Phylogenetic analysis of 23 accessions of Indonesian banana cultivars based on Internal Transcribed Spacer 2 (ITS2) region

Karlia Meitha(1), Intan Fatmawati(2), Fenny Martha Dwivany(3*), Agus Sutanto(4), Sigit Nur Pratama(5), Husna Nugrahapraja(6), Ketut Wikantika(7)

(1) School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
(2) School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
(3) School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia; Bali International Research Center for Banana, Jl. Raya Kampus UNUD, Badung, Bali 80361, Indonesia; Center for Remote Sensing, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
(4) Indonesia Tropical Fruit Research Institute, Jl. Raya Solok Aripan KM 8, Solok, Sumatera Barat 27356, Indonesia
(5) School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
(6) School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
(7) Center for Remote Sensing, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia; Bali International Research Center for Banana, Jl. Raya Kampus UNUD, Badung, Bali 80361, Indonesia
(*) Corresponding Author


Pisang Kepok (Musa spp. [ABB ’Saba’ subgroup]) has several unique characteristics, such as tolerance to drought and Fusarium Foc (TR4) disease. Currently, the genetic diversity of Pisang Kepok in Indonesia is not well identified, although it is widely cultivated. Information on genetic diversity is essential for developing breeding strategies to achieve efficient cultivar improvement in the future. Aims of this research were to analyze the genetic variation of Pisang Kepok from some islands in Indonesia and to determine the genetic relationship between Pisang Kepok and other accessions banana cultivars based on ITS2 region, as a basis for future research in improving banana quality through molecular breeding. We have conducted the multiple sequence alignment and built the phylogenetic tree analysis using the Bayesian Inference Phylogeny method of one million generations (ngen = 1,000,000). The ITS2 region showed two clade ingroups: first clade consists of banana with B genome (balbisiana), while the second clade consists of banana with only A genome (acuminata). In general, all accessions of Pisang Kepok cultivars were clustered in the B genome of bananas cultivars. In addition, the ITS2 sequences and secondary structures among Pisang Kepok from various regions are identical, suggesting that there was no genetic variation in the ITS2 region of Pisang Kepok from multiple areas in Indonesia.


Pisang Kepok; Musa spp. (ABB ‘Saba’ subgroup); ITS2; phylogenetic; ITS2 secondary structure

Full Text:



Ahmad F, Megia RITA, Poerba YS. 2014. Genetic Diversity of Musa balbisiana Colla in Indonesia Based on AFLP Marker. HAYATI J Biosci. 21(1):39–47. doi:10.4308/hjb.21.1.39.

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215(3):403–410. doi:10.1016/S0022­ 2836(05)80360­2.

Baral A. 2019. Bananas tackling drought and heat – with DREBs and more. Physiol Plant. 165(2):128–130. doi:10.1111/ppl.12905.

Boonruangrod R, Desai D, Fluch S, Berenyi M, Burg K. 2008. Identification of cytoplasmic ancestor genepools of Musa acuminata Colla and Musa balbisiana Colla and their hybrids by chloroplast and mitochondrial haplotyping. Theor Appl Genet. 118(1):43–55. doi:10.1007/s00122­008­0875­3.

Burgos­Hernández M, González D, Castillo­Campos G. 2017. Phylogenetic position of the disjunct species Musa ornata (Musaceae): first approach to understand its distribution. Genet Resour Crop Evol. 64(8):1889–1904. doi:10.1007/s10722­016­0479­8.

Campbell NA, Reece J. 2000. Biology. Boston: Benjamin Cummings Pearson. Chen S, Yao H, Han J, Liu C, Song J, Shi L, Zhu Y, Ma X, Gao T, Pang X, et al. 2010. Validation of the ITS2 Region as a Novel DNA Barcode for Identifying Medicinal Plant Species. PLoS One. 5(1):e8613. doi:10.1371/journal.pone.0008613.

Coleman AW. 2007. Pan­eukaryote ITS2 homologies revealed by RNA secondary structure. Nucleic Acids Res. 35(10):3322–3329. doi:10.1093/nar/gkm233.

Crooks GE, Hon G, Chandonia JM, Brenner SE. 2004. WebLogo: a sequence logo generator. Genome Res. 14(6):1188–1190. doi:10.1101/gr.849004.

Daniells J, O’Keefe V, Smyth H, Gething K, Fanning K, Telford P. 2013. Planet of the Cavendish ­ understanding the domination. In: Acta Horticulturae, 986. Int Soc Hort Sci (ISHS), Leuven, Belgium. p. 219–224. doi:10.17660/ActaHortic.2013.986.23.

