou CH, Chiang TY. 2001b. Organelle DNA phylogeography of Cycas taitungensis, a relict species in Taiwan. Mol Ecol 10: 2669–2681.
Huang JC, Wang WK, Peng C I and Chiang TY. 2005. Phylogeography and Conservation Genetics of Hygrophila pogonocalyx (Acanthaceae) Based on atpB – rbcL Noncoding Spacer cpDNA. Journal of Plant Research 118: 1 – 11.
Hughes M, Girmansyah D. 2011. A revision of Begonia sect. Sphenanthera (Hassk.) Warb. from Sumatra. Gardens’ Bulletin Singapore 62 (2): 27-39.
Hughes M, Hollingsworth PM. 2008. Population genetic divergence corresponds with species level biodiversity patterns in the large genus Begonia. Molecular ecology.17 (11): 2643-265.
Hughes, M., Moonlight, P.W., Jara-Muñoz, A., Tebbitt, M.C., Wilson, H.P. & Pullan, M. 2015–. Begonia Resource Centre. Online database available from http://padme.rbge.org.uk/begonia/.
Janssens S, Geuten K, Yuan, YM, Song Y, Kupfer P, Smets E. 2006. Phylogenetics of Impatiens and Hydrocera (Balsaminaceae) using Chloroplast atpB-rbcL Spacer Sequences. Systematic Botany 31(1): pp. 171–180.
Jiao LJ, Shui YM. 2013. Evaluating candidate DNA barcodes among Chinese Begonia (Begoniaceae) species. Plant Div Resour 35 (6): 715-724. DOI: 10.7677/ynzwyj201313064
Kanno M, Yokoyama J, Suyama Y, Ohyama M, Itoh T, Suzuki M.2003. Geographical distribution of two haplotypes of chloroplast DNA in four oak species (Quercus) in Japan. J. Plant Res 116:311–317.
Li C, Chen J-L, Li Y-Y, Tian D-K, 2018. Genetic diversity of Begonia versicolor (Begoniaceae), a narrow endemic species in southeast Yunnan of China. Taiwania 63(1): 49-53.
Li WH. 1997. Molecular Evolution. Sinauer, Sunderland, MA.
Liu F, Zhao S Y, Li W, Chen J M and Wang Q F. 2010. Population Genetic Structure and Phylogeographic Patterns in the Chinese Endemic Species Sagittaria lichuanensis, Inferred from cpDNA atpB – rbcL Intergenic Spacers. Botany 88: 886 – 92.
Liu C, Wang G, Wang H, Xia T, Zhang S, Wang Q, Fang Y. 2015. Phylogenetic Relationships in the Genus Rosa Revisited Based on rpl16, trnL-F, and atpB-rbcL Sequences. Hortscience 50 (11): 1618–1624.
Manen J, Natali A. 1995. Comparison of the evolution of ribulose-1, 5-biphosphate carboxylase (rbcL) and atpB-rbcL spacer sequences in a recent plant group, the tribe Rubieae (Rubiaceae). J. Mol. Biol. 41: 920-927.
Matolweni LO, Balkwill K, McLellan T. 2000. Genetic diversity and gene flow in the morphologically variable, rare endemics begonia dregei and begonia homonyma (begoniaceae). American journal of botany 87(3): 431-439.
Moonlight PW, Ardi WH, Padilla LA, Chung K-F, Fuller D, Girmansyah D, Hollands R, Jara-Muñoz A, Kiew R, Leong W-C, Liu Y, Mahardika A, Marasinghe LDK, O’Connor M, Peng C-I, Pérez AJ, Phutthai T, Pullan M, Rajbhandary S, Reynel C, Rubite RR, Sang J, Scherberich D, Shui Y-M, Tebbitt MC, Thomas DC, Wilson HP, Zaini NH, and Hughes, M. 2018. Dividing and conquering the fastest-growing genus: towards a natural sectional classification of the mega-diverse genus Begonia (Begoniaceae). Taxon 67 (2): 267-323.
Mori GM and Kajita T. 2016. Mangrove Conservation Genetics Journal of Integrated Field Science 13:13–9.
Mukhopaddhyay T, Bhattacharjee S. 2016. Genetic Diversity: Importance and Measurements. In Mir AH and Bhat NA (Eds), Conserving biological diversity: A multiscaled approach. Research India Publications, New Delhi, India.
