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.

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.

scholarly journals Relationships of Nematodirus Species and Nematodirus battus Isolates (Nematoda: Trichostrongyloidea) Based on Nuclear Ribosomal DNA Sequences

2000 ◽  
Vol 86 (3) ◽  
pp. 588 ◽  
Author(s):  
Steven A. Nadler ◽  
Eric P. Hoberg ◽  
Deborah S. S. Hudspeth ◽  
Lora G. Rickard
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Nuclear Ribosomal Dna

scholarly journals Phylogenetics of Taxus Using the Internal Transcribed Spacers of Nuclear Ribosomal DNA and Plastid trnL-F Regions

Horticulturae ◽  
2020 ◽  
Vol 6 (1) ◽  
pp. 19
Author(s):  
Patricia Coughlan ◽  
James C. Carolan ◽  
Ingrid L. I. Hook ◽  
Lisa Kilmartin ◽  
Trevor R. Hodkinson
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Intergenic Spacer ◽  
Its Region ◽  
Single Species ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Trnl Intron ◽  
Group Status ◽  
Haplotype Networks

Taxus is a genus of trees and shrubs with high value in horticulture and medicine as a source of the anticancer drug paclitaxel. The taxonomy of the group is complex due to the lack of diagnostic morphological characters and the high degree of similarity among species. Taxus has a wide global geographic distribution and some taxonomists recognize only a single species with geographically defined subgroups, whereas others have described several species. To address these differences in taxonomic circumscription, phylogenetic analyses were conducted on DNA sequences using Maximum Likelihood, Bayesian Inference and TCS haplotype networks on single and combined gene regions obtained for the nuclear ribosomal ITS region and the plastid trnL intron and trnL-F intergenic spacer. Evidence is presented for the sister group status of Pseudotaxus to Taxus and the inclusion of Amentotaxus, Austrotaxus, Cephalotaxus and Torreya within Taxaceae. Results are consistent with the taxonomic recognition of nine species: T. baccata, T. brevifolia, T. canadensis, T. cuspidata, T. floridana, T. fuana, T. globosa, T. sumatrana and T. wallichiana, but evidence is found for less species distinction and considerable reticulation within the T. baccata, T. canadensis and T. cuspidata group. We compare the results to known taxonomy, biogeography, present new leaf anatomical data and discuss the origins of the hybrids T. ×media and T. ×hunnewelliana.

Phylogenetics of Helotiales and Rhytismatales Based on Partial Small Subunit Nuclear Ribosomal DNA Sequences

Mycologia ◽  
2001 ◽  
Vol 93 (5) ◽  
pp. 915 ◽  
Author(s):  
David S. Gernandt ◽  
Jamie L. Platt ◽  
Jeffrey K. Stone ◽  
Joseph W. Spatafora ◽  
Arne Holst-Jensen ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Small Subunit ◽  
Nuclear Ribosomal Dna

Phylogeny of the Genus Omphalotus Based on Nuclear Ribosomal DNA-Sequences

Mycologia ◽  
2004 ◽  
Vol 96 (6) ◽  
pp. 1253 ◽  
Author(s):  
Martin Kirchmair ◽  
Sandra Morandell ◽  
Daniela Stolz ◽  
Reinhold Poder ◽  
Christian Sturmbauer
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Nuclear Ribosomal Dna

Characterization of Trichuris trichiura from humans and T. suis from pigs in China using internal transcribed spacers of nuclear ribosomal DNA

2012 ◽  
Vol 88 (1) ◽  
pp. 64-68 ◽  
Author(s):  
G.H. Liu ◽  
W. Zhou ◽  
A.J. Nisbet ◽  
M.J. Xu ◽  
D.H. Zhou ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Sequence Variation ◽  
Animal Health ◽  
Trichuris Trichiura ◽  
Its Rdna ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Economic Losses ◽  
Molecular Characteristics ◽  
Rdna Sequences

