Phylogenetic Analysis of the Lichen Family Umbilicariaceae based on nuclear ITS1 and ITS2 rDNA Sequences

1999 ◽  
Vol 31 (5) ◽  
pp. 477-489 ◽  
Author(s):  
Natalia V. Ivanova ◽  
Paula T. Depriest ◽  
Vera K. Bobrova ◽  
Alexey V. Troitsky
Keyword(s):  
Phylogenetic Analyses ◽  
Current Treatment ◽  
Taxon Sampling ◽  
Its2 Rdna ◽  
Separate Genus ◽  
Rdna Sequences ◽  
Representative Species ◽  
Phylogenetic Hypotheses ◽  
Its1 And Its2 Rdna ◽  
Its1 And Its2

AbstractThe lichen family Umbilicariaceae is accepted by most lichenologists as consisting of two genera, Lasallia and Umbilicaria. The monophyly of these two genera was examined by phylogenetic analyses of nucleotide sequences of ITS 1 and ITS2 rDNA. Sequences of these regions from three Lasallia and 17 Umbilicaria species were aligned to those of seven representatives of the outgroup taxa including Eurotiales, Onygenales and Caliciales (Mycocaliciaceae) and subjected to maximum parsimony, maximum likelihood and neighbour-joining analyses. The resulting phylogenetic hypotheses supported the monophyly of the representative species of Lasallia. However, the species of Umbilicaria did not form a monophyletic sistergroup to Lasallia due to the basal placement of other Umbilicaria species in some analyses. Based on these analyses, if Lasallia is recognized as a separate genus then Umbilicaria appears to be paraphyletic. Although further taxon sampling is required to resolve the monophyly of Umbilicaria, for the present we recommend retaining the current treatment of Lasallia as separate from Umbilicaria.

Phylogenetic Analysis of the Lichen Family Umbilicariaceae based on nuclear ITS1 and ITS2 rDNA Sequences

1999 ◽  
Vol 31 (05) ◽  
pp. 477 ◽  
Author(s):  
Natalia V. Ivanova ◽  
Paula T. Depriest ◽  
Vera K. Bobrova ◽  
Alexey V. Troitsky
Keyword(s):  
Phylogenetic Analysis ◽  
Its2 Rdna ◽  
Rdna Sequences ◽  
Its1 And Its2 Rdna ◽  
Its1 And Its2

First records of Knufia marmoricola from limestone outcrops in the Wyżyna Krakowsko-Częstochowska Upland, Poland

Phytotaxa ◽  
2018 ◽  
Vol 357 (2) ◽  
pp. 94 ◽  
Author(s):  
MAGDALENA OWCZAREK-KOŚCIELNIAK ◽  
KATJA STERFLINGER
Keyword(s):  
Mediterranean Basin ◽  
Phylogenetic Analyses ◽  
High Variability ◽  
Potato Dextrose Agar ◽  
Malt Extract ◽  
Its2 Rdna ◽  
Rdna Sequences ◽  
Microcolonial Fungi ◽  
Molecular Phylogenetic ◽  
The Mediterranean Basin

Studies on microcolonial fungi (MCF) inhabiting limestone formations in the Wyżyna Krakowsko-Częstochowska Upland (Poland) resulted in isolation of Knufia marmoricola. This is the first report of this species in Poland, which was previously known from the Mediterranean basin. Morphological analyses have shown a high variability dependent on used mycological media. Malt extract agar (MEA) proved to be the most suitable medium for morphological observations. Cultivation on potato dextrose agar (PDA) and dichloran rose-Bengal with chloramphenicol medium (DRBC) resulted in growth of mycelium lacking in repetitive diagnostical features. Growth on a synthetic nutrient-poor agar (SNA) medium resulted in flattening of the colonies, decreased melanization and reduction of the colony density. Molecular phylogenetic analyses, based on ITS1­-5.8S-­ITS2 rDNA sequences, confirmed assignment of Polish isolates to Knufia marmoricola. Nomenclatural clarification of Knufia petricola is presented.

scholarly journals Molecular phylogenetic analyses of Drakaeinae: Diurideae (Orchidaceae) based on DNA sequences of the internal transcribed spacer region

2014 ◽  
Vol 27 (1) ◽  
pp. 3 ◽  
Author(s):  
Joseph T. Miller ◽  
Mark A. Clements
Keyword(s):  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Internal Transcribed Spacer Region ◽  
Orchid Species ◽  
Weak Support ◽  
Separate Genus ◽  
Rdna Sequences ◽  
Molecular Phylogenetic ◽  
Taxonomic Summary

