Systematics of the Salmonid Genus Salvelinus Inferred from Ribosomal DNA Sequences

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.

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

Notulae Botanicae Horti Agrobotanici Cluj-Napoca ◽

10.15835/nbha48311997 ◽

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.

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

Edinburgh Journal of Botany ◽

10.1017/s0960428600000196 ◽

2000 ◽

Vol 57 (2) ◽

pp. 261-270 ◽

Cited By ~ 31

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.

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

Journal of Clinical Microbiology ◽

10.1128/jcm.37.12.3957-3964.1999 ◽

1999 ◽

Vol 37 (12) ◽

pp. 3957-3964 ◽

Cited By ~ 124

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.

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A molecular perspective on the genera Paragonimus Braun, Euparagonimus Chen and Pagumogonimus Chen

Journal of Helminthology ◽

10.1017/s0022149x99000499 ◽

1999 ◽

Vol 73 (4) ◽

pp. 295-299 ◽

Cited By ~ 33

Author(s):

D. Blair ◽

B. Wu ◽

Z.S. Chang ◽

X. Gong ◽

T. Agatsuma ◽

...

Keyword(s):

Ribosomal Dna ◽

Dna Sequences ◽

Internal Transcribed Spacer ◽

Morphological Study ◽

Type Species ◽

Phylogenetic Trees ◽

Nuclear Ribosomal Dna ◽

Mitochondrial Cytochrome ◽

The Status ◽

Second Internal Transcribed Spacer

The status of the genera Euparagonimus Chen, 1963 and Pagumogonimus Chen, 1963 relative to Paragonimus Braun, 1899 was investigated using DNA sequences from the mitochondrial cytochrome c oxidase subunit I (CO1) gene (partial) and the nuclear ribosomal DNA second internal transcribed spacer (ITS2). In the phylogenetic trees constructed, the genus Pagumogonimus is clearly not monophyletic and therefore not a natural taxon. Indeed, the type species of Pagumogonimus,P. skrjabini from China, is very closely related to Paragonimusmiyazakii from Japan. The status of Euparagonimus is less obvious. Euparagonimus cenocopiosus lies distant from other lungflukes included in the analysis. It can be placed as sister to Paragonimus in some analyses and falls within the genus in others. A recently published morphological study placed E. cenocopiosus within the genus Paragonimus and probably this is where it should remain.

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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 ◽

10.1163/156854105775142937 ◽

2005 ◽

Vol 7 (5) ◽

pp. 713-725 ◽

Cited By ~ 7

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.

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Utility of ITS2 sequence data of nuclear ribosomal DNA: Molecular evolution and phylogenetic reconstruction of Lathyrus spp.

Scientia Horticulturae ◽

10.1016/j.scienta.2015.08.030 ◽

2015 ◽

Vol 194 ◽

pp. 313-319 ◽

Cited By ~ 1

Author(s):

Sonia Marghali ◽

Imen Fadhlaoui ◽

Maroua Gharbi ◽

Nadia Zitouna ◽

Neila Trifi-Farah

Keyword(s):

Molecular Evolution ◽

Ribosomal Dna ◽

Sequence Data ◽

Phylogenetic Reconstruction ◽

Its2 Sequence ◽

Nuclear Ribosomal Dna

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Systematic Relationship of Weeping Katsura Based on Nuclear Ribosomal DNA Sequences

HortScience ◽

10.21273/hortsci.37.3.595 ◽

2002 ◽

Vol 37 (3) ◽

pp. 595-598 ◽

Cited By ~ 4

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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