Van İlinde Bulunan <i>Centaurea</i> Cinsine Ait Beş Türün Moleküler Analizi ve <i>Centaurea depressa</i>’ nın Taksonomik Pozisyonunun Belirlenmesi

Bu çalışmada, Van Yüzüncü Yıl Üniversitesi kampüsünde doğal olarak yetişen Centaurea cinsine ait beş farklı türün (C. depressa, C. virgata, C. iberica, C. solstitialis ve C. balsamita) filogenetik ilişkileri çalışılarak taksonomik açıdan akrabalık dereceleri belirlenmeye çalışılmıştır. Ayrıca, bazı araştırmacılar tarafından C. depressa türünün Cyanus cinsi içerisine aktarılmasının moleküler seviyede desteklenip desteklenmediği de tartışılmıştır. Moleküler belirteç olarak, evrimsel çalışmalarda en fazla tercih edilen ve nüklear DNA’da bulunan ITS ve kloroplast DNA’da bulunan matK bölgeleri kullanılmıştır. Çalışılan türlerin teşhisinden emin olmak ve daha önceki çalışılan türlerle olan ilişkilerini de göstermek için NCBI veritabanından ilave sekanslar alınmıştır. ITS bölgesi ITS1, 5.8S ve ITS2 alt bölgelerini kapsamakta olup yaklaşık 630 baz çifti, matK bölgesi ise tamamen ekson bölgesinden oluşan yaklaşık 1200 baz çifti uzunluğundadır. ITS bölgesinde 100’den fazla, matK bölgesinde ise 24 nükleotit varyasyonu görülmüştür. ITS ve matK bölgeleri dizileri birleştirilerek yapılandırılan UPGMA ağacında, Cyanus cinsine transfer edilen C. depressa değil, C. balsamita türü evrimsel olarak uzak konumlanmıştır. Bu sonuçlar dikkate alındığında C. depressa türünün Centaurea cinsten çıkarılarak Cyanus cinsine aktarılması moleküler seviyede desteklenememiştir

Comparative molecular phylogenetics of Astragalus L. sections from Turkey with New World Astragalus species using nrDNA ITS sequences

Comparative molecular phylogenetic study using nrDNA internal transcribed spacer region (ITS) sequences was carried out on species from three Astragalus L. (Fabaceae) sections from Turkey (Old World species) and the New World. A total of 56 taxa (179 accessions) including 30 species from Incani DC., 15 species from Hypoglottidei DC. and 11 species from Dissitiflori DC. section were used in the current study. The total length of the ITS region was 642 bp with 56 (8.7 %) parsimony-informative and 9 insertion\deletion sites. The constructed phylogenetic tree suggested that the section Incani had the most conserved ITS region among the studied Astragalus sections, evolutionarily separated from other sections and monophyletic. Also, DNA sequences of several New World (Neo-) Astragalus species analyzed comparatively with those from the current study indicated that New World aneuploid species of Astragalus clearly formed a monophyletic group separated from the species of the Old World

Elymus L. ve akraba cinslerin (Poaceae) nüklear ribozomal iç transkripsiyonu aralayıcı dizisi kullanılarak filogenetik akrabalıkları

