scholarly journals Sequence Analysis of the Internal Transcribed Spacer (ITS) Region of the Nuclear Ribosomal DNA (nrDNA) and Chloroplast trnL-F Region (cpDNA) of Some Lactuca L. (Asteraceae) Species in Turkey

2016 ◽  
Vol 8 (4) ◽  
pp. 444-450 ◽  
Author(s):  
Emre SEVİNDİK ◽  
Veysel UZUN ◽  
Fatih COŞKUN
Keyword(s):  
Sequence Analysis ◽  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Its Region ◽  
Nucleotide Composition ◽  
Nuclear Ribosomal Dna ◽  
Sequencing Data ◽  
Plant Materials ◽  
F Region ◽  
Lactuca Species

In the current study, sequence analysis of some Turkish Lactuca L. species using nrITS DNA and trnL-F cpDNA sequences were performed to elucidate phylogenetic relationships among the taxa under study. Hieracium umbellatum was used as an outgroup. Different plant materials of Lactuca were collected from different parts of Turkey during excursions of summer 2013. Plant materials were either kept in silica gel or kept fresh for immediate DNA isolation. Both phenol chloroform-isoamyl alcohol method and commercial kits were used to extract genomic DNA for PCR reactions. ITS4 and ITS5A primers were utilized for ITS region, while trnLe and trnLf primers were used to amplify the trnL-F region. Obtained DNA sequences were edited both manually and by using BioEdit 7.0.4.1. Sequencing data were aligned via ClustalW program and analyzed using PAUP 4.01b10 software. nrITS sequences varied from 639 nucleotides to 735 nucleotides. Average nucleotide composition for nrITS was 22.1% (T), 27.9% (C), 23.2% (A) and 26.8% (G). It was also found that divergence values differed between 0.0000 and 0.10290. The trnL-F sequences varied from 296 nucleotides to 385 nucleotides. Average nucleotide composition of trnL-F sequences was 34.1% (T), 18.4% (C), 31.6% (A) and 16.0% (G). It was also found that divergence values differed between 0.0000 and 0.09674. Neighbour Joining (NJ) trees were constructed in order to identify the relationships among Lactuca species. Phylogenetic trees based on ITS region were found to be more useful than phylogenetic trees based on trnL-F region. After analysis of the results obtained, the data suggest that Lactuca contains 2 clades, with clade 1 having 2 subclades. These results support the prior phylogenetic studies on Lactuca and hence provide an up to date review of Turkish Lactuca species.

scholarly journals Molecular characterization based on chloroplast (trnl-f) DNA sequence of the apple genotypes in Ardahan/Turkey

2019 ◽  
Vol 48 (4) ◽  
pp. 1099-1106
Author(s):  
Emre Sevindik ◽  
Zehra Tuğba Murathan ◽  
Sümeyye Filiz ◽  
Kübra Yalçin
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Tree ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Nucleotide Composition ◽  
Neighbor Joining ◽  
Sequencing Data ◽  
F Region ◽  
Phylogenetic Studies

Genetic diversity among Turkish apple genotypes in Ardahan province was conducted based on cpDNA trnL-F sequences. Apple genotypes were plotted on a phylogenetic tree where Pyrus x bretschneideri was used as the outgroup. The plant samples were collected from different locations and genomic DNA was isolated from healthy and green leaves. For sequence in trnL-F region trnLe and trnFf primers were used. Later obtained DNA sequences were edited using the BioEdit and FinchTV. Sequencing data were analyzed using MEGA 6.0 software. Neighbor joining and bootstrap trees were constructed in order to verify the relationships among the apple genotypes. Phylogenetic tree consisted of two clades. The divergence values of trnL-F sequences differed between 0.000 and 0.005. Average nucleotide composition was 38.3 T, 14.9 C, 31.9 A and 14.9% G. The phylogenetic tree constructed based on trnL-F region sequences was nearly parallel to prior phylogenetic studies on apple genotypes.

scholarly journals Phylogenetics of Taxus Using the Internal Transcribed Spacers of Nuclear Ribosomal DNA and Plastid trnL-F Regions

