Phylogenetic relationships of the Hamamelidaceae inferred from sequences of internal transcribed spacers (ITS) of nuclear ribosomal DNA

1999 ◽  
Vol 86 (7) ◽  
pp. 1027-1037 ◽  
Author(s):  
Jianhua Li ◽  
A. Linn Bogle ◽  
Anita S. Klein
Keyword(s):  
Ribosomal Dna ◽  
Phylogenetic Relationships ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna

Phylogenetic relationships of three tribes of cloacinine nematodes (Strongylida: Chabertiidae) from macropodid marsupials

2018 ◽  
Vol 93 (04) ◽  
pp. 486-493 ◽  
Author(s):  
N.B. Chilton ◽  
F. Huby-Chilton ◽  
A. Koehler ◽  
R.B. Gasser ◽  
I. Beveridge
Keyword(s):  
Ribosomal Dna ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Host Genus ◽  
Single Host

AbstractThe phylogenetic relationships of 42 species of cloacinine nematodes belonging to three tribes (Coronostrongylinea, Macropostrongylinea and Zoniolaiminea) were examined based on sequence data of the first and second internal transcribed spacers (ITS-1 and ITS-2) of the nuclear ribosomal DNA. All nematodes examined are parasites of Australian macropodid marsupials. None of the three nematode tribes was monophyletic. Paraphyly was also encountered in three genera: Papillostrongylus, Monilonema and Wallabinema. Species within the genus Thallostonema were limited to a single host genus (i.e. Thylogale), whereas species within the five principal genera (Coronostrongylus, Macropostrongylus, Popovastrongylus, Wallabinema and Zoniolaimus) were found to occur in multiple host genera. Potential modes of evolution among these nematodes are discussed.

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.

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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