Neale, S, Goodall-Copestake W, Kidner CA. 2006. The evolution of diversity in Begonia. In: Floriculture, Ornamental and Plant Biotechnology, Teixeira da Silva, JA. (ed.).Global Science books.Middlesex, UK.
Nei M, Wen-Hsiung L.1979. Mathematical Model for Studying Genetic Variation in Terms of Restriction Endonucleases. PNAS. 76 (10): 5269–73.
Nei M, 1987. Molecular evolutionary genetics. Columbia University Press, New York.
Ningrum WDA, Atmaja MB, Daryono BS, Purnomo. 2020. Genetic variability of Begonia longifolia Blume from Indonesia based on Nuclear DNA internal transcribed spacer (ITS) sequence data. Biodiversitas 21 (12): 5778-5785.
Ohsako T, Ohnishi O.2000. Intra- and interspecific phylogeny of wild Fagopyrum (Polygonaceae) species based on nucleotide sequences of noncoding regions in chloroplast DNA. Am J Bot 87:573–582.
Peng C-I, Chiang T-Y. 2000. Molecular confirmation of unidirectional hybridization in Begonia x taipeiensis Peng (Begoniaceae) from Taiwan. Annals of the Missouri Botanical Garden 87 (1): 273 – 285.
Philippe H, Brinkmann H, Lavrov DV, Littewood DTJ, Manuel M, Worheide G and Baurain D. 2011. Resolving Difficult Phylogenetic Question: Why More Sequences Are Not Enough. Plos Biology, 9(3): e1000602. doi:10.1371/journal.pbio.1000602.
Plana V, Gascoigne A, Forrest LL, Harris D, Pennington RT. 2004. Pleistocene and pre-Pleistocene Begonia speciation in Africa. Mol Phylogenet Evol 31 (2): 449-461. DOI: b10.1016/j.ympev.2003.08.023 .
Priyadi H, Takao G, Rahmawati I, Supriyanto B, Nursal WI, Rahman I. 2010. Five hundred plant species in Gunung Halimun Salak National Park, West Java: a checklist including Sundanese names, distribution and use. CIFOR, Bogor, Indonesia.
Purwantoro RS, Hartutiningsih, Siregar M, Sudarmono, Fijridiyanto IA, Satyanti A. 2010. Potensi Lamiaceae, Begoniaceae, dan Lamiaceae sebagai Bahan Baku Obat dan Aspek Konservasinya. Laporan Akhir Tahun Program Insentif Peneliti dan Perekayasa LIPI. Departemen Pendidikan Nasional dan Lembaga Ilmu Pengetahuan Indonesia [Indonesian].
Purwantoro RS, Siregar HM, Satyanti A, Wihermanto, Kusuma YWC, Sumanto. 2011. Characterization of active components in Begonia baliensis extract and Lasianthus obscurus (Rubiaceae) as medicinal raw materials and conservation aspects. Proposal of Researcher and Engineer Incentive Activities LIPI, Research and Technology, LIPI, Bogor.
Putri NHS, Nurdiwiyati D, Lestari S, Ramdhan B, Efendi M, Nurhidayat N. 2019. Antibacterial Activity of Begonia multangula Blume. Stem and Leaf Extract on Porphyromonas gingivalis. Jurnal Biologi Universitas Andalas 7(1): 51-58.
Schradin C. 2013. Intraspecific variation in social organization by genetic variation, developmental plasticity, social flexibility or entirely extrinsic factors. Phil Trans R Soc B 368: 20120346. DOI: 10.1098/rstb.2012.0346.
Siregar, HM, Wahyuni S, Ardaka IM. 2018. Karakterisasi morfologi daun Begonia alam (Begoniaceae): Prospek pengembangan koleksi tanaman hias daun di Kebun Raya Indonesia. Jurnal Biologi Indonesia 14(2), 201–211.
Šmarda P, Bureš P, Horová L et al (2014) Ecological and evolutionary significance of genomic GC content diversity in monocots. Proc Natl Acad Sci U S A 111:E4096–E4102.
Susanto AH, Nuryanto A and Daryono BS. 2018 High Connectivity Among Synedrella nodiflora Populations in Java Island Based on Intergeneric Spacer atpB – rbcL. Biosaintifika: Journal of Biology & Biology Education. 10: 41 – 7.
