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Bazı Önemli Bitki Türlerinin Kloroplast matK Geni Filogenisi

Year 2005, Volume: 18 Issue: 2, 157 - 162, 01.09.2005

Abstract

Bu çalışmada, genomda bulunan genlerin çoğundan daha fazla varyasyon gösteren ve kloroplasta bulunan matK geninin moleküler filogeni çalışmalarında kullanımı araştırılmıştır. Çalışma da kloroplast matK geni DNA sekansları kullanılarak 26 farklı familyaya ait 142 bitki türünde, takım, familya, cins ve türler arasındaki evrimsel ilişkilerin belirlenebilmesi amaçlanmıştır. Cins ya da türler arasındaki genetik akrabalıkların belirlenmesi modern ve geleneksel ıslah metodları kullanılarak gerçekleştirilecek genetik ilerlemeler için çok önemlidir. 730-1545 nükleotid dizilimli kloroplast matK geni sekansı Gen Bankası’ndan alınmış ve Clustal W programı kullanılarak bu DNA sekanslarının sekansta bulanan baz içerikleri sıralanmıştır. “PAUP*” programı kullanılarak “Maksimum parsimony” metoduyla filogenetik ilişkiler belirlenmiştir. Parsimony analizinden elde edilen filogeni sonuçları daha önceden yapılmış olan tekli ve çoklu gen analizleri sonuçlarıyla benzerlik gösterdiği gibi elde edilen sonuçlar önemli türlerin akrabalıklarını belirlemede de daha iyi sonuçlar vermiştir. Analiz sonuçları açık tohumlu bitki türlerinin (Pinus thunbergii, Pinus attenuata and Ginko biloba) monokotiledonlar ve dikotiledonlardan oluşan kapalı tohumlu bitki türlerinden oldukça farklı olduğunu göstermiştir. Ayrıca C4 metabolizmasına sahip bitkilerden Cynodon dactylon, Panicum capilare, Zea mays ve Saccharum officiarum’un ortak atadan gelmelerine karşın C3 metabolizmasına sahip Triticum, Avena, Hordeum, Oryza ve Phalaris bitkilerinde farklı ya da benzer atadan yayıldıkları tespit edilmiştir. Bu çalışmada ayrıca Fabaceae (Fabales), Rosaceae (Rosales), Moraceae (Uriticales), Cannabeceae (Uriticales) and Uriticaceae (Uriticales). Malvaceae (Malvales) ve Brassicaceae (Brassicales) arasındaki veya içerisindeki ilişkiler tartışılmıştır. Genel olarak alınan sonuçlar matK gen sekansı Tek Dizi Polimorfizmi (TDP) çalışmalarında, veya Polimeraz Zincir Reaksiyonu, (PZR) analizleriyle familya, cins ve türlerin kendi içlerinde ve türler arasındaki ilişkileri en iyi şekilde belirlenmesini sağlayabileceği gibi bitki sistematiğinde de başarıyla kullanılabileceğini göstermiştir

