PENGELOMPOKKAN SEPULUH VARIETAS TEMBAKAU (Nicotiana tabacum) BERDASARKAN KERAGAMAN RUNUTAN BASA PARSIAL GEN PMT(PUTRESCINE N-METHYLTRANSFERASE) Clustering of ten tobacco (Nicotiana tabacum) varieties based on the partial PMT (putrescine N-methyltranfera

Sesanti Basuki, Sudarsono Sudarsono

Abstract


PMT gene is the gene encoded putrescine N-methiltransferase which is related to nicotine biosinthesis in tobacco (Nicotiana  tabacum). Ten tobacco varieties with different nicotine level were used inthis study. The aims of this study were: (1) to analyze thepartial PMT gene sequence diversity among ten tobacco varieties, and (2) to evaluate the closed-relationship amongten tobacco varieties based on their partialPMT gene sequences diversity.Sequence diversity was analyzed by multiple sequence alignment between the partialPMT gene sequence of the ten tobacco varietiesand Ntpmt_Sindoro1 sequence deposited in the NCBI gene-bank database.The phylogenetic relationship amongthe sequences was inferred by genetic distancebetween pairs of sequences using the pairwise and multiple sequence alignment analysis. Analysis of the sequences showed that all varieties analyzed had varied in size and number of the PMT gene fragments yielded. The analysis also revealed that thepartialPMT gene sequencesarecoming from the same ancestor which related to nicotine biosynthesis in tobacco. Phylogenetic analysis separated the partialPMT gene sequences into two different branches significantly (bootstrap value = 100), and clustered together based on tobacco types with different nicotine level in whichcould be due to some baseschanged on the specific sites of thePMT gene sequences.  This information could be used to study the relationship between some bases changed on the specific sites of thePMT gene sequences and the nicotine content variation yielded by the ten tobacco varieties that is happened during evolution time.

Key words: Clustering analysis, PMT gene, nicotine, Nicotiana tabacum

 

Abstrak

Gen PMT adalah gen penyandi enzim putresina N-metiltransferase (PMT) yang berperan dalam lintasan biosintesis nikotin pada tanaman tembakau (Nicotiana tabacum). Sepuluh varietas tembakau yang memiliki perbedaan tingkat kadar nikotin diuji untuk mempelajari: (1) keragaman runutan basa parsial gen PMT dari masing-masing varietas, dan (2) kekerabatan antara sepuluh varietas tembakau yang diuji berdasarkan keragaman runutan basa parsial gen PMT. Keragaman runutan basa dianalisis dengan mensejajarkan data runutan basa dari sepuluh varietas tembakau yang diuji dengan runutan basa dari Ntpmt_Sindoro1 (JQ438825) yang telah tersimpan dalam database genbank NCBI. Hasil pensejajaran digunakan untuk menghitung matriks jarak, yang selanjutnya digunakan untuk menganalisis hubungan kekerabatan diantara sepuluh varietas tembakau. Hasil analisis memperlihatkan adanya variasi ukuran dan jumlah runutan basaparsial gen PMT asal sepuluh varietas tembakau yang dianalisis. Hasil analisis juga memperlihatkan bahwa runutan basa parsial gen PMT tersebut berasal/diturunkan dari sumber (ancestor) yang sama dan  terkait dengan biosintesis nikotin pada tembakau. Runutan basaparsial gen PMT dari sepuluh varietas yang dianalisis memisahkan antara kelompok tembakau introduksi (kadar nikotin rendah-sedang) dengan kelompok tembakau lokal (kadar nikotin sedang-tinggi). Dua kelompok memisah berdasarkan level kadar nikotin, danperbedaan/perubahan susunan basa pada situs-situs tertentu dari runutan basaparsial gen PMT  yang dianalisis. Informasi tentang mutasi yang terjadi pada situs-situs runutan basa dari parsial gen PMT dapat digunakan untuk mempelajari keterkaitan antara perubahan basa pada fragmen gen PMT dengan kandungan nikotin total tembakau yang terjadi selama proses evolusi.