Horticulturae ◽  
2020 ◽  
Vol 6 (1) ◽  
pp. 19
Author(s):  
Patricia Coughlan ◽  
James C. Carolan ◽  
Ingrid L. I. Hook ◽  
Lisa Kilmartin ◽  
Trevor R. Hodkinson
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Intergenic Spacer ◽  
Its Region ◽  
Single Species ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Trnl Intron ◽  
Group Status ◽  
Haplotype Networks

Taxus is a genus of trees and shrubs with high value in horticulture and medicine as a source of the anticancer drug paclitaxel. The taxonomy of the group is complex due to the lack of diagnostic morphological characters and the high degree of similarity among species. Taxus has a wide global geographic distribution and some taxonomists recognize only a single species with geographically defined subgroups, whereas others have described several species. To address these differences in taxonomic circumscription, phylogenetic analyses were conducted on DNA sequences using Maximum Likelihood, Bayesian Inference and TCS haplotype networks on single and combined gene regions obtained for the nuclear ribosomal ITS region and the plastid trnL intron and trnL-F intergenic spacer. Evidence is presented for the sister group status of Pseudotaxus to Taxus and the inclusion of Amentotaxus, Austrotaxus, Cephalotaxus and Torreya within Taxaceae. Results are consistent with the taxonomic recognition of nine species: T. baccata, T. brevifolia, T. canadensis, T. cuspidata, T. floridana, T. fuana, T. globosa, T. sumatrana and T. wallichiana, but evidence is found for less species distinction and considerable reticulation within the T. baccata, T. canadensis and T. cuspidata group. We compare the results to known taxonomy, biogeography, present new leaf anatomical data and discuss the origins of the hybrids T. ×media and T. ×hunnewelliana.

Molecular systematics of Australian Podolepis (Asteraceae: Gnaphalieae): evidence from DNA sequences of the nuclear ITS region and the chloroplast matK gene

2000 ◽  
Vol 13 (5) ◽  
pp. 709 ◽  
Author(s):  
N. Konishi ◽  
K. Watanabe ◽  
K. Kosuge
Keyword(s):  
Dna Sequences ◽  
Its Region ◽  
Chromosomal Evolution ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Base Number ◽  
Monophyletic Clade ◽  
Matk Gene ◽  
Nuclear Its ◽  
Generic Relationships

The generic circumscription and intra-generic relationships of the genus Podolepis Labill., with various chromosome numbers from n = 12 to n = 3, were examined by sequences of the internal transcribed spacers (ITS) of nuclear ribosomal DNA and the matK gene of chloroplast DNA. The topology of the ITS tree for 17 species and the matK tree for 18 species of the genus Podolepis sensu Davis (1957) and Anderberg (1991) and 15 taxa from eight related genera (Anderberg 1989, 1991, 1994) are basically concordant. Except for P. georgei Diels andP. kendallii F.Muell., parsimony analyses support the monophyly of the genus Podolepis sensu Davis (1957) and Anderberg (1991). The genera of Asteridea Lindl. and Pterochaeta Steetz are sisters toPodolepis in the combined tree based on the ITS and matK sequences. Within the monophyletic clade of the genus Podolepis, three lineages are identified. The chromosome base number of x = 12 may be ancestral in the genus Podolepis. The dysploidal reduction in chromosome number from n = 12 to n = 10 and 9, from n = 12 to n = 8 and 7, and from n = 12 to n = 11 and 3 in three lineages, respectively, is the primary mode of chromosomal evolution in this genus. Total karyotypic length (= genome size) is much greater in perennials than in annuals within the genus Podolepis. The number of pappus bristles on outer female florets tends to decrease and they are absent in some annuals of this genus, while myxogenic cells on the pericarp become prominent.

