Pistacia Türlerinin rbcL Kloroplast Gen Bölgesi ile Filogenetik Analizi

Öz

Pistacia cinsindeki beş türün filogenisi, plastid rbcL gen bölgesi kullanılarak değerlendirilmiştir. Yaprak dokusundan genomik DNA izole edilmiş ve rbcL gen bölgesi primeriyle PZR analizi ve DNA dizilemesi yapılmıştır. Elde edilen dizi verileri kullanılarak Pistacia türleri arasındaki filogenetik ilişkileri ortaya çıkarmak için filogenetik ve PCoA (Principle Component Analysis) analizleri gerçekleştirilmiştir. Filogenetik analiz sonucuna göre, P. vera, P. khinjuk ve P. atlantica arasında; P. palaestina ve P. terebinthus arasında dallarda daha yakın gruplaşma gözlenmiştir. PCoA sonuçları filogenetik analiz sonucunu desteklemiştir. Sonuç olarak, rbcL gen bölgesi tür bazlı gruplandırmada güçlü bulunmuştur. Kloroplast gen bölgesi dizi bilgisi, yerel fıstık gen havuzu üzerinde yürütülecek ıslah programları kapsamında hazırlanacak moleküler bir veri tabanı için güvenilirdir.

Anahtar Kelimeler

• Pistacia
• kloroplast geni
• rbcL
• filogeni

Phylogenetic Analysis of Pistacia Species with rbcL Chloroplast Gene Region

Öz

The phylogeny of five species in the genus Pistacia was assessed using the plastid rbcL gene region. Genomic DNA was isolated from leaf tissue and PCR analysis with primer of rbcL gene region and DNA sequencing were performed. Using obtained sequence data, phylogenetic and PCoA (Principle Component Analysis) analyses were performed for reveal the phylogenetic relationships among Pistacia species. According to the result of phylogenetic analysis, closer grouping in clades was observed between P. vera; P. khinjuk and P. atlantica; between P. palaestina and P. terebinthus. Result of PCoA analysis supported the result of phylogenetic analysis. As a result, rbcL gene region was found powerful at species-based grouping. Revealed sequence information of chloroplast gene region is reliable to elaborate a molecular database to conduct breeding programs on local pistachio gene pool.

Anahtar Kelimeler

• Pistacia
• chloroplast gene
• rbcL
• phylogeny

Kaynakça

1. [1] Catalan, L., Alvarez‐Ortí, M., Pardo‐Giménez, A., Gomez, R., Rabadan, A., and Pardo, J.E. (2017). Pistachio oil: A review on its chemical composition, extraction systems, and uses. European Journal of Lipid Science and Technology, 119(5), 1600126.
2. [2] Dar, A.A., Mudigunda, S., Mittal, P.K., and Arumugam, N. (2017). Comparative assessment of genetic diversity in Sesamum indicum L. using RAPD and SSR markers. 3 Biotech, 7, 1-12.
3. [3] Sharma, S., Pradhan, S., Khajuria, P., and Dar, A.A. (2017). Genetic diversity studies in cucumber (Cucumis sativus L.) using RAPD markers. Vegetable Science, 44(1), 34-37.
4. [4] Altıntaş, S., Toklu, F., Kafkas, S., Kilian, B., Brandolini, A., and Özkan, H. (2008). Estimating genetic diversity in durum and bread wheat cultivars from Turkey using AFLP and SAMPL markers. Plant breeding, 127(1), 9-14.
5. [5] Hormaza, J.I., Dollo, L., and Polito, V.S. (1994). Determination of relatedness and geographical movements of Pistacia vera (Pistachio; Anacardiaceae) germplasm by RAPD analysis. Economic Botany, 349-358.
6. [6] Parfitt, D.E., and Badenes, M.L. (1997). Phylogeny of the genus Pistacia as determined from analysis of the chloroplast genome. Proceedings of the National Academy of Sciences, 94(15), 7987-7992.
7. [7] Kafkas, S., and Perl-Treves, R. (2001). Morphological and molecular phylogeny of Pistacia species in Turkey. Theoretical and Applied Genetics, 102, 908-915.
8. [8] Yaltirik, F. (1967). Anacardiaceae. In: Flora of Turkey, P.H., Davis (ed.), Volume 2, Edinburgh University Press, Edinburgh, UK, p. 544–548. [9] Kafkas, S., and Perl-Treves, R. (2002). Interspecific relationships in Pistacia based on RAPD fingerprinting. HortScience, 37(1), 168-171.

