Evaluation of Phylogenetic Relationships by Using psbA-trnH IGS Region of Chloroplast DNA in the Species of the Genus Quercus L.

Year 2020, Volume: 8 Issue: 1, 1185 - 1192, 31.01.2020

Aykut Yılmaz

https://doi.org/10.29130/dubited.637842

Abstract

The psbA-trnH IGS region belonging to chloroplast genome is one of the regions which most frequently used in plants for barcoding because of it’s nucleotide sequence differences. For this purpose, this region was chosen in this study in order to contribute to the solution of taxonomic problems in oaks and to evaluate phylogenetic relationships between species. Firstly, the sequence information of the psbA-trnH IGS region was obtained from NCBI for analysis. Then, these sequences were aligned and analysis for variable sites such as substitution from one base to another base, transition / transversion ratios, and base frequencies were performed using the MEGA X program. Finally, Neighbor-joining dendrogram was prepared and analyzed in order to evaluate the phylogenetic relationships between the species. Although this region has sufficient variation for sectional separation of oak species, sequence variations were found to be insufficient in species separation and identification. As a result of the study, it is suggested that the psbA-trnH IGS sequence alone is insufficient for barcoding in oaks, however it will be beneficial to use it with different barcoding regions together.

Keywords

psbA-trnH IGS, NCBI, MEGA X, Transition/transversion, Neighbor-joining dendrogram, Barcoding

Quercus L. Cinsine Ait Türlerde Kloroplast DNA’ya Ait psbA-trnH IGS Bölgesinin Kullanılarak Filogenetik İlişkilerin Değerlendirilmesi

Abstract

Kloroplast genoma ait psbA-trnH IGS bölgesi, en fazla nükleotid dizi farklılığı içeren bölgelerden biri olmasından dolayı barkodlama amacı ile bitkilerde sıklıkla kullanılan bölgelerden biridir. Bu amaçla meşelerde var olan taksonomik problemlerin çözümüne katkı sağlamak ve türler arasındaki filogenetik ilişkileri değerlendirmek adına bu bölge bu çalışmada tercih edilmiştir. İlk olarak psbA-trnH IGS bölgesine ait sekans bilgisi analizler için NCBI’den sağlanılmıştır. Daha sonra bu sekanslar hizalandırılmış ve varyasyon gösteren bölgeler için bir bazın diğerine değişim oranları, transisyon/transversiyon oranları, baz frekansları gibi analizler MEGA X programı kullanılarak yapılmıştır. Son olarak, türlerin birbirleri ile olan filogenetik ilişkilerini değerlendirmek adına Neighbor-joining dendrogram hazırlanmış ve analiz edilmiştir. Bu bölgenin meşe türlerinin seksiyonel ayrımı için yeterli varyasyona sahip olmasına karşın, tür ayrımında ve tanımlamasında sekans varyasyonlarının yetersiz kaldığı görülmüştür. Çalışmanın sonucu olarak psbA-trnH IGS sekansının meşelerde barkodlama amacı ile tek başına yetersiz olduğu, bununla birlikte farklı barkodlama bölgeleri ile kullanımının fayda sağlayacağı önerilmektedir.

Keywords

psbA-trnH IGS, NCBI, MEGA X, Transisyon/transversiyon, Neighbor-joining dendrogram, Barkodlama

