MatK ve trnH-psbA Barkot Genleri Kullanılarak Bazı Bitki Taksonlarının Moleküler Olarak Sınıflandırılması

Yıl 2019, Cilt: 6 Sayı: 1, 87 - 93, 28.02.2019

Behcet İnal , Mehmet Karaca

https://doi.org/10.19159/tutad.488296

Cited By: 2

Öz

Canlıların sınıflandırılması ve canlı birliklerine
ait sınırların çizilmesi gözleme ve deneye dayalı sistemli bilgi üretmeye
başlanmasıyla birlikte karşılaşılan en karmaşık problemlerden biri olmuştur. Bu
amaçla araştırmacılar birçok kuram ve metot geliştirerek var olan canlı
çeşitliliğini saptamaya çalışmışlardır. Çekirdek kökenli barkot bölgeleri,
plastid kökenli barkot bölgelerine göre çok daha fazla bilgi içermesine karşın,
tek lokus kullanılarak barkotlama yapıldığında, farklı bitki gruplarını
karşılaştırabilmek için yeterli bilgiye sahip olunmamaktadır. Tüm bitki
türlerinde kullanılabilecek tek bir barkot bölgesi henüz mevcut değildir ve bu
nedenle farklı barkot bölgelerinin birlikte kullanılması, türlerin ayırt
edilebilme gücünü arttırabilmektedir. Çalışmanın ana hedefi, bitki moleküler
filogenetiğini konu alan çalışmalarda etkin olarak kullanılabilecek gen, gen
bölgesi ve gen sayısını değerlendirmektir. Bu çalışmada, 15 farklı bitki
ailesine ait toplam 60 bitki türüne ait filogenetik ilişkiyi değerlendirmek
için matK, ve trnH-psbA barkot genler
kullanılarak MAFFT (Multiple Alignment Using Fast Fourier Transform) yazılımı
ile diziler hizalanmış ve Bayesian metodu ile konsensus filogenetik ağaç elde
edilmiştir. Sonuçlar bitki moleküler filogenetik çalışmalarında matK gen dizilerinin trnH-psbA
gen dizilerine göre daha yüksek ardıl olasılık değerli ağaç üretebildiğini
göstermiştir. Ancak daha fazla genlerin çalışması ile olası filogenetik ilişki
daha da iyi bir şekilde tahmin edilebilir.

Anahtar Kelimeler

Filogeni, moleküler sistematik, biyoinformatik, barkot gen

Molecular Classification of Some Plant Taxa Using MatK and trnH-psbA Barcode Genes

Öz

The classification of living creatures and the
demarcation of living units have been one of the most complex problems
encountered as a result of observing experimental and systematic information.
For this purpose, researchers have tried to determine the diversity of living
creatures by developing many theories and methods. Although the nuclear genome
barcode regions contain much more information than the barcode regions of
plastid, they do not have enough information to compare different plant groups
when barcoding with a single locus. A single barcode region that can be used in
all plant species is not yet available, and therefore, the use of different
barcode regions may increase the distinguishing power of species. Main
objective of this study was to determine gene, gene region and numbers of genes
suitable for plant molecular phylogentic studies. In
this study, matK, and trnH-psbA
barcode genes were used to evaluate the phylogenetic relationship of 60 plant
species belonging to 15 different plant families. Sequences were aligned with
MAFFT (Multiple Alignment Using Fast Fourier Transform) software and a
consensus phylogenetic tree was constructed by the Bayesian method. Results
indicated that matK gene was
much more suitaable in comparison to trnH-psbA region since the use of matK produced trees with higher posterior
probability values. However, further studies clearly showed that increased
number of genes produced much better phylogenetic estimations.