Phylogenetic relationships of the monogenomic species of the wheat tribe, Triticeae (Poaceae), inferred from nuclear rDNA (internal transcribed spacer) sequences

Genome ◽  
1995 ◽  
Vol 38 (2) ◽  
pp. 211-223 ◽  
Author(s):  
C. Hsiao ◽  
N. J. Chatterton ◽  
K. H. Asay ◽  
K. B. Jensen
Keyword(s):  
Phylogenetic Relationships ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Trees ◽  
Parallel Evolution ◽  
Diploid Species ◽  
Its Region ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
The Arctic ◽  
Cytogenetic Evidence

Phylogenetic relationships of 30 diploid species of Triticeae (Poaceae) representing 19 genomes were estimated from the sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA. The ITS sequence phylogeny indicated that: (i) each genome group of species is monophyletic, concordant with cytogenetic evidence; (ii) Hordeum (I) and Critesion (H) are basal; (iii) Australopyrum (W) is closely related to Agropyron (P); (iv) Peridictyon (G), Heteranthelium (Q), and Dasypyrum (V) are closely related to Pseudoroegneria (S); (v) most of the annuals, Triticum s.l. (A, B, D), Crithopsis (K), Taeniatherum (T), Eremopyrum (F), Henrardia (O), Secale (R), and two perennials, Thinopyrum (J) and Lophopyrum (E), all of Mediterranean origin, are a monophyletic group. However, phylogenetic trees based on morphology group these Mediteranean species with various perennial lineages of the Arctic-temperate region. The molecular data and biogeography of the tribe suggest that the Mediterranean lineage is derived from the Arctic-temperate lineage and that the two lineages have evolved in parallel. Extensive morphological parallelism apparently obscures the true genealogical history of the tribe when only morphology is considered.Key words: Poaceae, Triticeae, rDNA sequence, molecular phylogeny, parallel evolution.

scholarly journals Phylogenetic analysis of the genus Conringia Heist. Ex Fabr. (Brassicaceae) in Turkey based on nuclear (nrITS) and chloroplast (trnL-F) DNA sequences

2021 ◽  
Vol 13 (3) ◽  
pp. 11034
Author(s):  
Emre SEVINDIK ◽  
Melike AYDOGAN ◽  
Mehmet Y. PAKSOY
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Nuclear Ribosomal Dna ◽  
Neighbor Joining ◽  
F Region ◽  
Brassicaceae Species ◽  
Nj Tree ◽  
Brassicaceae Family

In this study, phylogenetic analysis of Turkish Conringia (Brassicaceae) species was conducted based on nuclear ribosomal DNA (nrITS) and chloroplast DNA (trnL-F) sequences. In addition, the relationships between the sequences of some Brassicaceae family species retrieved from NCBI, and Conringia species were documented. All of the plant specimens were collected at their flowering and vegetation periods from different regions of Turkey, and brought to the laboratory. Total genomic DNA was extracted using the GeneMark kit. In PCR analyses, ITS4 and ITS5A primers were used for the amplification of the nrITS region, while the trnLe and trnLf primers were used for the cpDNA trnL-F region. The DNA sequences obtained were then edited using BioEdit and FinchTV, and analyzed using MEGA 6.0 software. Neighbor joining (NJ) and bootstrap trees were constructed in order to identify the relationships among Conringia taxa. The nrITS sequences ranged between 573 and 672 nucleotides, while the trnL-F sequences ranged between 346 and 764 nucleotides. The divergence values of nrITS sequences differed between 0.177 and 0.00 and divergence values of trnL-F sequences differed between 0.902 and 0.00. NJ tree generated using nrITS and trnL-F sequences consisted of two clades. In trees generated with both the nrITS and trnL-F sequences, C. orientalis, C. grandiflora and C. austriaca appeared within the same group. In addition, according to the phylogenetic analysis results obtained with other Brassicaceae species, it is revealed that the Conringia genus is polyphyletic.

scholarly journals Two new species of Hygrophorus from temperate Himalayan Oak forests of Pakistan

