scholarly journals Molecular phylogeny based on its sequences of nrDNA of some species belonging to dodder (Cuscuta L.) genus from various ecological sites of Turkey

2020 ◽  
Vol 48 (3) ◽  
pp. 1332-1340
Author(s):  
Ilhan KAYA ◽  
Ibrahim DEMIR ◽  
Mustafa USTA ◽  
Hikmet M. SIPAHIOĞLU
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Sequence Data ◽  
Its Sequences ◽  
Nuclear Ribosomal Dna ◽  
Universal Primers ◽  
Morphological Examination ◽  
Internal Transcribed Spacer Region ◽  
Tissue Samples ◽  
Geographical Regions

Nuclear ribosomal DNA (nrDNA) sequence data of the Cuscuta genus, which have been considered as one of the most popular sequences for phylogenetic inference in plants, have been studied from a phylogenetic perspective in agricultural and non-agricultural lands of Turkey. The samples of Cuscuta spp. were collected from different geographical regions of Turkey between the years of 2013-2015. Some other species, not available locally, were taken from the herbarium samples of some research units. In order to study the phylogenetic relations of collected species, DNA isolations were made from body tissue samples. Conserved regions on ribosomal DNA (rDNA) were amplified by universal primers via PCR method and cloned into a proper cloning vector. The cloned DNA fragments were sequenced and analysed by web-based and computer programs. DNA sequences of certain species were recorded to the National Center for Biotechnology Information (NCBI) database. Based on the morphological examination and molecular analyses of fresh and the herbarium specimen, 8 species were identified. The identified species were C. hyalina (Gene bank accession no. KY020420), C. monogyna (KY020421), C. europaea (KY020422), C. palaestina (KY020423), C. approximata (KY020424), C. kurdica (KY020427), C. kotschyana (KY020430) and C. babylonica (KY020431). The ITS (Internal Transcribed Spacer) region contains several indels in identified Cuscuta species with the length varying from 668 to 730 bp. Sequence divergence ranges from 1.00% to 8.00% within Cuscuta spp. Based on our findings, the ITS sequences provided phylogenetically informative results in combination with the secondary structures.

Evolutionary relationships ofHyphodiscus hymeniophilus(anamorphCatenulifera rhodogena) inferred from β-tubulin and nuclear ribosomal DNA sequences

2006 ◽  
Vol 84 (2) ◽  
pp. 243-253 ◽  
Author(s):  
Wendy A. Untereiner ◽  
Françoise A. Naveau ◽  
Jason Bachewich ◽  
Andrea Angus
Keyword(s):  
Phylogenetic Relationship ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Its Sequences ◽  
Nuclear Ribosomal Dna ◽  
Phialocephala Fortinii ◽  
Piptoporus Betulinus ◽  
Close Phylogenetic Relationship ◽  
Relationship Of ◽  
Β Tubulin

During an investigation of lignicolous ascomycetes from Luxembourg, we isolated a Phialophora -like species that produced striking red colonies. To confirm the identity of this fungus as Catenulifera rhodogena , we compared it with isolates of Catenulifera rhodogena and Hyphodiscus hymeniophilus on a variety of media. Portions of the β-tubulin gene and the nuclear ribosomal DNA cistron (internal transcribed spacers (ITS) and large subunit (LSU)) were sequenced to examine the relationship of isolates of Catenulifera rhodogena and Hyphodiscus hymeniophilus from different substrates and to test the hypothesis that Cadophora and Catenulifera are congeneric. The phylogenetic position of Catenulifera within the Ascomycota was investigated based on the analysis of the small-subunit (SSU) rDNA sequences. The isolates examined were indistinguishable micromorphologically and closely related phylogenetically. Three strains of Catenulifera rhodogena from bark or wood and one strain from Piptoporus betulinus formed a strongly supported clade in analyses of β-tubulin and ITS sequences. This clade did not encompass the ex-type isolates of Cistella rubescens and Scopulariopsis rhodogena or a second isolate of Catenulifera rhodogena from Piptoporus betulinus. Analysis of partial LSU sequences confirmed the close phylogenetic relationship of Catenulifera rhodogena and Hyphodiscus hymeniophilus but provided no evidence that the isolates could be grouped by substrate or that Catenulifera is synonymous with Cadophora. The position of Catenulifera within the Helotiales was not resolved based on the comparison of LSU and SSU sequences, but the isolate for which we obtained complete SSU sequence grouped with the root endophyte Phialocephala fortinii. Comparison of ITS sequences confirmed the close phylogenetic relationship of Hyphodiscus to members of the Dermateaceae and Hyaloscyphaceae.

