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.

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

1999 ◽  
Vol 73 (4) ◽  
pp. 295-299 ◽  
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.

Characterization of the complete nuclear ribosomal DNA sequences of Eurytrema pancreaticum

2017 ◽  
Vol 92 (4) ◽  
pp. 484-490 ◽  
Author(s):  
X. Su ◽  
Y. Zhang ◽  
X. Zheng ◽  
X.X. Wang ◽  
Y. Li ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
18S Rdna ◽  
Internal Transcribed Spacer ◽  
28S Rdna ◽  
Nuclear Ribosomal Dna ◽  
Economic Losses ◽  
Length Variation ◽  
5.8S Rdna ◽  
Rdna Sequences

AbstractEurytrema pancreaticum is one of the most common trematodes of cattle and sheep, and also infects humans occasionally, causing great economic losses and medical costs. In this study, the sequences of the complete nuclear ribosomal DNA (rDNA) repeat units of five E. pancreaticum individuals were determined for the first time. They were 8306–8310 bp in length, including the small subunit (18S) rDNA, internal transcribed spacer 1 (ITS1), 5.8S rDNA, internal transcribed spacer 2 (ITS2), large subunit (28S) rDNA and intergenic spacer (IGS). There were no length variations in any of the investigated 18S (1996 bp), ITS1 (1103 bp), 5.8S (160 bp), ITS2 (231 bp) or 28S (3669 bp) rDNA sequences, whereas the IGS rDNA sequences of E. pancreaticum had a 4-bp length variation, ranging from 1147 to 1151 bp. The intraspecific variations within E. pancreaticum were 0–0.2% for 18S rDNA, 0–0.5% for ITS1, 0% for 5.8S rDNA and ITS2, 0–0.2% for 28S rDNA and 2.9–20.2% for IGS. There were nine types of repeat sequences in ITS1, two types in 28S rDNA, but none in IGS. A phylogenetic analysis based on the 18S rDNA sequences classified E. pancreaticum in the family Dicrocoeliidae of Plagiorchiata, closely related to the suborder Opisthorchiata. These results provide useful information for the further study of Dicrocoeliidae trematodes.

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.

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.

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