MycoKeys ◽  
2019 ◽  
Vol 56 ◽  
pp. 33-47 ◽  
Author(s):  
Arooj Naseer ◽  
Abdul Nasir Khalid ◽  
Rosanne Healy ◽  
Matthew E. Smith
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Large Subunit ◽  
Its Region ◽  
Morphological Characters ◽  
Nuclear Ribosomal Dna ◽  
Oak Forests ◽  
Rdna Genes ◽  
Two New Species ◽  
Dark Green

The genus Hygrophorus is poorly studied from Asia. From Pakistan, only one species has been reported so far. Two new species in the genus have been collected from Himalayan oak forests of Pakistan. Hygrophorusalboflavescens (section Pudorini, subgenus Colorati) is characterised by its pure white, centrally depressed pileus, occurrence of white stipe with yellow patches at lower half and broader (4.98 μm) basidiospores. Hygrophorusscabrellus (section Hygrophorus, subgenus Hygrophorus) is characterised by its yellowish-green stipe with white apex that has fine scales on the entire stipe, an off-white pileus with dark green and greyish fibrils, ovoid to ellipsoid basidiospores and clavate 4-spored basidia. Macro- and micromorphological descriptions have revealed that both these taxa are not yet described. Phylogenetic estimation based on DNA sequences from the internal transcribed spacer (ITS) region and large subunit (LSU) of the nuclear ribosomal DNA (rDNA) genes, is congruent with the morphological characters that help to delimit these as new species of Hygrophorus. Allied taxa are also compared.

scholarly journals Analyses of molecular markers and leaf morphology of two rare birches, Betula obscura and B. pendula var. carelica

2020 ◽  
Vol 63 (2) ◽  
pp. 121-137
Author(s):  
Katarzyna Anna Jadwiszczak ◽  
Lidia Vetchinnikova ◽  
Agnieszka Bona ◽  
Łukasz Tyburski ◽  
Tatiana Kuznetsova ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Leaf Morphology ◽  
Phylogenetic Signal ◽  
Distinct Species ◽  
Nuclear Ribosomal Dna ◽  
Gene Sequences ◽  
Length Polymorphisms ◽  
Adh Gene

Trees and shrubs belonging to the Betula L. genus seem to represent one of the most confused interspecific relationships, and hybridization is considered to be one of the main factors responsible for the substantial genetic and morphological variation of birches. In the present investigation, the internal transcribed spacer ITS1 and ITS2 regions of nuclear ribosomal DNA, nuclear alcohol dehydrogenase (ADH) gene sequences and amplified fragment length polymorphisms (AFLPs) as well as the Atkinson discriminant function (ADF) of leaf morphology were used to verify hypotheses concerning the origin of the dark barked Betula obscura and B. pendula var. carelica with the patterned wood. Both plants were considered by different authors to be distinct species, intraspecific forms of common B. pendula or B. pubescens, or hybrid taxa between B. pendula and B. pubescens. In the phylogenetic trees, the ITS and ADH gene sequences of both B. obscura and B. pendula var. carelica clustered with those of B. pendula, whereas B. pubescens trees were somewhat distinct. In turn, the AFLPs revealed genetic similarity of B. pendula var. carelica to both frequent species, whereas B. obscura was clearly distinct from other birches. Values of the ADF indices of the rare birches were typical for B. pendula. In the light of the results obtained, we imply that B. obscura and B. pendula var. carelica represent an intraspecific variation of B. pendula, they are neither intraspecific taxa of B. pubescens nor hybrid species between the common birches. Different grouping of B. obscura in the AFLPs and DNA sequences analyses is likely a result of an unreliable phylogenetic signal of the former molecular markers.

scholarly journals DNA Authentication of St John’s Wort (Hypericum perforatum L.) Commercial Products Targeting the ITS Region

Genes ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 286
Author(s):  
Howard ◽  
Hill ◽  
Kreuzer ◽  
Mali ◽  
Masiero ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Hypericum Perforatum ◽  
Its Region ◽  
Qpcr Assay ◽  
Plant Materials ◽  
Commercial Products ◽  
Synthetic Dna ◽  
Hypericum Perforatum L ◽  
Species Specific ◽  
Its1 And Its2