References

• [1] R. Govaerts and D. G. Frodin, “World checklist and bibliography of Fagales (Betulaceae, Corylaceae, Fagaceae and Ticodenraceae,)” Royal Botanic Garden, Great Britain: Kew, 1998.
• [2] A. Maryam, R. Fatima and S. Abbas, “Genetic variation among Iranian oaks (Quercus ssp.) using random amplified polymorphic DNA (RAPD) markers,” Afr. J. Biotechnol., vol. 11, no. 45, pp. 10291–10296, 2012.
• [3] A. Yılmaz, “Cytotaxonomic study of Quercus L. species from section Quercus in Turkey,” Caryologia, vol. 70, no. 2, pp. 141–146, 2017.
• [4] A. Borazan and M. T. Babaç, “Morphometric leaf variation in oaks (Quercus) of Bolu, Turkey,” Annales Botanici Fennici, vol. 40, pp. 233–242, 2003.
• [5] A. Gonzalez-Rodrıguez, D. M. Arıas, S. Valencıa and K. Oyama, “Morphological and RAPD analysis of hybridization between Quercus affinis and Q. laurina (Fagaceae), two Mexican red oaks,” Am. J. Bot., vol. 91, pp. 401–409, 2004.
• [6] F. Tılkı and C. U. Alptekın, “Variation in acorn characteristics in three provenances of Quercus aucheri Jaub. Et Spach and provenance, temperature and storage effects on acorn germination,” Seed Sci. Technol., vol. 33, pp. 441–447, 2005.
• [7] A. Boratynskı, K. Marcysıak, A. Lewandowska, A. Jasınska, G. Iszkulo and J. Burczyk, “Differences in leaf morphology between Quercus petraea and Q. robur adult and young individuals, ” Silva Fenn., vol. 42, pp. 115–124, 2008.
• [8] A. Yılmaz, E. Uslu and M. T. Babaç, “Morphological variability of evergreen oaks (Quercus) in Turkey,” Bangladesh Journal of Plant Taxonomy, vol. 24, no. 1, pp. 39–47, 2017.
• [9] J. Franjic, Z. Liber, Z. Skvorc, M. Idzojtic, R. Sostaric and Z. Stancic, “Morphological and molecular differentiation of the Croation populations of Quercus pubescens (Fagaceae),” Acta Soc. Bot. Pol., vol. 75, pp. 123–130, 2006.
• [10] Z. Faltusova, L. Kucera and J. Ovesna, “Genetic diversity of Brassica oleracea var. capitata gene bank accessions assessed by AFLP,” Electron. J. Biotechnol., vol. 14, no. 4, 2011.
• [11] R. Pıredda, M. C. Sımeone, M. Attımonellı, R. Bellarosa and B. Schırone, “Prospects of barcoding the Italian wild dendroflora: oaks reveal severe limitations to tracking species identity,” Molecular Ecology Resources, vol. 11, pp. 72–83, 2011.
• [12] J. Yang, L. Vazquez, X. Chen, H. Li, H. Zhang, Z. Liu and G. Zhao, “Development of Chloroplast and Nuclear DNA Markers for Chinese Oaks (Quercus Subgenus Quercus) and Assessment of Their Utility as DNA Barcodes,” Frontiers in Plant Science, vol. 8, pp. 816, 2017.
• [13] D. Selvaraj, R. K. Sarma and R. Sathishkumar, “Phylogenetic analysis of chloroplast matK gene from Zingiberaceae for plant DNA barcoding,” Bioinformation, vol. 3, no. 1, pp. 24–27, 2008.
• [14] E. Filiz ve İ. Koç, “Bitkilerde DNA barkotları,” Afyon Kocatepe Üniversitesi Fen Bilimleri Dergisi, c. 12, ss. 53–57, 2012.
• [15] K. Hürkan, “Karasal bitkilerde DNA barkodlama: Bazı DNA barkod bölgelerinin incelenmesi,” The International Journal of Innovative Approaches in Science Research, c. 1, s. 1, ss. 57–67, 2017.
• [16] W. J. Kress and D. L. Erickson, “A two-locus global DNA barcode for land plants: The coding rbcL gene complements the non-coding trnH-psbA spacer region,” PLoS ONE, vol. 2, no. 6, pp. 508, 2007.
• [17] CBOL Plant Working Group, “Plant barcode protocol matK and rbcL, ” pp. 599, 2009.
• [18] F. Yaltirik, Türkiye meşeleri teşhis kılavuzu, İstanbul, Türkiye: Yenilik Basımevi, 1984.
• [19] NCBI. (2019, September 24). GenBank Overview [Online]. Available: www.ncbi.nlm.nih.gov/genbank.
• [20] R. Piredda, INSDC. DAF, University of Tuscia,Via C. De Lellis, 01100, ITALY, 2011
• [21] J. Shaw, E. B. Lickey, E. E. Schilling and R. L. Small, “Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: The tortoise and the hare III,” American Journal of Botany, vol. 94, no. 3, pp. 275–288, 2007.
• [22] C. C. Chang, H. C. Lin, I. P. Lin, T. Y. Chow, H. H Chen, W. H. Chen and S. M. Chaw, “The chloroplast genome of Phalaenopsisaphrodite (Orchidaceae): Comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications,” Molecular Biology and Evolution, vol. 23, no. 2, pp. 279–291, 2006.
• [23] M. W. Chase, R. S. Cowan, P. M. Hollingsworth, C. Van Den Berg, S. Madriñán, G. Petersen et al., “A proposal for a standardised protocol to barcode all land plants,” Taxon, vol. 56, no. 2, pp. 295–299, 2007.
• [24] N. Saitou and M. Nei, “The neighbor-joining method: A new method for reconstructing phylogenetic trees,” Molecular Biology and Evolution, vol. 4, pp. 406–425, 1987.
• [25] T. Borsch and D. Quandt, “Mutational Dynamics and phylogenetic utility of noncoding chloroplast DNA,” Plant Systematics and Evolution, vol. 282, pp. 169–199, 2009.