Anahtar Kelimeler

Phylogeny, molecular systematics, bioinformatics, barcode gene

Kaynakça

• Allan, G.J., Francisco-Ortega, J., Santos-Guerra, A., Boerner, E., Zimmer, E.A., 2004. Molecular phylogenetic evidence for the geographic origin and classification of canary ısland lotus (Fabaceae: Loteae). Molecular Phylogenetics and Evolution, 32(1): 123-138.
• Cohen, B.L., Weydmann, A., 2005. Molecular evidence that phoronids are a subtaxon of brachiopods (brachiopoda: phoronata) and that genetic divergence of metazoan phyla began long before the early cambrian. Organisms Diversity & Evolution, 5(4): 253-273.
• Ford, C., Ayres, K., Toomey, N., Haider, N., Stahl, J., Kelly, L., Wikstrom, N., Hollingsworth, P., Duff, R., Hoot, S., Cowan, R., Chase, M., Wilkinson, M., 2009. Selection of candidate coding DNA barcoding regions for use on land plants. Botanical Journal of the Linnean Society, 159(1): 1-11.
• Graham, S.W., Olmstead, R.G., 2000. Utility of 17 Chloroplast genes for ınferring the phylogeny of the basal angiosperms. American journal of Botany, 87(11): 1712-1730.
• Hilu, K.W., Liang, H., 1997. The matK gene: sequence variation and application in plant systematics. American Journal of Botany, 84(6): 830-839.
• Hochbach, A., Linder, H.P., Röser, M., 2018. Nuclear genes, matK and the phylogeny of the Poales. Taxon, 67(3): 521-536.
• Hollingsworth, P.M., Graham, S.W., Little, D.P., 2011. Choosing and using a plant DNA barcode. PLoS ONE, 6(5): e19254.
• İnal, B., Aydın, A., İnce, A.G., Karaca, M., 2017. Genetic relationships among continental cotton species based on ITS1 gene region aligned with different alignment tools. Journal of Molecular Biology and Biotechnology, 1(2): 1-6.
• Johnson, L.A.N., Soltis, D.E., 1994. matK DNA sequences andphylogenetic reconstruction in Saxifragaceae s. str. Sysematic Botany, 19(1): 143-156.
• Kress, W.J., Erickson, D.L., 2007. A two-locus global DNA barcode for land plants: the coding rbcL gene gomplements the non-coding trnH-psbA spacer region. PLoS One, 2(6): e508.
• Lahaye, R., Bank, M.V.D., Bogarin, D., Warner, J., Pupulin, F., Gigot, G., Maurin, O., Duthoit, S., Barraclough, T.G., Savolainen, V., 2007. DNA barcoding the floras of biodiversity hotspots. Pnas, 105(8): 2923-2928.
• Lahaye, R., Van Der Bank, M., Bogarin, D., Warner, J., Pupulin, F., Gigot, G., Savolainen, V., 2008. DNA barcoding the floras of biodiversity hotspots. Proceedings of the National Academy of Sciences, 105(8): 2923-2928.
• Lei, Y.X., Liu, J., Fan, X., Sha, L.N., Wang, Y., Kang, H.Y., Zhang, H.Q., 2018. Phylogeny and maternal donor of Roegneria and its affinitive genera (Poaceae: Triticeae) based on sequence data for two chloroplast DNA regions (ndhF and trnH–psbA), Journal of Systematics and Evolution, 56(2): 105-119.
• Li, X., Yang, Y., Henry, R.J., Rossetto, M., Wang, Y., Chen, S., 2015. Plant DNA barcoding: from gene to genome. Biological Reviews, 90(1): 157-166.
• Phong, D.T., Hien, V.T.T., Lieu, T.T., 2018. Nucleotıde diversity of 15 conifer species in vietnam’s central highlands based on the analysis of ITS, trnH-psbA, matK, trnL and rpoC1 gene regions. Vietnam Journal of Science and Technology, 56(1): 47-63.
• Piredda, R., Simeone, M.C., Attimonelli, M., Bellarosa, R., Schirone, B., 2010. Prospects of barcoding the Italian wild dendroflora: oaks reveal severe limitations to tracking species identity. Molecular Ecology Resources, 11(1): 72-83.
• Qui, Y.L., Lee, J.H., Bernasconi-Quadroni, F., Soltis, D.E., Soltis, P.S., Zanis, M., Zimmer, E.A., Chen, Z.D., Savolainen, V., Chase, M.W., 1999. The earliest angiosperms,evidence from mitochondrial, plastid and nuclear genoms. Nature, 402: 404-407.
• Ren, B.Q., Xiang, X.G., Chen, Z.D., 2010. Species identification of Alnus (Betulaceae) using nrDNA and cpDNA genetic markers. Molecular Ecology Resources, 10(4): 594-605.
• Ro, K.E., Keener, C.S., Mcpheron, B.A., 1997. Molecular phylogenetic study of the Ranunculaceae: Utility of the nuclear 26s ribosomal DNA in inferring intrafamilial relationships. Molecular Phylogenetics and Evolution, 8(2): 117-127.
• Ronquist, F., Huelsenbeck, J., 2003. Mrbayes 3: bayesian phylogenetic inference under mixed models. Bioinformatics, 19(12): 1572-1574.
• Von Crautlein, M., Korpelainen, H., Pietilainen, M., Rikkinen, J., 2011. DNA barcoding: a tool for improved taxon identification and detection of species diversity. Biodiversity and Conservation, 20(2): 373-389.
• Wen, J., Vanek-Krebitz, M., Hoffmann-Sommergruber, K., Scheiner, O., Breiteneder, H., 1997. The potential of betv1homologues, a nuclear multigene family, as phylogenetic markers in flowering plants. Molecular Phylogenetics and Evolution, 8(3): 317-333.
• Yang, Z., Zhao, T., Ma, Q., Liang, L., Wang, G., 2018. Comparative genomics and phylogenetic analysis revealed the chloroplast genome variation and ınterspecific relationships of corylus (Betulaceae) species. Frontiers in Plant Science, 9: 927.
• Yokoyama, J., Suzuki, M., Iwatsuki, K.,, Hasebe, M., 2000. Molecular phylogeny of Coriaria, with special emphasis on the disjunct distribution. Molecular Phylogenetics and Evolution, 14(1): 11-19.