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

2015 ◽  
Vol 194 ◽  
pp. 313-319 ◽  
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

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.

Synonymy of the three Villaria Rolfe species (Rubiaceae): evidence from morphological and nuclear ribosomal DNA sequence data

Acta Manilana ◽  
2010 ◽  
Vol 56 (0) ◽  
Author(s):  
GJD Alejandro ◽  
DLA Arlegui ◽  
PMO Detabali ◽  
EA Espino ◽  
EG Layson ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Ribosomal Dna ◽  
Sequence Data ◽  
Nuclear Ribosomal Dna ◽  
Dna Sequence Data ◽  
Ribosomal Dna Sequence

Molecular analysis of selected paramphistome isolates from cattle in southern Africa

2015 ◽  
Vol 90 (6) ◽  
pp. 784-788 ◽  
Author(s):  
S. Dube ◽  
M.S. Sibula ◽  
Z. Dhlamini
Keyword(s):  
Sequence Data ◽  
Animal Health ◽  
Phylogenetic Reconstruction ◽  
Morphological Characterization ◽  
Its2 Sequence ◽  
Molecular Techniques ◽  
Its2 Rdna ◽  
African Countries ◽  
Rdna Sequences ◽  
The Individual

AbstractParamphistomes are parasites of domestic and wild ruminants, the effects of which in animal health remain underestimated. Very few studies in Africa have been done using molecular techniques to resolve situations associated with taxonomical groupings and epidemiology of these parasites. In this study, the genetic variability of nine representative paramphistome isolates collected from southern African countries, namely Botswana, South Africa, Zambia and Zimbabwe, was assessed using both morphological and internal transcribed spacer 2 (ITS2) rDNA sequence data. Morphological characterization and identification were carried out using median sagittal sections of the paramphistomes. DNA of the individual paramphistomes was isolated, the ITS2 rDNA was amplified, purified and sequenced. The sequences were submitted to GenBank, which assigned them the following accession numbers: KP639631, KP639630, KP639632, KP639633, KP639634, KP639635, KP639636, KP639637 and KP639638. These sequences were used for phylogenetic analysis using MEGA 6. Morphological characterization revealed three species of paramphistomes belonging to three different sub-families: one Stephanopharynx compactus isolate, a member of the Stephanopharyngidae sub-family; one Carmyerius dollfusi isolate, a member of the Gastrothylacidae sub-family; and seven Calicophoron microbothrium isolates belonging to the Paramphistomidae sub-family. ITS2 sequence analysis using BlastN results indicated that this is the first report of S. compactus (KP639630) and C. dollfusi (KP639636). Phylogenetic reconstruction of the paramphistome isolates revealed three separate clades representing the three species. However, the clade with all the C. microbothrium isolates was the only one that was supported by a higher bootstrap value of 92%, although there was no differentiation of the isolates according to geographical locations. The low divergence values on the ITS2 sequences of the C. microbothrium isolates indicate that ITS rDNA sequences can be used as a molecular tool to infer knowledge for resolving taxonomic groupings.

Molecular systematics of subtribe Banksiinae (Banksia and Dryandra; Proteaceae) Based on cpDNA and nrDNA sequence data: Implications for taxonomy and biogeography

1998 ◽  
Vol 11 (4) ◽  
pp. 321 ◽  
Author(s):  
Austin R. Mast
Keyword(s):  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Morphological Characters ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Base Substitution ◽  
Trnl Intron ◽  
Single Root ◽  
Cladistic Analyses ◽  
Molecular Characters

Despite considerable research interest in the subtribe Banksiinae (Banksia L.f. and Dryandra R.Br.), no strongly supported phylogenetic hypothesis for the relationship between the genera exists, nor have molecular characters been sampled for phylogenetic reconstruction at any level. In this study, DNA sequence characters were sampled from chloroplast DNA (cpDNA; the trnL intron, the trnL 3′ exon, and the spacer between the trnL 3′ exon and trnF) and nuclear ribosomal DNA (nrDNA; both internal transcribed spacers) of 18 species of Banksia and five of Dryandra, with six outgroup taxa from the subfamily Grevilleoideae. The molecular characters provided the opportunity to code taxa outside of Banksia for cladistic comparison with the genus—an opportunity not previously provided by morphological characters. Cladistic analyses, using parsimony, explored the effects of various weightings of transition to transversion events and base substitution to insertion and deletion events to determine which relationships in the cladograms were robust. The trnL/trnF and ITS characters strongly supported a paraphyletic Banksia with respect to a monophyletic Dryandra. The molecular results supported a single root for Thiele and Ladiges’(1996) unrooted morphological cladogram along the branch between the Isotylis to B. fuscolutea clade and the Grandes to B. tricuspis clade. George’s (1981) subgenus Banksia and section Banksia appeared dramatically non-monophyletic. The distribution of eastern taxa at derived positions on the molecular cladograms suggested considerable cladogenesis in the the genus prior to the formation of the Nullarbor Plain during the Tertiary.

scholarly journals PCR identification of Fusarium genus based on nuclear ribosomal-DNA sequence data

2003 ◽  
Vol 2 (4) ◽  
pp. 82-85 ◽  
Author(s):  
A. Abd-Elsalam Kamel ◽  
N. Aly Ibrahim ◽  
A. Abdel-Satar Mohmed ◽  
S. Khalil Mohmed ◽  
A. Verreet Joseph
Keyword(s):  
Dna Sequence ◽  
Ribosomal Dna ◽  
Sequence Data ◽  
Nuclear Ribosomal Dna ◽  
Dna Sequence Data ◽  
Pcr Identification ◽  
Ribosomal Dna Sequence

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.

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.

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