Systematics of the Salmonid Genus Salvelinus Inferred from Ribosomal DNA Sequences

1994 ◽  
Vol 51 (S1) ◽  
pp. 198-204 ◽  
Author(s):  
Ruth B. Phillips ◽  
Susan A. Manley ◽  
Thomas J. Daniels
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Brook Trout ◽  
Lake Trout ◽  
Sequence Data ◽  
Distance Matrix ◽  
Its2 Sequence ◽  
Nuclear Ribosomal Dna ◽  
Bull Trout ◽  
Second Internal Transcribed Spacer

DNA sequences of the second internal transcribed spacer (ITS2) of the nuclear ribosomal DNA were determined for six species of the genus Salvelinus: S. alpinus (Arctic char), S. malma (Dolly Varden), S. confluentus (bull trout), S. leucomaenis (Japanese char), S. fontinalis (brook trout), and S. namaycush (lake trout), and for Hucho perryi (huchen). The ITS2 sequence data (approximately 375 base pairs (bp)) were combined with previously determined sequence data for the ITS1 (approximately 575 bp), giving a total of 981 bp of aligned sequence for each species. Phylogenetic analysis of the aligned sequences was done using maximum parsimony, maximum likelihood, and distance matrix methods with H. perryi as an outgroup. The results were consistent with previous work based on comparisons of morphologies, allozymes, and karyotypes. Comparison of these results with those based on mitochondrial DNA sequences suggests that hybridization may have occurred between S. confluentus and S. alpinus or S. malma.

PHYLOGENY OF HEDYCHIUM AND RELATED GENERA (ZINGIBERACEAE) BASED ON ITS SEQUENCE DATA

2000 ◽  
Vol 57 (2) ◽  
pp. 261-270 ◽  
Author(s):  
T. H. WOOD ◽  
W. M. WHITTEN ◽  
N. H. WILLIAMS
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Interspecific Hybrid ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Cladistic Analysis ◽  
Monophyletic Group ◽  
Nuclear Ribosomal Dna ◽  
Its Sequence ◽  
Limited Sample

The phylogeny of Hedychium J. Koenig was estimated using sequence data of internal transcribed spacer regions 1 and 2 (ITS1, ITS2) and 5.8S nuclear ribosomal DNA. Sequences were determined for 29 taxa, one interspecific hybrid of Hedychium and one species in each of 16 other genera of Zingiberaceae representing tribes Hedychieae, Globbeae, Zingibereae and Alpinieae. Cladistic analysis of these data strongly supports the monophyly of Hedychium, but relationships to other genera are poorly supported. Within Hedychium, four major clades are moderately supported. These clades are also distinguishable on the basis of number of flowers per bract and distribution. Stahlianthus, Curcuma, and Hitchenia also form a strongly supported clade. Based on this limited sample, the currently defined tribes of Zingiberoideae are not monophyletic. The Asiatic genera form a monophyletic group within this broadly defined Hedychieae. The taxonomy and biogeography of Hedychium are reviewed.

scholarly journals Inclusion of Kickxia abhaica D.A. Sutton in the genus Nanorrhinum (Plantaginaceae): Evidence from its nuclear ribosomal DNA sequences

2018 ◽  
Vol 25 (2) ◽  
pp. 209-214
Author(s):  
M. Ajmal Ali
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Molecular Phylogenetics ◽  
Taxonomic Status ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Universal Primers ◽  
Discrimination Power ◽  
Molecular Phylogenetic ◽  
Endemic Taxon