To help in the clarification of the taxonomic status of Elymus L. and related genera Agropyron Gaertn., Leymus Hochst., Hordelymus (Jess.) Harz, and Brachypodium P.Beauv., the sequence diversity in the internal transcribed spacer (ITS) region of nuclear ribosomal DNA was studied. ITS data of 64 Triticeae accessions including 40 Elymus, 12 Agropyron, 7 Leymus, and 4 Hordelymus, and 1 Brachypodium as an out-group were analysed. The molecular diversity statistics indicated that the most diverse genus is Elymus among the studied genera. The constructed phylogenetic tree by the maximum parsimony method revealed that one specimen of Elymus, E. pycnanthus (Godr.) Melderis, clustered with species of Agropyron. Molecular diversity statistics also indicated that E. pycnanthus is distantly related to other species of Elymus, but is closer to Agropyron species. The finding of strong affinity of Elymus to the species of Leymus and Agropyron supports the view that the taxonomy of Elymus is further complicated by the role of hybridisation among different ancestral genera.Elymus L. ve bu cinse akraba Agropyron Gaertn., Leymus Hochst., Hordelymus (Jess.) Harz ve Brachypodium P.Beauv. cinslerinin taksonomik statülerini açıklamaya yardımcı olmak için nüklear ribozomal DNA bölgesinde bulunan iç transkripsiyonu aralayıcı (ITS) bölgesinin dizi çeşitliliği çalışılmıştır. 40 Elymus, 12 Agropyron, 7 Leymus, 4 Hordelymus ve dış-grup olarak kullanılan 1 Brachypodium olmak üzere 64 Triticeae örneğinin ITS bölgesinden alınan verileri analiz edilmiştir. Moleküler çeşitlilik verileri, çalışılan cinsler içerisinde en fazla çeşitliliğin Elymus cinsinde varolduğunu göstermiştir. Maximum parsimony metodu kullanılarak elde edilen filogenetik ağaç, Elymus cinsi içerisinde bulunan bir türün, E. pycnanthus (Godr.) Melderis, Agropyron cinsi ile beraber grup oluşturduğunu göstermiştir. Aynı zamanda moleküler çeşitlilik verileri, E. pycnanthus türünün Elymus cinsine ait türlere daha uzak, fakat Agropyron türlerine daha yakın olduğunu göstermiştir. Elymus cinsinin Leymus ve Agropyron cinsine ait olan türlerle yakın ilişkisi, Elymus taksonomisinin farklı atasal cinslerle aralarında gerçekleşen melezlenme ile dahada karmaşıklaştığı görüşünü desteklemektedir

Phylogenetic relationships of Elymus L. and related genera (Poaceae) based on the nuclear ribosomal internal transcribed spacer sequences

To help in the clarification of the taxonomic status of Elymus L and related genera Agropyron Gaertn Leymus Hochst Hordelymus (Jess) Harz and Brachypodium P Beauv, the sequence diversity in the internal transcribed spacer (ITS) region of nuclear ribosomal DNA was studied ITS data of 64 Triticeae accessions including 40 Elymus 12 Agropyron 7 Leymus and 4 Hordelymus and 1 Brachypodium as an out group were analysed The molecular diversity statistics Indicated that the most diverse genus is Elymus among the studied genera The constructed phylogenetic tree by the maximum parsimony method revealed that one specimen of Elymus, E pycnanthus (Godr) Melderis, clustered with species of Agropyron Molecular diversity statistics also indicated that E pycnanthus is distantly related to other species of Elymus but is closer to Agropyron species The finding of strong affinity of Elymus to the species of Leymus and Agropyron supports the view that the taxonomy of Elymus is further complicated by the role of hybridisation among different ancestral gener

Barley germplasms developed for scald disease resistance exhibited a high level of genetic diversity based on SRAP markers

The objective of this study was to assess the genetic diversity and genetic relationships among 59 Turkish barley (Hordeum vulgare L.) germplasm lines (maintained for scald disease resistance breeding) using sequence-related amplified polymorphism (SRAP) markers. Seventeen SRAP primer combinations produced 83 polymorphic markers, with a mean polymorphism of 73.5%. The dendrogram created based on Nei's unweighted-pair group method using arithmetic average (UPGMA) indicated that there were 4 main clusters, which was supported by principle component analysis (PCA). Cluster I primarily included only scald-resistant germplasm lines, while clusters III and IV consisted of only scald-sensitive lines, but cluster 11 had both scald-resistant and scald-sensitive barley germplasm lines. The coefficients of genetic similarity among the genotypes ranged from 0.58 to 0.96, with a cophenetic correlation (r = 0.71) suggesting that the cluster analysis moderately represented the similarity matrix. The results indicate that a large amount of the genetic diversity present could be of great use in the development of future scald-resistant barley lines

Phylogeography and phylogeny of genus Quercus L. (Fagaceae) in Turkey implied by variations of trnT (UGU) -L (UAA) -F (GAA) chloroplast DNA region