Kata kunci: Analisis pengelompokkan, gen PMT,Nikotin, Nicotiana tabacum

 


Keywords


Phylogenetic analysis;PMT gene;Nicotine;Nicotiana tabacum

Full Text:

PDF

References


Basuki, S., Mattjik, N.A., Suwarso, Wirnas, D. & Sudarsono (2011) Isolasi fragmen gen penyandi putresin N-metil transferase dan quinolinat fosforibosiltransferaseasal tembakau lokal Temanggung (Nicotiana tabacum). Jurnal Littri. 17:109-117.

Basuki, S., Suwarso, Yulaikah, S. & Rochman, F. (2005). Status Plasma Nutfah Tanaman Tembakau (Nicotiana sp.) dalam: Buku Pedoman Pengelolaan Plasma Nutfah (editor: Luntungan, H.T., Karmawati, E., & Hartati, Rr.). Pusat Penelitian dan Pengembangan Perkebunan. Badan Penelitian dan Pengembangan Pertanian. Halaman: 183-200.

Bombarely, A., Rosli, H.G., Vrebalov, J., Moffett, P., Mueller, L. & Martin, G. (2012) A draft genome sequence of Nicotiana benthamiana to enhance molecular plant-microbe biology research. Molecular Plant-Microbe Interactions. 25:1523-1530.

Bowman, D., Corbin, T. & Tart, G. (1984) TOBACCO Measured Crop Performance. Res Rep (97). NC State Univ. 32 pps.

Champell, N.A., Reece, J.B., Taylor, M.A., Simon, E.J., Dickey, J.L. &Hogan, K. (2015) Biology eighth edition. Pearson Ed. Inc. USA. 780 pp.

Charlesworth, D., Charlesworth, B. & McVean, G.A.T. (2001) Genome sequences and evolutionary biology, a two-way interaction. Trends in Ecology & Evolution. 16: 235–242.

Chen, S., Matsubara, K., Omori, T., Kokubun, H., Kodama, H., Watanabe, H., Hashimoto, G., Marchesi, E., Bullrich, L. & Ando, T. (2007) Phylogenetic analysis of the genus Petunia (Solanaceae) based on the sequence of the Hf1 gene. Journal of Plant Research (Japan). 120:385-397.

Dekkers, J.C.M. & Hospital, F. (2002) The use of molecular genetics in the improvement of agricultural populations. Nat Rev Genet. 3:22–32.

Dewey, R.E. & Xie, J. (2013) Molecular genetics of alkaloid biosynthesis in Nicotiana tabacum. Phytochemistry. 94:10–27.

Edwards, D. & Batley, J. (2010) Plant genome sequencing: applications for crop improvement. Plant Biotechnology Journal. 8:2–9.

Hashimoto, T., Shoji, T., Mihara, T., Oguri, H., Tamaki, K., Suzuki, K.I. & Yamada, Y. (1998) Intraspecific variability of the tandem repeats in Nicotiana putrescine N-methyltransferases. Plant Molecular Biology. 37:25–37.

Hibi, N. (1994) Gene Expression in Tobacco Low-Nicotine Mutants. the Plant Cell Online. 6:723–735.

Kidd, S.K., Melillo, A.A., Lu, R., Reed, D.G., Uchida, K., Furuya, M. & Jelesko, J.G. (2006) The A and B loci in tobacco regulate a network of stress response genes, few of which are associated with nicotine biosynthesis. Plant Molecular Biology. 60:699–716.

Kumar, S., Tamura, K. & Nei, M. (2004) MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Briefings in Bioinformatics. 5:150–163.

Leffingwell, J.C. (1999) Leaf Chemistry Basic Chemical Constituents of Tobacco Leaf and Differences among Tobacco Types. Dalam: DAVIS D.L. and M.T. NIELSEN (ed.) Tobacco, Production, Chemistry, and Technology. Cambridge (GB) Univ. Pr. p. 265–284.