The nuclear ribosomal DNA (nrDNA) internal transcribed spacers (ITS) sequences is extensively used in the plant molecular phylogenetics for plant taxonomic identification and DNA barcoding purposes because the nrDNA ITS gene is easy to amplify by using the universal primers, its length is shorter and thus easy to sequence, and has strong discrimination power to distinguish the taxon at the species level. The present molecular phylogenetic analysis of ITS nrDNA sequences focuses to determine the taxonomic status of an unresolved endemic taxon Kickxia abhaica D.A. Sutton (Family Plantaginaceae, tribe Antirrhineae) reported from Saudi Arabia. The analysis supports the transfer of K. abhaica under the genus Nanorrhinum.

scholarly journals Phylogeny and PCR Identification of Clinically Important Zygomycetes Based on Nuclear Ribosomal-DNA Sequence Data

1999 ◽  
Vol 37 (12) ◽  
pp. 3957-3964 ◽  
Author(s):  
Kerstin Voigt ◽  
Elizabeth Cigelnik ◽  
Kerry O'donnell
Keyword(s):  
Dna Sequence ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Sequence Data ◽  
Large Subunit ◽  
Gene Tree ◽  
Strong Support ◽  
Nuclear Ribosomal Dna ◽  
Syncephalastrum Racemosum ◽  
Dna Sequence Data

A molecular database for all clinically important Zygomycetes was constructed from nucleotide sequences from the nuclear small-subunit (18S) ribosomal DNA and domains D1 and D2 of the nuclear large-subunit (28S) ribosomal DNA. Parsimony analysis of the aligned 18S and 28S DNA sequences was used to investigate phylogenetic relationships among 42 isolates representing species of Zygomycetes reported to cause infections in humans and other animals, together with commonly cultured contaminants, with emphasis on members of the Mucorales. The molecular phylogeny provided strong support for the monophyly of the Mucorales, exclusive of Echinosporangium transversale andMortierella spp., which are currently misclassified within the Mucorales. Micromucor ramannianus, traditionally classified within Mortierella, and Syncephalastrum racemosum represent the basal divergences within the Mucorales. Based on the 18S gene tree topology, Absidia corymbiferaand Rhizomucor variabilis appear to be misplaced taxonomically. A. corymbifera is strongly supported as a sister group of the Rhizomucor miehei-Rhizomucor pusillusclade, while R. variabilis is nested withinMucor. The aligned 28S sequences were used to design 13 taxon-specific PCR primer pairs for those taxa most commonly implicated in infections. All of the primers specifically amplified DNA of the size predicted based on the DNA sequence data from the target taxa; however, they did not cross-react with phylogenetically related species. These primers have the potential to be used in a PCR assay for the rapid and accurate identification of the etiological agents of mucormycoses and entomophthoromycoses.

Differentiation of the Xiphinema americanum-group nematodes X. brevicollum, X. incognitum, X. diffusum and X. oxycaudatum in Taiwan by morphometrics and nuclear ribosomal DNA sequences

Nematology ◽  
2005 ◽  
Vol 7 (5) ◽  
pp. 713-725 ◽  
Author(s):  
Yung-Hsiung Cheng ◽  
Tung-Tsuan Tsay ◽  
Hui-Fang Ni ◽  
Diann-Yih Chen ◽  
Jyh-Herng Yen
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Nuclear Ribosomal Dna ◽  
Pairwise Comparisons ◽  
Geographical Regions ◽  
Juvenile Stages ◽  
Stylet Length ◽  
Second Internal Transcribed Spacer ◽  
Species Being

