Bazı Önemli Bitki Türlerinin Kloroplast matK Geni Filogenisi

AKDENİZ ÜNİVERSİTESİ ZİRAAT FAKÜLTESİ DERGİSİ, 2005, 18(2), 157-162 CHLOROPLAST matK GENE PHYLOGENY OF SOME IMPORTANT SPECIES OF PLANTS Ayşe Gül İNCE1 1 Mehmet KARACA2 A. Naci ONUS1 Mehmet BİLGEN2 Akdeniz University Faculty of Agriculture Department of Horticulture, 07059 Antalya, Turkey Akdeniz University Faculty of Agriculture Department of Field Crops, 07059 Antalya, Turkey Correspondence addressed E-mail: 2 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. Keywords: Bootstrap, Plant Families, Chloroplast, matK, Molecular Phylogeny Bazı Önemli Bitki Türlerinin Kloroplast matK Geni Filogenisi Özet 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. Anahtar Kelimeler: Bootstrap, Bitki Familyaları, Kloroplast, matK, Moleküler Filogeni Chloroplast matK Gene Phylogeny of Some Important Species of Plants 1. Introduction Recent advances in DNA sequencing technologies and molecular biology enable us to characterize genomes of organisms and now many ongoing genome projects for various species are providing valuable insights into their biology and utilizations. The application of molecular biology information to systematic and evolution has resulted in significant contributions to plant systematics and in the emergence of molecular systematics as a solid interdisciplinary field (Mort et al., 2001). Nucleotide sequence variability in chloroplast DNA (cpDNA or plastid DNA) at inter-(between families or genus) and intra-specific level (within species or varieties) has been surveyed primarily in order to analyze the phylogenetic relationships and plant identification studies (Tamura et al., 2004). The matK gene, a chloroplast genome encoded locus located within the intron of the chloroplast gene trnK, encodes a maturase on the large single-copy section adjacent to the inverted repeat of every plant families, has high rates of substitution compared to other chloroplast genes and its DNA sequence is one of the least conserved plastid genes; therefore, has been effectively used in plant evolution and addresses the phylogenetic questions in various taxonomic levels (Ito et al., 1999; Fuse and Tamura, 2000). The matK gene has several advantages in comparison to other genes including the organelle genome genes. First of all the matK gene evolves approximately three times faster than the widely used plastid genes rbcL and atpB. It is in the chloroplast genome and in many cases it is maternally inherited. This gene has a reasonable size, high rate of substitution, large proportion of variation at the first and the second codon positions, low transitiontransversion ratio, and the presence of mutationally conserved sectors. Research has shown that the variations at nucleic acid (DNA) and amino acid levels evenly distributed throughout the entire gene, and the 5’ region of the matK gene appears to have more variation than the 3’ region in 158 many monocotyledon (...truncated)