Filogenetik Jenis-jenis Annonaceae dari Jawa Timur Koleksi Kebun Raya Purwodadi Berdasarkan Coding dan Non-coding sekuen DNA

https://doi.org/10.22146/jtbb.28308

Dewi Ayu Lestari(1*), Rodiyati Azrianingsih(2), H. Hendrian(3)

(1) Purwodadi Botanic Garden, Indonesian Institute of Sciences, Malang
(2) Department of Biology, Faculty of Mathematics and Natural Sciences, Brawijaya University, Malang
(3) Purwodadi Botanic Garden, Indonesian Institute of Sciences, Malang
(*) Corresponding Author

Abstract


Annonaceae species of Purwodadi Botanic Garden collections from East Java encountered problems in species identification based on morphological characters. In addition, the unavailability of molecular data to support identification based on morphological characters hinders accurate identification of species. The aim of this research is to discern phylogenetic of Annonaceae species from East Java collections of Purwodadi Botanic Garden based on coding and non-coding sequence DNA. Annonaceae species used in this study are 30 species, includes outgroup from family of Magnoliaceae. Materials for DNA analysis were young leaves which were processed through DNA extraction, DNA amplification through PCR technique, DNA sequencing and data analysis with Maximum Likelihood (ML), Maximum Parsimony (MP) and Neighbour-Joining (NJ) method analysis. The results show that phylogenetic tree is divided into two subfamilies, i.e. Annonoideae and Malmeoideae. The topology of phylogenetic tree from three DNA molecular marker shows that non-coding sequence DNA (trnL-F molecular marker) has the best grouping of relationship and be able to explain the relationship between species of Annonaceae than rbcL and matK molecular marker as coding sequence DNA. Bootstrap value of trnL-F tree is very weak to high (36-100%) while rbcL is very weak to weak (17-63%) and matK tree is high (98-99%).


Keywords


Annonaceae, coding DNA, non-coding DNA, phylogenetic

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References

Barthet, M.M. & Hilu, K.W., 2007, Expression of matK: functional and evolutionary implications, American Journal of Botany 94(8), 1402-1412.

Bioversity International, 2008, Descriptors for cherimoya (Annona cherimola Mill.), Rome, Italy.

Chaowasku, T. & Keβler, P.J.A., 2013, Phylogeny of Miliusa (Magnoliales: Annonaceae: Malmeoideae: Miliuseae), with descriptions of two new species from Malesia, European Journal of Taxonomy 54, 1-21.

Chatrou, L.W., Pirie, M.D., van Velzen, R. & Bakker, F.T., 2014, Annonaceae substitution rates – a codon model perspective, Fevereiro 36, 108-117.

Chatrou, L.W., Pirie, M.D., Erkens, R.H.J., Couvreur, T.L.P., Neubig, K.M., Abbott, R.J., Mols, J.B., Maas, J.W., Saunders, R.M.K. & Chase, M.W., 2012, A new subfamily and tribal classification of the pantropical flowering plant family Annonaceae informed by molecular phylogenetics, Botanical Journal of Linnean Society 169, 5-40.

Chen, C.W., Huang, Y.M., Kuo, L.Y., Nguyen, Q.D., Luu, H.T., Callado, J.R., Farrar, D.R. & Chiou, W.L., 2013, trnL-F is a powerful marker for DNA identification of field vittarioid gametophytes (Pteridaceae), Annals of Botany, 1-11. doi:10.1093/aob/mct004.

Couvreur, T.L.P., Richardson, J.E., Sosef, M.S.M., Erkens, R.H.J. & Chatrou, L.W., 2008, Evolution syncarpy and other morphological characters in African Annonaceae: a posterior mapping approach, Molecular Phylogenetics and Evolution 47, 302-318.

Erkens, R.H.J., Chatrou, L.W., Maas J.W. & Pirie M.D., 2007, Phylogenetic relationships, saturation and marker-use in the Long Branch Clade of Annonaceae, PhD Thesis, pp 25-41.

Fatchiyah, Arumingtyas, E.L., Widyarti, S., & Rahayu, S., 2011, Biologi Molekuler: Prinsip Dasar Analisis, PT Erlangga, Jakarta.

Folorunso, A.E. & Olorode, O., 2008, Biosystematic studies in Annonaceae II. Vegetative and floral morphological studies of some marga of Annonaceae in Nigeria, Research Journal of Botany 3, 1-8.

Hidayat, T. & Pancoro, A., 2008, Kajian filogenetika molekuler dan peranannya dalam menyediakan informasi dasar untuk meningkatkan kualitas sumber genetik anggrek, Jurnal AgroBiogen 4(1), 35-40.

Hoggard, G.D., Kores, P.J., Molvray, M. & Hoggard, R.K., 2004, The phylogeny of Gaura (Onagraceae) based on ITS, ETS, and trnL-F sequence data, American Journal of Botany 91(1), 139-148.

Hollingsworth, P.M., Graham S.W. & Little, D.P., 2011, Choosing and using a plant DNA barcode, PLOS, https://doi.org/10.1371/journal.pone.0019254.

Kessler P.J.A., 1993, Annonaceae, Translated Kubitzki K, Rohwer JG, Bittrich V, eds. The sukues and marga of vascular plants, Volume 2, Springer-Verlag, Berlin.