References

  • Brochmann, C., Xiang, Q. Y., Brunsfeld, S. J., Soltis, D. E. and Soltis, P. S. 1998. Molecular evidence for polyploidy origins in Saxifraga (Saxifragaceae): the narrow arctic endemic S. svalbardensis and its widespread allies. Amer. J. Botany, 85: 135–143.
  • Crayn, D. M., Winter, K. and Smith, J. A. C. 2004. Multiple origins of crassulacean acid metabolism and the epiphytic habit in the Neotropical family Bromeliaceae. PNAS, 101: 3703–3708.
  • Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39: 783–791.
  • Fuse, S. and Tamura, M. N. 2000. A phylogenetic analysis of the plastid matK gene with emphasis on Melanthiaceae sensu lato. Plant Biol., 2: 415–427.
  • Ito, M., Kawamoto, A., Kita, Y., Yukawa, T. and Kurita, S. 1999. Phylogenetic relationships of Amaryllidaceae based on matK sequence data. J. Plant Res., 112: 207–216.
  • Kilel, B. 2004. Comparative analysis and relationships of six important crop species chloroplast genomes using whole genome web-based informatics tools. Afr. Biotech., 3: 210-214.
  • Koch, M., Haubold, B. and Mitchell-Olds, T. 2001. Molecular Systematics of the Brassicaceae: Evidence from coding plastidic matK and nuclear chs sequences. Amer. J. Botany, 88: 534–544.
  • Mort, M. E., Soltis, D. E., Soltis, P. S., Francisco- Ortega, J. and Santos-Guerra, A. 2001. Phylogenetic relationships and evolution of Crassulaceae inferred from matK sequence data. Amer. J. Botany, 88: 76–91.
  • Steele, K. P. and Vilgalys, R. 1994. Phylogenetic analysis of Polemoniaceae using nucleotide sequences of the plastid gene matK. Systematic Botany, 19: 126–142.
  • Swofford, D. L. 2002. PAUP*: Phylogenetic analysis using parsimony (*and other methods), version 4.0b10. Sinauer, Sunderland.
  • Tamura, M. N., Yamashita, J., Fuse, S. and Haraguchi, M. 2004. Molecular phylogeny of monocotyledons inferred from combined analysis of plastid matK and rbcL gene sequences. Journal of Plant Research, 117: 109–120.
  • Thompson, J. D., Higgins, D. G. and 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.

CHLOROPLAST matK GENE PHYLOGENY OF SOME IMPORTANT SPECIES OF PLANTS

Year 2005, Volume: 18 Issue: 2, 157 - 162, 01.09.2005

Abstract

In this study using the chloroplast matK DNA sequence, a chloroplast-encoded locus that has been shown to be much more variable than many other genes, from one hundred and forty two plant species belong to the families of 26 plants we conducted a study to contribute to the understanding of major evolutionary relationships among the studied plant orders, families genus and species (clades) and discussed the utilization of matK for molecular phylogeny. Determined genetic relationship between the species or genera is very valuable for genetic improvement studies. The chloroplast matK gene sequences ranging from 730 to 1545 nucleotides were downloaded from the GenBank database. These DNA sequences were aligned using Clustal W program. We employed the maximum parsimony method for phylogenetic reconstruction using PAUP* program. Trees resulting from the parsimony analyses were similar to those generated earlier using single or multiple gene analyses, but our analyses resulted in strict consensus tree providing much better resolution of relationships among major clades. We found that gymnosperms (Pinus thunbergii, Pinus attenuata and Ginko biloba) were different from the monocotyledons and dicotyledons. We showed that Cynodon dactylon, Panicum capilare, Zea mays and Saccharum officiarum (all are in the C4 metabolism) were improved from a common ancestors while the other cereals Triticum Avena, Hordeum, Oryza and Phalaris were evolved from another or similar ancestors. In this study, relationships within and between Fabaceae (Fabales), Rosaceae (Rosales), Moraceae (Uriticales), Cannabeceae (Uriticales) and Uriticaceae (Uriticales). Malvaceae (Malvales) and Brassicaceae (Brassicales) were also discussed. Overall, our results indicated that matK gene provides well-defined relationships within and among the families, genus and species; therefore its sequence can be successfully used in Single Nucleotide Polymorphism (SNP) or part of the sequence as DNA fragment analysis using PCR in plant systematic.

