The Use of DNA Barcoding and Phylogenetic Analysis to Improve Identification of Usnea spp. Based on ITS rDNA

https://doi.org/10.22146/jtbb.58635

Miftahul Jannah(1*), Muhammad Rifqi Hariri(2), Rina Sri Kasiamdari(3), Niken Satuti Nur Handayani(4)

(1) Biology Department, As-Syafi`iyah Islamic University
(2) Research Center for Plant Conservation and Botanic Gardens – Indonesian Institute of Sciences
(3) Faculty of Biology, Gadjah Mada University
(4) Faculty of Biology, Gadjah Mada University
(*) Corresponding Author

Abstract


Lichen of the genus Usnea is quite common being used as a traditional herbal remedy. This genus is characterized by thallus, which is very similar among the species, leads to some difficulties in distinguishing them. In Indonesia, such research report on the availability of this genus based on their morphological characteristic is minimal. This might be due to too high morphological similarities among them. The molecular character, which is based on the DNA Barcode of Internal Transcribed Spacer (ITS) rDNA sequences, with its conserved region (5.8S) and varied region (ITS1 and ITS2), are becoming essential characters on identifying as well as analyzing the phylogenetic. The current study then proposed to identify and draw the species dendrogram of species within the Usnea genus obtained from Mount Lawu Forest of Central Java and Turgo Forest of Yogyakarta based on their phylogenetic and phenetic analysis. The dendrogram was constructed with UPGMA using the simple matching coefficient, whereas the phylogenetic tree was constructed with Maximum Likelihood (ML) using Kimura-2 parameter with 1000 bootstrap. The data were unable to draw phenetic relationships among the subgenus Usnea and Eumitria members. The phylogenetic tree shows the primary two clades, distinguishing the subgenus Usnea and Eumitria. The ITS rDNA sequence was able to identify most of the Usnea species.


Keywords


Usnea; DNA Barcode; ITS rDNA; phylogenetic

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References

Articus, K, 2004, Phylogenetic Studies in Usnea (Parmeliaceae) and Allied Genera, Comprehensive Summaries of Uppsala Dissertations From the Faculty of Science and Technology, Acta Universitatis Upsaliensis.

Articus, K, Mattison, J.E, Tibell, L, Grube, M, & Wedin, M. 2002. 'Ribosomal DNA and b-tubulin data do not support the separation of the lichens Usnea florida and U. subfloridana as distinct species', Mycological Society, 106(4), pp.412-418.

Campbell, Reecerry, Cain, Wasserman, Minorsky, & Jackson, 2008, Biologi Edisi Kedelapan Jilid 2, Jakarta, Penerbit Erlangga.

Clerc, 1998, Species Concepts In The Genus Usnea (Lichenized Ascomycetes), Lichenologist, 30(4-5), pp.321–340.

Del-Prado, R., Cubas, P. Lumbsch, H.T, Divakar, P.K, Blanco, O., De Paz, G.A., Molina, M.C., & Crespo, A, 2010, Genetic distances within and among species in monophyletic lineages of Parmeliaceae (Ascomycota) as a tool for taxon delimitation, Molecular Phylogenetic & Evolution, 56, pp.125-133.

Divakar, P.K., Crespo, A., Blanco, O., & Lumbsch, H.T, 2006, Phylogenetic Significance of Morphological Character in the Tropical Hypotrachyna clade of Parmelioid Lichens (Parmeliaceae, Ascomycota), Molecular Phylogenetic & Evolution, 40, pp.448-458.

Hawksworth, D.L, Krik, P.M., Sutton, B.C. & Pelger, D.N., 1995, Ainsworth & Bisby`s Dictionary of the Fungi, CAB International, Wallingford, Cambridge University Press.

Jannah, M. & Afifah, N. 2019a, Study of Kayu Angin (Usnea spp.) as a traditional medicine, Case Study: Traditional Markets in Jakarta, Teknosains, 14 (1), pp.61-67.

Jannah, M. & Rahayu, D.A., 2019b, DNA Barcode of Indonesian animals and plants, Yayasan Inspirasi Ide Berdaya Press, Jakarta.

Korabecna, 2007, The Variability in the Fungal Ribosomal DNA (ITS1, ITS2, and 5.8 S rRNA Gene): Its Biological Meaning and Application in Medical Mycology, Applied Microbiology, 48, pp.301.

Kelly, L.J, Hollingsworth, P.M., Coppins, B.J., Ellis, C.J., Harrold, P., Tosh, J., & Yahr, R., 2011, DNA Bacording of Lichenized Fungi Demonstrates High Identification Success in a Floristic Context, New Phytologist, 191, pp.288-300.

Ohmura, Y., 2002, Phylogenetic evaluation of infrageneric groups of the genus Usnea based on ITS regions in rDNA, Journal of Hattori Botanical Laboratory, 92, pp.231-243.

Ohmura, Y., 2012, A Synopsis of the Lichen Genus Usnea (Parmeliaceae, Ascomycota) in Taiwan, Memoirs of the National Museum of Nature and Science, 48, pp.91-137.

Sokal, PH.A. & Sneath, R.R, 1963, Numerical taxonomy: The Principle and Practice of Numerical Classification, Monografija, San Frasisco. USA.

Swinscow, T. D. V. & Krog, H., 1978, Pendulous species of Usnea in East Africa, Norwegian Journal of Botany, 25, pp.221–241.

White, T.J., Bruns, S.L., & Taylor,1990, Amplification and Direct Sequencing of Fungal Ribosomal RNA Genes For Phylogenetic, Academic press.Inc.

Zachariah, S.A & Varghese, S.K., 2018, The Lichen Symbiosis: A Review, International Journal of Scientific Research and Reviews, 7(3), pp.1160-1169.



DOI: https://doi.org/10.22146/jtbb.58635

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