Reviewing lymnaeid vectors of fascioliasis by ribosomal DNA sequence analyses

2005 ◽  
Vol 79 (3) ◽  
pp. 257-267 ◽  
Author(s):  
M.D. Bargues ◽  
S. Mas-Coma
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Fasciola Hepatica ◽  
Rdna Sequence ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Nuclear Rdna ◽  
Natural Classification ◽  
The Family

AbstractSnails of the family Lymnaeidae are of great parasitological importance due to the numerous helminth species they transmit, mainly trematodiases (such as fascioliasis) of considerable medical and veterinary impact. The present knowledge of the genetics and host–parasite relationships of this gastropod group is far from adequate. Fascioliasis is caused by two species, Fasciola hepatica and F. gigantica, which, as in the case of other trematodes, show a marked snail host specificity. Many lymnaeid species involved in fascioliasis transmission still show a confused systematic-taxonomic status. The need for tools to distinguish and characterize species and populations of lymnaeids is evident and the present review concerns new molecular tools developed in recent years using nuclear ribosomal DNA sequences. The small subunit or 18S gene and the internal transcribed spacers ITS-2 and ITS-1 are analysed and evaluated as markers for taxon differentiation and relationships within the Lymnaeidae from genus and species levels to subspecies and population levels. rDNA sequence differences and genetic distances, and their value for reconstructing phylogenetic trees using different methods are considered. Nuclear rDNA sequences are appropriate tools on which to base a review of the systematics and taxonomy of the family Lymnaeidae, without excluding other valuable snail characteristics already available. A reconstruction of the lymnaeid system towards a more natural classification will undoubtedly be helpful in understanding parasite transmission and epidemiological features as well the dispersion of an emerging-reemerging disease such as fascioliasis. Nomenclature for nuclear rDNA genotyping in lymnaeids includes the main rDNA sequence regions able to furnish important information on interspecific differentiation and grouping as well as intraspecific variability of lymnaeid species. The composite haplotype code includes the rDNA markers arranged in order according to their well-known usefulness, in its turn related to their respective, more or less rapid evolutionary ratios, to distinguish between different taxonomic levels, from supraspecific taxa to the species level and up to the population level.

Towards a molecular phylogeny for the lichen family Pannariaceae (Lecanorales, Ascomycota)

2002 ◽  
Vol 80 (6) ◽  
pp. 625-634 ◽  
Author(s):  
Stefan Ekman ◽  
Per Magnus Jørgensen
Keyword(s):  
Monte Carlo ◽  
Markov Chain ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Sampling Procedure ◽  
Nuclear Ribosomal Dna ◽  
Dna Phylogeny ◽  
Green Algal ◽  
The Family ◽  
Optimal Trees

The phylogeny of the family Pannariaceae (Lecanorales, lichenized Ascomycota) was investigated using ITS1–5.8S–ITS2 nuclear ribosomal DNA sequences representing 21 species. Phylogenetic estimations were performed using parsimony and a Bayesian Markov chain Monte Carlo (MCMC) tree sampling procedure. Several phylogenetic null hypotheses were tested, also using MCMC. The results indicate that Pannariaceae, as currently treated, is polyphyletic and that Degelia sect. Amphiloma, Fuscopannaria subg. Micropannaria, and Moelleropsis s.str. do not belong in the family. The inclusion of Parmeliella in the Pannariaceae could not be rejected, although it falls outside the family in the optimal trees. Psoroma, Santessoniella, Protopannaria, Fuscopannaria subg. Fuscopannaria, Moelleropsis s.str., and Pannaria unequivocally belong to the family. The Pannaria sphinctrina group belongs in Pannaria despite its green-algal photobiont. Protopannaria pezizoides is not, as sometimes treated, a Pannaria, although a relationship with Psoroma could not be ruled out. In the optimal trees, Moelleropsis s.str. is nested inside Fuscopannaria subg. Fuscopannaria and Santessoniella inside Psoroma, but null hypotheses of their independence from these genera could not be rejected. Pannaria cannot be divided into two monophyletic subgenera, Pannaria and Chryopannaria. The photobiont has changed twice or three times and the ascus apex and hymenial amyloidity twice within the Pannariaceae.Key words: lichens, Pannariaceae, ITS, ribosomal DNA, phylogeny, MCMC.

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 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 Hemicriconemoides mangiferae and H. litchi (Nematoda: Criconematina) based on morphometrics and nuclear ribosomal DNA sequences

Nematology ◽  
2011 ◽  
Vol 13 (2) ◽  
pp. 165-175 ◽  
Author(s):  
Ruey-Shyang Chen ◽  
Hui-Fang Ni ◽  
Tung-Tsuan Tsay ◽  
Diann-Yih Chen
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Sequence Divergence ◽  
Its Region ◽  
Rdna Sequence ◽  
Nuclear Ribosomal Dna ◽  
Molecular Characteristics ◽  
Species Differentiation ◽  
Sequence Information ◽  
Lateral Field

Abstract Hemicriconemoides mangiferae and H. litchi, which have been considered as junior synonyms of H. strictathecatus, are morphologically similar, making identification difficult. In the present study, six populations of Hemicriconemoides spp. were collected from mango and litchi in Taiwan and were differentiated based on morphometrics and molecular characteristics. By comparing morphometric data from females and males, three populations collected from mango were identified as H. mangiferae and another three populations from litchi were identified as H. litchi. According to SEM, both of the H. mangiferae and H. litchi males had an areolated lateral field with four incisures; caudal alae were not found. The internal transcribed spacer (ITS) sequences of ribosomal DNA (rDNA) from these nematode populations were sequenced and aligned. The sequence identity of the ITS region was 89-95% between H. mangiferae and H. litchi populations, suggesting rDNA sequence divergence could be a taxonomic aid for species differentiation. Since H. mangiferae and H. litchi are closely related to H. strictathecatus, more rDNA sequence information could be valuable to deal with molecular phylogenetic relationships of these species in depth.