References

  • Brochmann, C., Xiang, Q. Y., Brunsfeld, S. J., Soltis, D. E. and Soltis, P. S. 1998. Molecular evidence for polyploidy origins in Saxifraga (Saxifragaceae): the narrow arctic endemic S. svalbardensis and its widespread allies. Amer. J. Botany, 85: 135–143.
  • Crayn, D. M., Winter, K. and Smith, J. A. C. 2004. Multiple origins of crassulacean acid metabolism and the epiphytic habit in the Neotropical family Bromeliaceae. PNAS, 101: 3703–3708.
  • Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39: 783–791.
  • Fuse, S. and Tamura, M. N. 2000. A phylogenetic analysis of the plastid matK gene with emphasis on Melanthiaceae sensu lato. Plant Biol., 2: 415–427.
  • Ito, M., Kawamoto, A., Kita, Y., Yukawa, T. and Kurita, S. 1999. Phylogenetic relationships of Amaryllidaceae based on matK sequence data. J. Plant Res., 112: 207–216.
  • Kilel, B. 2004. Comparative analysis and relationships of six important crop species chloroplast genomes using whole genome web-based informatics tools. Afr. Biotech., 3: 210-214.
  • Koch, M., Haubold, B. and Mitchell-Olds, T. 2001. Molecular Systematics of the Brassicaceae: Evidence from coding plastidic matK and nuclear chs sequences. Amer. J. Botany, 88: 534–544.
  • Mort, M. E., Soltis, D. E., Soltis, P. S., Francisco- Ortega, J. and Santos-Guerra, A. 2001. Phylogenetic relationships and evolution of Crassulaceae inferred from matK sequence data. Amer. J. Botany, 88: 76–91.
  • Steele, K. P. and Vilgalys, R. 1994. Phylogenetic analysis of Polemoniaceae using nucleotide sequences of the plastid gene matK. Systematic Botany, 19: 126–142.
  • Swofford, D. L. 2002. PAUP*: Phylogenetic analysis using parsimony (*and other methods), version 4.0b10. Sinauer, Sunderland.
  • Tamura, M. N., Yamashita, J., Fuse, S. and Haraguchi, M. 2004. Molecular phylogeny of monocotyledons inferred from combined analysis of plastid matK and rbcL gene sequences. Journal of Plant Research, 117: 109–120.
  • Thompson, J. D., Higgins, D. G. and 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.
There are 12 citations in total.

Details

Primary Language Turkish
Subjects Agricultural Engineering
Journal Section Articles
Authors

A. G. İnce This is me

M. Karaca This is me

A. N. Onus This is me

M. Bilgen This is me

Publication Date September 1, 2005
Published in Issue Year 2005 Volume: 18 Issue: 2

Cite

APA İnce, A. G., Karaca, M., Onus, A. N., Bilgen, M. (2005). Bazı Önemli Bitki Türlerinin Kloroplast matK Geni Filogenisi. Akdeniz University Journal of the Faculty of Agriculture, 18(2), 157-162.
AMA İnce AG, Karaca M, Onus AN, Bilgen M. Bazı Önemli Bitki Türlerinin Kloroplast matK Geni Filogenisi. Akdeniz University Journal of the Faculty of Agriculture. September 2005;18(2):157-162.
Chicago İnce, A. G., M. Karaca, A. N. Onus, and M. Bilgen. “Bazı Önemli Bitki Türlerinin Kloroplast MatK Geni Filogenisi”. Akdeniz University Journal of the Faculty of Agriculture 18, no. 2 (September 2005): 157-62.
EndNote İnce AG, Karaca M, Onus AN, Bilgen M (September 1, 2005) Bazı Önemli Bitki Türlerinin Kloroplast matK Geni Filogenisi. Akdeniz University Journal of the Faculty of Agriculture 18 2 157–162.
IEEE A. G. İnce, M. Karaca, A. N. Onus, and M. Bilgen, “Bazı Önemli Bitki Türlerinin Kloroplast matK Geni Filogenisi”, Akdeniz University Journal of the Faculty of Agriculture, vol. 18, no. 2, pp. 157–162, 2005.
ISNAD İnce, A. G. et al. “Bazı Önemli Bitki Türlerinin Kloroplast MatK Geni Filogenisi”. Akdeniz University Journal of the Faculty of Agriculture 18/2 (September 2005), 157-162.
JAMA İnce AG, Karaca M, Onus AN, Bilgen M. Bazı Önemli Bitki Türlerinin Kloroplast matK Geni Filogenisi. Akdeniz University Journal of the Faculty of Agriculture. 2005;18:157–162.
MLA İnce, A. G. et al. “Bazı Önemli Bitki Türlerinin Kloroplast MatK Geni Filogenisi”. Akdeniz University Journal of the Faculty of Agriculture, vol. 18, no. 2, 2005, pp. 157-62.
Vancouver İnce AG, Karaca M, Onus AN, Bilgen M. Bazı Önemli Bitki Türlerinin Kloroplast matK Geni Filogenisi. Akdeniz University Journal of the Faculty of Agriculture. 2005;18(2):157-62.