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.

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.

The status of Thamnobryum maderense (Kindb.) Hedenäs and T. fernandesii C. Sergio

2006 ◽  
Vol 28 (1) ◽  
pp. 149-154
Author(s):  
Jan-Peter Frahm ◽  
Marko Sabovljevic
Keyword(s):  
Ribosomal Dna ◽  
Tree Species ◽  
Internal Transcribed Spacer ◽  
Morphological Study ◽  
Full Rank ◽  
Molecular Methods ◽  
Nuclear Ribosomal Dna ◽  
Morphological Evidence ◽  
Molecular Studies ◽  
The Status

Th. maderense was regarded either as synonymous with Th. alopecurum, as a variety of the latter and also as a good species. A morphological study revealed that it clearly distinguished from Th. alopecurum by four ranked instead of eight-ranked leaves and thus deserves full rank of a species. Th. fernandesii has eight-ranked leaves and is therefore more related to Th. alopecurum than to Th. maderense. A comparison of the sequences of the Internal Transcribed Spacer of the nuclear ribosomal DNA region in the tree species supports the morphological evidence. Previous molecular studies of Th. maderense (showing almost no differences to Th. alopecurum) were based on misidentifications. The status of Th. fernandesii is not clear. The multistratose leaves with broad costa indicate that it is a mutant as proved in several other cases by molecular methods. It differs, however, genetically too much from Th. alopecurum that it cannot be interpreted as a mutant of the latter.

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.

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.

On the origins of the tetraploid Bromus species (section Bromus, Poaceae): insights from internal transcribed spacer sequences of nuclear ribosomal DNA

Genome ◽  
1997 ◽  
Vol 40 (5) ◽  
pp. 730-743 ◽  
Author(s):  
Malika L. Ainouche ◽  
Randall J. Bayer
Keyword(s):  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Trees ◽  
Direct Sequencing ◽  
Diploid Species ◽  
Pcr Amplification ◽  
Nuclear Ribosomal Dna ◽  
Species Introduction ◽  
Bromus Hordeaceus ◽  
Allotetraploid Species

The internal transcribed spacer (ITS) region of nuclear ribosomal DNA from 22 diploid and tetraploid annual Bromus species of section Bromus (Poaceae) and three species belonging to other Bromus sections, Bromus catharticus (section Ceratochloa), Bromus anomalus (section Pnigma), and Bromus sterilis (section Genea), were investigated by PCR amplification and direct sequencing. The length of the ITS-1 region varied from 215 to 218 bp, and that of the ITS-2 region from 215 to 216 bp, in the species analyzed. ITS-1 was more variable and provided more informative sites (49) than ITS-2 (32). No variation was encountered within species. In pairwise comparison among species of section Bromus, sequence divergence ranged from 0.0 to 8.0% for the combined ITS-1 and ITS-2 regions. Parsimony analysis using Avena longiglumis and Hordeum vulgare as outgroups resulted in well-resolved phylogenetic trees and showed that section Bromus is monophyletic according to the species analyzed outside of the section. The analysis clarified the phylogenetic relationships among monogenomic (diploid) species. Introduction of the allotetraploid species did not change the general topology of the trees obtained using only the diploid species. Although some tetraploid–diploid species relationships will have to be clarified with faster evolving markers, the ITS sequences are shown to be useful for assessing evolutionary relationships among closely related Bromus species, as well as for clarifying taxonomic problems in previously controversial cases (e.g., Bromus alopecuros and Bromus caroli–henrici). New hypotheses are proposed concerning the origin of several allotetraploid species. For example, it is shown that the tetraploid Bromus hordeaceus diverged earlier than all other species of section Bromus, excluding the diploid B. caroli–henrici, which is found to be basal in this group. The tetraploid Bromus arenarius, which was considered a hybrid between sections Bromus and Genea, and the tetraploid Bromus adoensis are sister taxa within section Bromus; they belong in a weakly differentiated clade with the diploids Bromus brachystachys, Bromus japonicus, Bromus squarrosus, Bromus arvensis, and Bromus intermedius.Key words: Bromus, allopolyploidy, ITS, ribosomal DNA, phylogeny.

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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