There is considerable potential for the use of DNA barcoding methods to authenticate raw medicinal plant materials, but their application to testing commercial products has been controversial. A simple PCR test targeting species-specific sequences within the nuclear ribosomal internal transcribed spacer (ITS) region was adapted to screen commercial products for the presence of Hypericum perforatum L. material. DNA differing widely in amount and extent of fragmentation was detected in a number of product types. Two assays were designed to further analyse this DNA using a curated database of selected Hypericum ITS sequences: A qPCR assay based on a species-specific primer pair spanning the ITS1 and ITS2 regions, using synthetic DNA reference standards for DNA quantitation and a Next Generation Sequencing (NGS) assay separately targeting the ITS1 and ITS2 regions. The ability of the assays to detect H. perforatum DNA sequences in processed medicines was investigated. Out of twenty different matrices tested, both assays detected H. perforatum DNA in five samples with more than 103 ITS copies µL−1 DNA extract, whilst the qPCR assay was also able to detect lower levels of DNA in two further samples. The NGS assay confirmed that H. perforatum was the major species in all five positive samples, though trace contaminants were also detected.

Characterization of the complete mitochondrial genome of Metastrongylus salmi (M. salmi) derived from Tibetan pigs in Tibet, China

2018 ◽  
Vol 63 (2) ◽  
pp. 280-286 ◽  
Author(s):  
Kun Li ◽  
Muhammad Shahzad ◽  
Hui Zhang ◽  
Khalid Mehmood ◽  
Xiong Jiang ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Translation Termination ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Phylogenetic Position ◽  
Protein Coding ◽  
Tibetan Pigs ◽  
Translation Termination Codon ◽  
Rna Genes

AbstractThe present study was designed to determine and analyze themtgenomes ofMetastrongylus salmi(M.salmi), and reveal the phylogenetic relationships of this parasite usingmtDNA sequences. Results showed that the completemtgenome ofM.salmiwas 13722 bp containing 12 protein-coding genes (cox1-3, nad1-6, nad4L, atp6 and cytb), 22 transfer RNA genes, and 2 ribosomal RNA genes (rrnL and rrnS). The overall A+T content was 73.54% and the nucleotide composition was A (23.52%), C (6.14%), G (19.60%), T (50.02%), and N (UCAG) (0.73%). A total of 4237 amino acids are encoded from the Tibetan isolates ofM. salmi mtgenomes. The ATA was predicted as the most common starting codon with 41.7% (5/12 protein genes); and 11 of the 12 protein genes were found to have a TAG or TAA translation termination codon. By clustering together the phylogenetic trees of TibetanM.salmiand AustrianM.salmi, theM.salmiisolated from Tibetan pigs was found to be highly homological with that stemmed from Austrian one. This information provides meaningful insights into the phylogenetic position of theM.salmiChina isolate and represents a useful resource for selecting molecular markers for diagnosis and population studies.

A new perennial Erysimum species from Turkey, E. nemrutdaghense (Brassicaceae)

Phytotaxa ◽  
2018 ◽  
Vol 336 (3) ◽  
pp. 239 ◽  
Author(s):  
BİROL MUTLU
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Its Region ◽  
Nuclear Ribosomal Dna ◽  
Similar Species ◽  
Sem Images ◽  
First Time ◽  
East Anatolia ◽  
A New Species ◽  
Different Parts

In this study, Erysimum nemrutdaghense Mutlu (Brassicaceae) is described as a new species from the province of Adıyaman in the South-east Anatolia. In order to determine the phylogenetic relationships of the new species, a portion of the nuclear ribosomal DNA sequences of ITS region was used. In addition to the new species, ITS regions of five Erysimum species were sequenced. Erysimum sintenisianum Bornm., E. lazistanicum (Rupr.) Lipsky, and E. stenophyllum Polatschek were sequenced in this study for the first time. The diagnostic morphological and phylogenetic characteristics are discussed with similar species. SEM images of trichomes on different parts of siliqua, stigma, and seed are given. Chromosome number of the new species is found to be 2n=16.

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