AbstractMorphometrics and molecular variability of the X. americanum-group collected in Taiwan were studied. Morphometric data, derived from the females and their developing juveniles, revealed that the 27 populations comprised four taxa: X. brevicollum, X. incognitum, X. diffusum and X. oxycaudatum, the last species being found to have only three juvenile stages. Further identifications were conducted by analysing the nucleotide sequences of the first internal transcribed spacer (ITS-1), 5.8S gene and second internal transcribed spacer (ITS-2) of ribosomal DNA (rDNA). Pairwise comparisons revealed the sequence differences among these taxa ranging from 3.5 to 21.8% for the ITS-1, 2.9 to 28.6% for the ITS-2 and 0 to 3.1% for the 5.8S. Little or no intraspecific variation was detected in the four species for which multiple populations from different geographical regions or hosts were sequenced. Although X. incognitum is morphometrically closer to X. diffusum than it is to X. brevicollum in mean body length, total stylet length, and percentage position of vulva, there is a higher degree of genetic similarity between X. incognitum and X. brevicollum.

Molecular phylogeny of Acacia subgenus Phyllodineae (Mimosoideae : Leguminosae) based on DNA sequences of the internal transcribed spacer region

2003 ◽  
Vol 16 (1) ◽  
pp. 19 ◽  
Author(s):  
Daniel J. Murphy ◽  
Joseph T. Miller ◽  
Randall J. Bayer ◽  
Pauline Y. Ladiges
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Its Region ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Internal Transcribed Spacer Region ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Dna Repeat ◽  
Outgroup Taxon

The largest monophyletic group within Acacia is subgenus Phyllodineae, with more than 950 predominately Australian species, the majority characterised by adult foliage consisting of phyllodes. Molecular sequence data from the internal transcribed spacers (ITS) of the nuclear ribosomal DNA repeat were used to investigate the monophyly of seven sections within the subgenus. A nested PCR approach was used to amplify the ITS region. Fifty-one species representative of all sections were sequenced together with one outgroup taxon Lysiloma divaricata (Ingeae).Phylogenetic parsimony analysis suggested that there are two main clades within Phyllodineae but that only one section, Lycopodiifoliae, is apparently monophyletic. In one of the main clades, Lycopodifoliae is related to some taxa in sections Alatae and Pulchellae and some members of section Phyllodineae. In the second main clade, sections Juliflorae, Plurinerves and Botrycephalae cluster with other members of section Phyllodineae. The two sections that are characterised by bipinnate foliage, Botrycephalae and Pulchellae, are nested within phyllodinous clades, indicating that at least two separate reversals to bipinnate leaves have occurred. Botrycephalae is paraphyletic with respect to taxa from section Phyllodineae that have single-nerved phyllodes and racemose inflorescences.

scholarly journals Systematic Relationship of Weeping Katsura Based on Nuclear Ribosomal DNA Sequences

HortScience ◽  
2002 ◽  
Vol 37 (3) ◽  
pp. 595-598 ◽  
Author(s):  
Jianhua Li ◽  
Michael S. Dosmann ◽  
Peter Del Tredici ◽  
Susyn Andrews
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Sequence Data ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Hybrid Origin ◽  
Morphological Evidence ◽  
Separate Species ◽  
Cultivar Group ◽  
Cercidiphyllum Japonicum

Sequences of the internal transcribed spacers (ITS) of nuclear ribosomal DNA were used to examine genetic divergence of the two species of katsura [Cercidiphyllum japonicum Sieb. & Zucc. and Cercidiphyllum magnificum (Nakai) Nakai] and four clones of weeping katsura (`Amazing Grace', `Tidal Wave', `Pendulum', and `Morioka Weeping'), and to characterize the affinity of these weeping katsura to both species. Our results indicate that C. japonicum and C. magnificum are genetically distinct, supporting the recognition of them as separate species. Based on our DNA sequence data and morphological evidence, all weeping selections are phylogenetically derived from C. japonicum, not C. magnificum; nor are they of a hybrid origin between C. japonicum and C. magnificum. We propose the new cultivar-group Cercidiphyllum japonicum Weeping Group to include all katsura clones of weeping or pendulous habit, and recognize the cultivar epithet `Morioka Weeping' and its application to the excurrent and upright clone obtained from Japan and distributed in North America by the Arnold Arboretum.

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