The genus Quercus L. is one of the most abundant and important genera of woody plants in the Northern Hemisphere as well as in Turkey. In the current study which is the most comprehensive study dealing with Turkish oaks, sequence variations of three noncoding regions (trnT(UGU)-L(UAA) IGS, trnL(UAA)intron, trnL(UAA)-F(GAA) IGS) of chloroplast DNA (cpDNA) were used for phylogeographic and phylogenetic analysis on 319 individuals representing 23 taxa (17 species). The trnT(UGU)-L(UAA) region was found to be the most variable and parsimony informative region. Twenty-eight cpDNA haplotypes were identified based on 34 substitutions and 22 indels. High number of haplotypes and hT > vT observed in populations of oaks in Turkey indicated that the Anatolian Peninsula might have been a refugium at Glacial Periods. Phylogeographic construction and molecular variance analysis revealed that Quercus cpDNA haplotypes were geographically structured. Although local haplotype sharing among species from same infrageneric clades was common, levels of hybridization differ between species pairs. Haplotype analysis revealed four infrageneric clades, namely Section Quercus, Section Cerris and two clades corresponding to Section Ilex, namely “Ilex” and “Coccifera.” Furthermore, a Section Cerris haplotype was detected in the Aegean members of Q. ilex and Q. coccifera. Section Ponticae was placed in the Section Quercus cluster. In contrast to the phylogenetic reconstructions based on the nuclear DNA sequence data, Group Ilex seems to be polyphyletic based on plastome phylogeny. Chloroplast phylogeny of oaks reflects the traces of recent and ancient introgression events during diversification of species. In addition to this, incomplete linkage sorting may also explain this polymorphic assemblage. Therefore, further investigation is required to clarify the cpDNA phylogeny of oaks, especially for Section Ilex

A Molecular Phylogeny Of Salvia Euphratica Sensu Lato (Salvia L., Lamiaceae) And Its Closely Related Species With A Focus On The Section Hymenosphace

To investigate the phylogenetic relationships of Salvia euphratica sensu lato and its closely related species with a focus on the section Hymenosphace, we screened five different regions; one nuclear ribosomal DNA region (Internal Transcribed Spacer, ITS) and four chloroplast DNA regions [trnT-trnL intergenic spacer (IGS), trnL intron, trnL-trnF IGS and trnV intron]. Based on 19 sequences of 7 Salvia taxa produced in the study and different number of sequences obtained from GenBank, our results supported latest taxonomic treatments on Salvia pseudeuphratica and S. cerino-pruinosa as they are resurrected and accepted different species from S. euphratica. The results confirmed the latest phylogenetic findings as “the section Hymenosphace is a non-monophyletic group, originated thick textured, non-expanding ancestral group, and expanding calyces with widely diverging lips in fruiting stage evolved several times in parallel, not only in Salvia but also in the Iranian genus Zhumeria”. The species of the sect. Hymenosphace are mostly distributed in three different geographic regions [(1) Southwest Asia, Turkey, Russia and Iran, (2) Canary Islands, (3) Southern Africa] with different morphological characters. The results showed that ITS had the highest resolution power for discriminating studied taxa and the highest number of haplotypes was also observed in this region. The resolutions of the chloroplast regions were too low for taxa native to Turkey, but quite enough to discriminate species from the different clades whose sequences were obtained from database. © 2015, Springer-Verlag Wien

Phylogenetic relationships between Oxytropis DC. and Astragalus L. species native to an Old World diversity center inferred from nuclear ribosomal ITS and plastid matK gene sequences

Oxytropis and Astragalus represent one of the largest angiosperm genera complexes. Although phylogenetic studies of this complex exist, the evolutionary relationships among Astragalus and Oxytropis species sharing similar habitats in the Old World have not been studied in detail. The phylogenetic relationships among 13 Oxytropis and 56 Astragalus species native to Turkey were inferred from nucleotide sequence variations in the nuclear ribosomal internal transcribed spacer (ITS) and chloroplast maturase-like protein (matK) gene regions. In addition to our samples, 36 Oxytropis ITS and 6 Oxytropis matK sequences were retrieved from GenBank and included in the analysis. Phylogenies derived from a maximum likelihood analysis of the sequences indicated that Oxytropis and Astragalus genera are more likely monophyletic. However, the results suggest that New World Oxytropis species did not evolve by a single adaptive radiation in the genus, but rather from different Old World lineages. The genetic divergence between genera was less when the matK region was analyzed. Although the Oxytropis species did not show high genetic diversity, one subcluster of the genus was always distinctly separated in both trees. This subcluster was formed by the species Oxytropis engizekensis Duman \& Vural and O. persica Boiss., which are also regarded as synonyms in regard to several morphological characters of the genus