9. [10] Werner, O., Sánchez-Gómez, P., Guerra, J., and Martı́nez, J.F. (2001). Identification of Pistacia× saportae Burnat (Anacardiaceae) by RAPD analysis and morphological characters. Scientia horticulturae, 91(1-2), 179-186.
10. [11] Katsiotis, A., Hagidimitriou, M., Drossou, A., Pontikis, C., and Loukas, M. (2003). Genetic relationships among species and cultivars of Pistacia using RAPDs and AFLPs. Euphytica, 132, 279-286.
11. [12] Golan-Goldhirsh, A., Barazani, O., Wang, Z.S., Khadka, D.K., Saunders, J.A., Kostiukovsky, V., and Rowland, L.J. (2004). Genetic relationships among Mediterranean Pistacia species evaluated by RAPD and AFLP markers. Plant Systematics and Evolution, 246, 9-18.
12. [13] Daniell, H., Lin, C. S., Yu, M., and Chang, W.J. (2016). Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome biology, 17, 1-29.
13. [14] Xing, G., Yu‐Ping, Z., Bao‐Cheng, W., Ya‐Mei, Z., Jian‐Qun, C., and Yue‐Yu, H. (2008). Phylogeny of Dioscorea sect. Stenophora based on chloroplast matK, rbcL and trnL-F sequences. Journal of Systematics and Evolution, 46(3), 315.
14. [15] Kress, W.J., Wurdack, K.J., Zimmer, E.A., Weigt, L.A., and Janzen, D.H. (2005). Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences, 102(23), 8369-8374.
15. [16] Li, F.W., Kuo, L.Y., Rothfels, C.J., Ebihara, A., Chiou, W.L., Windham, M.D., and Pryer, K.M. (2011). rbcL and matK earn two thumbs up as the core DNA barcode for ferns. PloS One, 6(10), e26597.
16. [17] Lahaye, R., Van der Bank, M., Bogarin, D., Warner, J., Pupulin, F., Gigot, G., Maurin, O., Duthoit, S., Barraclough, T.G., and Savolainen, V. (2008). DNA barcoding the floras of biodiversity hotspots. Proceedings of the National Academy of Sciences, 105(8), 2923-2928.
17. [18] Fazekas, A.J., Burgess, K.S., Kesanakurti, P.R., Graham, S.W., Newmaster, S.G., Husband, B.C., Percy, D.M., Hajibabaei, M., and Barrett, S.C. (2008). Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well. PloS One, 3(7), e2802.
18. [19] Hollingsworth, M.L., Andra Clark, A., Forrest, L.L., Richardson, J., Pennington, R.T., Long, D.G., Cowan, R., Chase, M.W., Gaudeul, M., and Hollingsworth, P.M. (2009). Selecting barcoding loci for plants: evaluation of seven candidate loci with species‐level sampling in three divergent groups of land plants. Molecular Ecology resources, 9(2), 439-457.
19. [20] Chen, S., Yao, H., Han, J., Liu, C., Song, J., Shi, L., Zhu, Y., Ma, X., Gao, T., Pang, X., Luo, K., Li, Y., Li, X., Jia, X., Lin, Y., and Leon, C. (2010). Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PloS One, 5(1), e8613.
20. [21] Doyle, J.J., and Doyle, J.L. (1987). A rapid DNA isolation procedure from small quantities of fresh leaf tissues. Phytochem. Bulletin. 19 (1): 11-15.
21. [22] Kafkas, S.K., Cetiner, G.D., Perl-Treves, R., and Nissim-Levi, A.N. (2001). Development of sex-associated RAPD markers in wild Pistacia species. The Journal of Horticultural Science and Biotechnology, 76(2), 242-246.
22. [23] Patterson, T.B., and Givnish, T.J. (2002). Phylogeny, concerted convergence, and phylogenetic niche conservatism in the core Liliales: insights from rbcL and ndhF sequence data. Evolution, 56(2), 233-252.
23. [24] Arabnezhad, H., Bahar, M., and Pour, A.T. (2011). Evaluation of genetic relationships among Iranian pistachios using microsatellite markers developed from Pistacia khinjuk Stocks. Scientia horticulturae, 128(3), 249-254.
24. [25] Talebi, M., Kazemi, M., and Sayed-Tabatabaei, B.E. (2012). Molecular diversity and phylogenetic relationships of Pistacia vera, Pistacia atlantica subsp. mutica and Pistacia khinjuk using SRAP markers. Biochemical Systematics and Ecology, 44, 179-185.
25. [26] Yi, T., Wen, J., Golan‐Goldhirsh, A., and Parfitt, D.E. (2008). Phylogenetics and reticulate evolution in Pistacia (Anacardiaceae). American Journal of Botany, 95(2), 241-251.
26. [27] Talebi, M., Akbari, M., Zamani, M., and Sayed-Tabatabaei, B.E. (2016). Molecular polymorphism in Pistacia vera L. using non-coding regions of chloroplast DNA. Journal of Genetic Engineering and Biotechnology, 14(1), 31-37.