Daniells JW, Arnaud E, Sharrock SL. 2001. Musalogue, a Catalogue of Musa Germplasm: Diversity in the Genus Musa. INIBAP. URL

De Langhe E. 2009. Relevance of banana seeds in archaeology. Ethnobot Res Appl. 7:271–281. doi:10.17348/era.7.0.271­281.

De Langhe E, Hribová E, Carpentier S, Dolezel J, Swennen R. 2010. Did backcrossing contribute to the origin of hybrid edible bananas? Ann Bot. 106(6):849–857. doi:10.1093/aob/mcq187.

Denham TP, Haberle SG, Lentfer C, Fullagar R, Field J, Therin M, Porch N, Winsborough B. 2003. Origins of Agriculture at Kuk Swamp in the Highlands of New Guinea. Science. 301(5630):189–193. doi:10.1126/science.1085255.

Dover G. 1982. Molecular drive: a cohesive mode of species evolution. Nature. 299(5879):111–117. doi:10.1038/299111a0.

Doyle JJ. 1990. Isolation of plant DNA from fresh tissue. Focus p. 13–15. FAO. 2019. Banana facts and figures. Technical report, Food and Agriculture Organizations of United Nation, Rome. URL{#}data/ QC.

FAO. 2020. Banana Market Review: Preliminary Results 2019. Technical report, Rome. URL http://www.fao. org/publications/card/en/c/CA7567EN/.

Gouy M, Guindon S, Gascuel O. 2010. SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol. 27(2):221–224. doi:10.1093/molbev/msp259.

Hřibová E, Čížková J, Christelová P, Taudien S, de Langhe E, Doležel J. 2011. The ITS1­5.8S­ITS2 Sequence Region in the Musaceae: Structure, Diversity and Use in Molecular Phylogeny. PLoS One. 6(3):e17863. doi:10.1371/journal.pone.0017863.

Hidayat T, Kelana HW, Ismanto DIA, Meitha K. 2018. Survey on ethnobotanic value of Banana (Musa spp; Musaceae) in Bali Province, Indonesia. HAYATI J Biosci. 25(1):31–39. doi:10.4308/hjb.25.1.31.

Holder M, Lewis PO. 2003. Phylogeny estimation: traditional and Bayesian approaches. Nat Rev Genet. 4(4):275–284. doi:10.1038/nrg1044. Jobes LV, Thien DB. 1997. A Conserved Motif in the 5.8S Ribosomal RNA (rRNA) Gene is a Useful Diagnostic Marker for Plant Internal Transcribed Spacer (ITS) Sequences. Plant Mol Biol Rep. 15(4):326–334. doi:10.1023/A:1007462330699.

Jumjunidang R, Soemargono A. 2012. Identification and distribution of Fusarium oxysporum f. sp. cubense isolates through analysis of vegetative compatibility group in Lampung province, Indonesia. ARPN J Agric Biol Sci. 7(4):297–284.

Koetschan C, Förster F, Keller A, Schleicher T, Ruderisch B, Schwarz R, Müller T, Wolf M, Schultz J. 2010. The ITS2 Database III—sequences and structures for phylogeny. Nucleic Acids Res. 38(suppl_1):D275–D279. doi:10.1093/nar/gkp966.

Kovarik A, Matyasek R, Lim KY, Skalicka K, Koukalova B, Knapp S, Chase M, Leitch AR. 2004. Concerted evolution of 18–5.8–26S rDNA repeats in Nicotiana allotetraploids. Biol J Linn Soc. 82(4):615–625. doi:10.1111/j.1095­8312.2004.00345.x.

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.

Maryani N, Lombard L, Poerba YS, Subandiyah S, Crous PW, Kema GH. 2019. Phylogeny and genetic diversity of the banana Fusarium wilt pathogen Fusarium oxysporum f. sp. cubense in the Indonesian centre of origin. Stud Mycol. 92:155–194. doi:10.1016/j.simyco.2018.06.003.

Merget B, Koetschan C, Hackl T, Förster F, Dandekar T, Müller T, Schultz J, Wolf M. 2012. The ITS2 Database. J Visualized Exp. (61):e3806. doi:10.3791/3806.

Molina A, Fabregar E, Sinohin V, Yi G, Viljoen A. 2009. Recent occurrence of Fusarium oxysporum f. sp. cubense tropical race 4 in Asia. In: D Jones, IV den Bergh, editors, III International Symposium on Banana: ISHS­ProMusa Symposium on Recent Advances in Banana Crop Protection for Sustainable Production and Improved Livelihoods, volume 828. p. 109–116. doi:10.17660/ActaHortic.2009.828.10.