Susanto AH, Dwiati M. 2019. Genetic difference between two phenotypically similar members of Asteraceae by the use of Intergenic Spacer atpB – rbcL. Biosaintifika 11(3): 393-399.
Tamam MB, Ramadani AH, Santoso H, Al Yamini TH. 2020. Diversity of Edible Flora and Biotourism Potential Development of Botany Adventure in Turgo, Mount Merapi National Park Yogyakarta. Jurnal Biota 6(2): 71-77.
Tamura K, Stecher G, Kumar S. 2021. MEGA11: Molecular Evolutionary Genetics Analysis Version 11 Molecular Biology and Evolution, 38 (7): 3022–3027.
Tan B, Liu K, Yue X L, Liu F, Chen J M and Wang Q F. 2008. Chloroplast DNA Variation and Phylogeographic Patterns in the Chinese Endemic Marsh Herb Sagittaria potamogetifolia. Aquatic Botany 89: 372 – 8.
Tebbitt MC. 2003. Taxonomy of Begonia longifolia (Begoniaceae) and related species. Brittonia 55 (1): 19–29. https://doi.org/10.1663/0007-196X(2003)055[0019:TOBLBB]2.0.CO;2
Tebbitt MC, Forrest LL, Santoriello A, Clement W, Swensen SM. 2006. Phylogenetic relationships of Asian Begonia, with an emphasis on the evolution of rain-ballist and animal dispersal mechanisms in sections Platycentrum, Sphenanthera and Leprosae. Syst. Bot. 31(2): 327–336.
Thomas, DC, Hughes M., Phutthai T, Rajbhandary S, Rubite R, Ardi WH, Richardson JE. 2011. A non-coding plastid DNA phylogeny of Asian Begonia (Begoniaceae): Evidence for morphological homoplasy and sectional polyphyly. Molecular Phylogenetics and Evolution 60 (3): 428-444.
Thomas, D.C., Hughes, M., Phuttai, T., Ardi, W.H., Rajhbandary, S., Rubite, R., Twyford, A.D., Richardson, J.E. (2012) West to east dispersal and subsequent rapid diversification of the mega-diverse genus Begonia (Begoniaceae) in the Malesian Archipelago. Journal of Biogeography 39: 98–113.
Tsai C-C, Sheue C-R, Chen C-H, Chou C-H. 2010. Phylogenetics and Biogeography of the Phalaenopsis violacea (Orchidaceae) Species Complex Based on Nuclear and Plastid DNA. J. Plant Biol. 53:453–460.
Tseng YH, Huang HY, Xu WB, Yang HA, Peng CI, Liu Y, Chung KF. 2019. Phylogeography of Begonia luzhaiensis suggests both natural and anthropogenic causes for the marked population genetic structure. Bot Stud 60 (20): 1-19. DOI: 10.1186/s40529-019-0267-9.
Undaharta NKE and Sutomo. 2016. Autecology of Begonia in Part of Mount Merapi National Park. Jurnal Biologi 20 (1): 29 – 34.
Widodo P, Chikmawati T, Kusuma YWC. 2019. Placement of Syzygium boerlagei (Merr.) Govaerts (Myrtaceae) confirmed with atpB-rbcL intergenic spacer. Biotropia 26(1): 9 – 15.
Wiriadinata H, Girmansyah D, Hoover S, Hunter J. 2002. Begonia Diversity in Gunung Halimun National Park. Berita Biologi 6(1): 91-97.
Yuwa-amornpitak T, Vichitsoonthonkul T, Tanticharoen M. 2006. Molecular phylogeny of Dipterocarpaceae in Thailand using trnl-trnf and atpb-rbcl intergenic spacer region in chloroplast DNA. Pakistan Journal of Biological Sciences 9(4): 649-653.
Zeng X, Yuan Z, Tong X, Li Q, Gao W, Qin M, Liu Z. 2012. Phylogenetic study of Oryzoideae species and related taxa of the Poaceae based on atpB-rbcL and ndhF DNA sequences. Mol.Biol. Rep. 39:5737–5744.
Zhang Q-d, Jia R-Z, Meng C, Ti CW & Wang TY. 2015. Diversity and population structure of a dominant deciduous tree based on morphological and genetic data. AoB Plants.7:1-13.
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