Phylogenetic relationships in Dermocybe and related Cortinarius taxa based on nuclear ribosomal DNA internal transcribed spacers

1997 ◽  
Vol 75 (4) ◽  
pp. 519-532 ◽  
Author(s):  
Y. J. Liu ◽  
S. O. Rogers ◽  
Y. J. Liu ◽  
J. F. Ammirati
Keyword(s):  
Ribosomal Dna ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Molecular Data ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Herbarium Specimens ◽  
Data Reorganization ◽  
Taxonomic Groups

The genus Cortinarius Fr. (Cortinariaceae, Agaricales) is divided into four or more subgenera. Dermocybe (Fr.) Sacc. has been recognized as either a subgenus of Cortinarius or a separate genus, distinguished in part by the presence of various anthraquinonic pigments. Nucleotide sequences of ribosomal DNA 5.8S and internal transcribed spacers were used to investigate the phylogenetic relationships among species of Dermocybe and selected taxa from subgenera of Cortinarius. Sequence data from 47 herbarium specimens representing 31 taxa (28 species plus 3 varieties) of Dermocybe and Cortinarius were analyzed using parsimony, maximum likelihood, and neighbor joining. In general, molecular data support the morphological groupings of the taxa, although they more closely correspond to biochemical (anthraquinone and other) analyses. Phylogenetic trees showed that, while the sections Dermocybe and Malicoriae are monophyletic, and the concolorous or almost concolorous red species (section Sanguineae, such as D. sanguinea and relatives) together formed a coherent clade, the subgenus Dermocybe sensu lato itself is polyphyletic. Cortinarius californicus clusters with taxa in Cortinarius, subgenus Telamonia, section Armillati. Dermocybe olivaceopicta is more closely related to other subgenera of Cortinarius than to Dermocybe. Within the genus Cortinarius, certain of the subgenera may actually represent coherent genera. Of the subgenera examined, Telamonia, Phlegmacium, and possibly Sericeocybe appear to represent well defined taxonomic groupings. However, current assignments of taxa within Leprocybe and Myxacium were inconsistent with the molecular data. Reorganization of some taxa and taxonomic groups is suggested. Key words: Dermocybe, Cortinarius, molecular phylogeny, rDNA, ITS1, ITS2.

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.

Phylogenetic relationships of 10 grass species: an assessment of phylogenetic utility of the internal transcribed spacer region in nuclear ribosomal DNA in monocots

Genome ◽  
1994 ◽  
Vol 37 (1) ◽  
pp. 112-120 ◽  
Author(s):  
C. Hsiao ◽  
N. J. Chatterton ◽  
K. H. Asay ◽  
K. B. Jensen
Keyword(s):  
Oryza Sativa ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Brachypodium Distachyon ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Grass Species ◽  
Its Sequence ◽  
Internal Transcribed Spacer Region ◽  
Distance Method

Entire sequences of the internal transcribed spacers (ITSs) and 5.8S subunit of nuclear ribosomal DNA (nrDNA) were obtained from nine grass species by direct double-stranded sequencing of polymerase chain reaction (PCR) amplified DNA fragments. These sequences from subfamily Pooideae (Triticum aestivum, Crithodium monococcum, Sitopsis speltoides, Hordeum vulgare, Secale montanum, Avena longiglumis, Bromus inermis, Brachypodium distachyon) and subfamily Panicoideae (Sorghum bicolor) together with published ITS sequence of rice (Oryza sativa, Bambusoideae) were analyzed using Wagner parsimony (PAUP) and the neighbor-joining distance method to assess the phylogenetic utility of ITS sequences at various taxonomic levels. Among the aligned sequences that ranged from 588 to 603 nucleotides in length, 118 of 269 variable sites contained potential phylogenetic information. A member of Bromus, B. inermis, was the sister taxon to the Triticeae species. Brachypodium was more distantly related to Triticeae than was Bromus or Avena. These data, with Oryza sativa as the outgroup, indicate monophyly of the Pooideae species and of the members of the tribe Triticeae within Pooideae. Phylogenetic trees of the 10 grass species generated from the ITS sequence data were in general agreement with phylogenies based on molecular data from ribosomal RNA (rRNA) and chloroplast DNA (cpDNA) of similar grass taxa. This study reaffirms that sequences of the ITS region are useful for phylogenetic inference among closely related monocot species.Key words: Poaceae, Pooideae, Triticeae, DNA sequences, molecular phylogeny.

Sign in / Sign up

Export Citation Format

Share Document