Morpurgo R, Lopato SV, Afza R, Novak FJ. 1994. Selection parameters for resistance to Fusarium oxysporum f. sp. cubense race 1 and race 4 on diploid banana (Musa acuminata Colla). Euphytica. 75(1):121–129. doi:10.1007/BF00024539.

Němečková A, Christelová P, Čížková J, Nyine M, den houwe I, Svačina R, Uwimana B, Swennen R, Doležel J, Hřibová E. 2018. Molecular and Cytogenetic Study of East African Highland Banana). Front Plant Sci. 9(1371):1–13. doi:10.3389/fpls.2018.01371.

Opara UL, Jacobson D, Al­Saady NA. 2010. Analysis of genetic diversity in banana cultivars (Musa cvs.) from the South of Oman using AFLP markers and classification by phylogenetic, hierarchical clustering and principal component analyses. J Zhejiang Univ., Sci., B. 11(5):332–341. doi:10.1631/jzus.B0900310.

Ploetz RC, Kepler AK, Daniells J, Nelson SC. 2007. Banana and Plantain–an Overview with Emphasis on Pacific Island Cultivars. URL­content/uploads/201 8/06/banana­plantain­overview.pdf.

Poerba YS, Ahmad F. 2010. Genetic variability among 18 cultivars of cooking bananas and plantains by RAPD and ISSR markers. Biodiversitas. 11(3):118–123. doi:10.13057/biodiv/d110303.

Price N. 1995. The origin and development of banana and plant cultivation. In: S Gowen, editor, Banana and plantain. London: Chapman and HIll. p. 1–13. Ravi I, Uma S, Vaganan MM, Mustaffa MM. 2013. Phenotyping bananas for drought resistance. Front Physio. 4(9):1–15. doi:10.3389/fphys.2013.00009.

Rebouças TA, Haddad F, Ferreira CF, de Oliveira SAS, da Silva Ledo CA, Amorim EP. 2018. Identification of banana genotypes resistant to Fusarium wilt race 1 under field and greenhouse conditions. Sci Hortic. 239:308–313. doi:10.1016/j.scienta.2018.04.037.

Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 19(12):1572–1574. doi:10.1093/bioinformatics/btg180.

Schultz J, Maisel S, Gerlach D, Müller T, Wolf M. 2005. A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota. RNA. 11(4):361–364. doi:10.1261/rna.7204505.

Siddiqah M. 2002. Biodiversitas dan Hubungan Kekerabatan Berdasarkan Marker Morfologi Berbagai Plasma Nutfah Pisang.

Sievers F, Higgins DG. 2014. Clustal Omega, accurate alignment of very large numbers of sequences. In: D Russell, editor, Multiple Sequence Alignment Methods. Methods in Molecular Biology (Methods and Protocols), volume 1079. Totowa NJ: Humana Press. p. 105–116. doi:10.1007/978­1­62703­646­ 7_6.

Simmonds N. 1962. The evolution of the bananas. London: Longmas Inc.

Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25(24):4876–4882. doi:10.1093/nar/25.24.4876.

Valmayor RV, Jamaluddin SH, Silayoi B, Kusumo S, Danh LD, Pascua OC, Espino RC. 2000. Banana Cultivar Names and Synonyms in Southeast Asia. Laguna: INIBAP Regoional Office of Asia and The Pacific. p. 8–14.

Wang Z, Miao H, Liu J, Xu B, Yao X, Xu C, Zhao S, Fang X, Jia C, Wang J, et al. 2019. Musa balbisiana genome reveals subgenome evolution and functional divergence. Nat Plants. 5(8):810–821. doi:10.1038/s41477­019­0452­6.

Whittle CA. 2006. The influence of environmental factors, the pollen : ovule ratio and seed bank persistence on molecular evolutionary rates in plants. J Evol Biol. 19(1):302–308. doi:10.1111/j.1420­ 9101.2005.00977.x.

Xiong J. 2006. Essential Bioinformatics. New York: Cambrige University Press. doi:10.1017/CBO9780511806087.

Yao H, Song J, Liu C, Luo K, Han J, Li Y, Pang X, Xu H, Zhu Y, Xiao P, Chen S. 2010. Use of ITS2 region as the universal DNA barcode for plants and animals. PloS ONE. 5(10):e13102. doi:10.1371/journal.pone.0013102.

Zhang W, Yuan Y, Yang S, Huang J, Huang L. 2015. ITS2 Secondary Structure Improves Discrimination between Medicinal “Mu Tong” Species when Using DNA Barcoding. PloS ONE. 10(7):e0131185. doi:10.1371/journal.pone.0131185.


Article Metrics

Abstract views : 234 | views : 280


  • There are currently no refbacks.

Copyright (c) 2020 The Author(s)

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