Legg, P.D. & Collins, G.B. (1971) Genetic Parameters in Burley Populations of Nicotianatabacum L. I. ‘Ky 10’ × ‘Burley 21’1. Crop Science. 11:365–367.

McGinnis, S. & Madden, T.L. (2004) BLAST: At the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Research. 32:20–25.

Moore, J.M. (2013) Tobacco Variety Information.http://www.caes.uga.edu/tobacco/2013.

SK. Menteri Pertanian. (2001) Pelepasan Varietas Unggul Tembakau Sindoro1. SK. Menteri Pertanian No.112/Kpts/TP240/2/2001. Hal. 3.

____________________. (2001a) Pelepasan Varietas Unggul Tembakau Kemloko1. SK. Menteri Pertanian No.113/Kpts/TP.240/2/2001. Hal. 3

____________________. (2005) Pelepasan Varietas Unggul Tembakau Kemloko 2. SK. Menteri Pertanian No.309/Kpts/SR.120/8/2005. Hal.3.

____________________.(2005a) Pelepasan Varietas Unggul Tembakau Kemloko 3. SK. Menteri Pertanian No.310/Kpts/SR.120/8/2005. Hal.3.

____________________. (2007) Pelepasan Varietas Unggul Tembakau Bligon1.SK. Menteri Pertanian No.127/Kpts/SR.120/2/2007.Hal.3.

____________________. (2007a) Pelepasan Varietas Unggul Tembakau Grompol Jatim1.SK. Menteri Pertanian No.131/Kpts/SR.120/2/2007. Hal.3.

Reed, D.G. & Jelesko, J.G. (2004) The A and B loci of Nicotiana tabacum have non-equivalent effects on the mRNA levels of four alkaloid biosynthetic genes. Plant Science. 167:1123–1130.

Robertson, K., Goldberg, E.E. & Igić, B. (2011) Comparative evidence for the correlated evolution of polyploidy and self-compatibility in solanaceae. Evolution. 65:139–155.

Rochman, F. (2013) Pengembangan varietas unggul tembakau temanggung tahan penyakit. Jurnal Litbang Pertanian. 32:30–38.

Saitou, N. & Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular biology and evolution. 4:406–425.

Saunders, J.W. & Bush, L.P. (1979) Nicotine biosynthetic enzyme activities in Nicotiana tabacum L. genotypes with different alkaloid levels. Plant Physiology. 64:236–240.

Tate, J.A., Acosta, M.C., McDill, J., Moscone, E.A., Simpson, B.B. & Cocucci, A.A. (2009) Phylogeny and Character Evolution in Nierembergia (Solanaceae): Molecular, Morphological, and Cytogenetic Evidence. Systematic Botany. 34:198–206.

Thompson, J.D., Higgins, D.G. & Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic acids research. 22: 4673–4680.

Vamdamme, A. (2009) Basic concepts of molecular evolution. Dalam: Lemey P., Salemi M., Vamdamme A.M. (ed.) The phylogenetic handbook. Cambridge (GB)Univ. Pr. p. 3-28.

Winz, R.A. & Baldwin, I.T. (2001) Molecular interactions between the specialist herbivore Manduca sexta (Lepidoptera, Sphingidae) and its natural host Nicotiana attenuata. I. Large-scale changes in the accumulation of growth- and defense-related plant mRNAs. Plant physiology. 125:683–700.

Wu, F. & Tanksley, S.D. (2010) Chromosomal evolution in the plant family Solanaceae.BMC Genomics. 11:182.




DOI: http://dx.doi.org/10.21082/littri.v23n1.2017.36-44

Refbacks

  • There are currently no refbacks.




Copyright (c) 2017 Jurnal Penelitian Tanaman Industri

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


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



P-ISSN: 0853-8212
E-ISSN: 2528-6870

Pusat Penelitian dan Pengembangan Perkebunan
Jln. Tentara Pelajar No 1, Kampus Penelitian Cimanggu
Bogor 16111 Indonesia
Phone: +62251-8313083
Fax: +62251-8336194
Email: littri_puslitbangbun@yahoo.co.id



View My Stats