Kress, W.J., Prince, L.M. & Williams, K.J., 2002, The phylogeny and a new classification of the gingers (Zingiberaceae): evidence from molecular data, Ann. J. Bot. 89, 1682-1696.

Lestarini, W., Matrani, Sulasmi, Trimanto, Fauziah, Laksono, R.A., Damaiyani, J. & Fiqa, A.P., 2012, An alphabetical list of plant species cultivated in Purwodadi Botanic Garden, Purwodadi Botanic Garden, Indonesian Institute of Sciences.

Ohsako, T. & Ohnishi O., 2001, Nucleotide sequence variation of the chloroplast trnK/matK region in two wild Fagopyrum (Polygonaceae) species, Fagopyrum leptopodum and Fagopyrum statice, Genes Genetics and Systematics 76, 39-46.

Ortiz-Rodriguez, A.E., Escobar-Castellanos, M.A. & Pérez-Farrera, M.A., 2016, Phylogenetic analyses and morphological characteristics support the description of a second species of Tridimeris (Annonaceae), PhytoKeys 74, 79-96. https://doi.org/10.3897/phytokeys.74.10371.

Patwardhan, A., Ray, S. & Roy, A., 2014, Molecular markers in phylogenetic studies – A review, Phylogenetics and Evolutionary Biology 2(2), 1-9. doi:10.4172/2329-9002.1000131.

Pirie, M.D., Vargas, M.P.B., Botermans, M., Bakker, F.T. & Chatrou, L.W., 2007, Ancient paralogy in the cpDNA trnL-F region in Annonaceae: implications for plant molecular systematics, American Journal of Botany 94(6), 1003-1016.

Pirie, M.D. & Doyle, J.A., 2012, Dating clades with fossils and molecules: the case of Annonaceae, Botanical Journal of the Linnean Society 169, 84-116.

Priyanti, 2001, A floristic study of the Annonaceaein the Bearu District, East Kalimantan, Indonesia, Thesis, Post Graduate Programme of Biology, Bogor Agricultural University, Bogor.

Rahayu, D.A. & Nugroho, E.D., 2015, Biologi molekuler dalam perspektif konservasi, Plantaxia, Yogyakarta.

Rasnovi, S., 2004, Species concepts: why phenetic or phylogenetic?, Floribunda 2(5), 138-143.

Richardson, J.E., Chatrou, L.W., Mols, J.B., Erkens, R.H.J. & Pirie, M.D., 2004, Historical biogeography of two cosmopolitan families of flowering plants: Annonaceae and Rhamnaceae, Philosophical Transactions of The Royal Society B: Biological Sciences 359(1450), 1495-1508. DOI: 10.1098/rstb.2004.1537.

Su, Y.C.F., Smith, G.J.D. & Saunders, R.M.K., 2008, Phylogeny of the basal angiosperm genus Pseuduvaria (Annonaceae) inferred from five chloroplast DNA regions, with interpretation of morphological character evolution, Molecular Phylogenetics and Evolution 48, 188-206.

Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. & Kumar, S., 2011, MEGA 5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance and maximum parsimony methods, Molecular Biology and Evolution 28(10), 2731-2739.

Tang, C.C., Thomas, D.C. & Saunders, R.M.K., 2015a, Molecular phylogenetics of the species-rich angiosperm genus Goniothalamus (Annonaceae) inferred from nine chloroplast DNA regions: synapomorphies and putative correlated evolutionary changes in fruit and seed morphology, Molecular Phylogenetics and Evolution 92, 124-139.

Tang, C.C., Thomas, D.C. & Saunders, R.M.K., 2015b, Molecular and morphological data supporting phylogenetic reconstruction of the genus Goniothalamus (Annonaceae), including a reassesment of previous infrageneric classifications, Data in Brief 4, 410-421.

Van Heusden, 1992, Flowers of Annonaceae: morphology, classification and evolution, BLUMEA Supplement 7, 1-218.

Wattoo, J.I., Saleem, M.Z., Shahzad, M.S., Arif, A., Hameed, A. & Saleem, M.A., 2016, DNA barcoding: amplification and sequence analysis of rbcL and matK genome regions in three divergent plant species, Advancements in Life Sciences 4(1), 3-7.

Young, N.D. & de Pamphilis, C.W., 2000, Purifying selection detected in plastid gene matK and flanking ribozyme regions within a group II intron of nonphotosynthetic plants, Molecular Biology and Evolution 17(12), 1933-1941.

Zhou, L., Su, Y.C.F. & Saunders, R.M.K., 2009, Molecular phylogenetic support for a broader delimitation of Uvaria (Annonaceae), inclusive of Anomianthus, Cyathostemma, Ellipeia, Ellipeiopsis and Rauwenhoffia, Systematics and Biodiversity 7(3), 249-258.

Zhou, L., Su, Y.C.F., Chalermglin, P. & Saunders, R.M.K., 2010, Molecular phylogenetics of Uvaria (Annonaceae): relationships with Balonga, Dasoclema and Australian species of Melodorum, Botanical Journal of the Linnean Society 163, 33-43.



DOI: https://doi.org/10.22146/jtbb.28308

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