AbstractTrichuris trichiura and Trichuris suis parasitize (at the adult stage) the caeca of humans and pigs, respectively, causing trichuriasis. Despite these parasites being of human and animal health significance, causing considerable socio-economic losses globally, little is known of the molecular characteristics of T. trichiura and T. suis from China. In the present study, the entire first and second internal transcribed spacer (ITS-1 and ITS-2) regions of nuclear ribosomal DNA (rDNA) of T. trichiura and T. suis from China were amplified by polymerase chain reaction (PCR), the representative amplicons were cloned and sequenced, and sequence variation in the ITS rDNA was examined. The ITS rDNA sequences for the T. trichiura and T. suis samples were 1222–1267 bp and 1339–1353 bp in length, respectively. Sequence analysis revealed that the ITS-1, 5.8S and ITS-2 rDNAs of both whipworms were 600–627 bp and 655–661 bp, 154 bp, and 468–486 bp and 530–538 bp in size, respectively. Sequence variation in ITS rDNA within and among T. trichiura and T. suis was examined. Excluding nucleotide variations in the simple sequence repeats, the intra-species sequence variation in the ITS-1 was 0.2–1.7% within T. trichiura, and 0–1.5% within T. suis. For ITS-2 rDNA, the intra-species sequence variation was 0–1.3% within T. trichiura and 0.2–1.7% within T. suis. The inter-species sequence differences between the two whipworms were 60.7–65.3% for ITS-1 and 59.3–61.5% for ITS-2. These results demonstrated that the ITS rDNA sequences provide additional genetic markers for the characterization and differentiation of the two whipworms. These data should be useful for studying the epidemiology and population genetics of T. trichiura and T. suis, as well as for the diagnosis of trichuriasis in humans and pigs.

Towards a new classification of tribe Stachydeae (Lamiaceae): naming clades using molecular evidence

2019 ◽  
Vol 190 (4) ◽  
pp. 345-358 ◽  
Author(s):  
Yasaman Salmaki ◽  
Günther Heubl ◽  
Maximilian Weigend
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Nuclear Ribosomal Dna ◽  
Molecular Evidence ◽  
New Classification ◽  
Formal Classification ◽  
Phylogenetic Nomenclature

AbstractStachydeae, comprising c. 470 species, are one of the most diverse and taxonomically puzzling groups in Lamioideae. In the present study, the phylogenetic relationships in the Eurystachys clade (a phylogenetic name for all genera attributed to Stachydeae except Melittis) were reconstructed utilizing nuclear ribosomal DNA sequences (nrETS, 5S-NTS) from 148 accessions in 12 genera. Our phylogenetic results recovered Stachys as paraphyletic with numerous traditionally recognized genera nested in it. A broadly defined Eurystachys clade, however, was monophyletic. Unlike previous studies, the present study was able to resolve the group into 12 well-supported clades, named here as (1) Eriostomum, (2) Stachys, (3) Prasium, (4) Setifolia, (5) Distantes, (6) Burgsdorfia, (7) Hesiodia, (8) Empedoclia, (9) Sideritis, (10) Marrubiastrum, (11) Swainsoniana and (12) Olisia. These 12 clades were formally named in a phylogenetic nomenclature for the Eurystachys clade. Several infrageneric units were retrieved as monophyletic, namely Sideritis sections Burgsdorfia, Empedoclia and Hesiodia, Sideritis subgenus Marrubiastrum and Stachys sections Eriostomum (including Stachys section Mucronata) and Setifolia. The findings of this study also provide the basis for a future formal classification, with two options: (1) splitting of the Eurystachys clade into 12 monophyletic genera, all of them based on pre-existing genus names and redefined to encompass additional taxa, but without clear morphological apomorphies; or (2) lumping of all segregates into a broadly defined Stachys, including widely recognized and well-defined segregates such as Prasium and Sideritis.

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