Results of the analysis of rDNA sequences based on 55 collections representative of 32 Drakaeinae orchid species and outgroups supported the monophyly of the subtribe, with weak support for the inclusion of Spiculaea, and revealed six strongly supported monophyletic, well defined morphological groups. Caleana is monophyletic. Chiloglottis s.lat. is monophyletic when Simpliglottis and Myrmechila are included. Our results also suggested that the segregate genus Phoringopsis is better treated as part of Arthrochilus.There is sufficient molecular and morphological support for recognition of the leafless, mycroheterotrophic Thynninorchis to be maintained as a separate genus. A taxonomic summary is provided, including reassignment of taxa at generic ranks and new combinations for Caleana alcockii (Hopper & A.P.Br.) M.A.Clem., Caleana brockmanii (Hopper & A.P.Br.) M.A.Clem., Caleana disjuncta (D.L.Jones) M.A.Clem., Caleana dixonii (Hopper & A.P.Br.) M.A.Clem., Caleana gracilicordata (Hopper & A.P.Br.) M.A.Clem., Caleana granitica (Hopper & A.P.Br.) M.A.Clem., Caleana hortiorum (Hopper & A.P.Br.) M.A.Clem., Caleana lyonsii (Hopper & A.P.Br.) M.A.Clem., Caleana parvula (Hopper & A.P.Br.) M.A.Clem., Caleana terminalis (Hopper & A.P.Br.) M.A.Clem. and Caleana triens (Hopper & A.P.Br.) M.A.Clem.

scholarly journals Comparison of the ITS1 and ITS2 rDNA in Eimeria callospermophili (Apicomplexa: Eimeriidae) from Sciurid Rodents

2011 ◽  
Vol 97 (2) ◽  
pp. 305-310 ◽  
Author(s):  
Dagmara Motriuk-Smith ◽  
R. Scott Seville ◽  
Leah Quealy ◽  
Clinton E. Oliver
Keyword(s):  
Its2 Rdna ◽  
Its1 And Its2 Rdna ◽  
Its1 And Its2

Comparison of ITS1 and ITS2 rDNA in 454 sequencing of hyperdiverse fungal communities

2013 ◽  
Vol 6 (1) ◽  
pp. 102-109 ◽  
Author(s):  
Anna L. Bazzicalupo ◽  
Miklós Bálint ◽  
Imke Schmitt
Keyword(s):  
454 Sequencing ◽  
Fungal Communities ◽  
Its2 Rdna ◽  
Its1 And Its2 Rdna ◽  
Its1 And Its2

Morphological and molecular characterisation of Longidorus pinus sp. n. (Nematoda: Longidoridae) from China and a key to known species of Longidorus in China

Nematology ◽  
2018 ◽  
Vol 20 (7) ◽  
pp. 617-639 ◽  
Author(s):  
Yumei Xu ◽  
Weimin Ye ◽  
Jianming Wang ◽  
Zengqi Zhao
Keyword(s):  
Phylogenetic Analyses ◽  
Geographic Origin ◽  
Morphological Characters ◽  
Rdna Sequences ◽  
Molecular Phylogenetic ◽  
Stage Juvenile ◽  
Juvenile Stages ◽  
Amphidial Fovea ◽  
Guide Ring ◽  
Its1 And Its2 Rdna

Summary Longidorus pinus sp. n. from China is characterised by females 3.3-4.9 mm long; lip region 8-12 μm diam., distinctly offset by a constriction; amphidial fovea pocket-shaped without basal lobes; a short odontostyle (67-81 μm); anteriorly located guide ring (30-38 μm); and short and conoid tail (31-40 μm long, c = 84-138, c′ = 1.2-1.9), with one or two pairs of caudal pores on each side. Males were not found. Three developmental juvenile stages were identified, the first-stage juvenile with conoid tail (c′ = 2.4-2.9). The polytomous key codes for the new species are: A2(3), B1, C23, D4, E1, F2, G23, H23, I1, J2, K6. Molecular phylogenetic analyses based on SSU, D2-D3 of LSU, ITS1 and ITS2 rDNA sequences indicate that L. pinus sp. n. is closely related to L. hangzhouensis, L. asiaticus, and L. camelliae, all of which apparently share a common Asiatic geographic origin. In addition, a key for identification of Longidorus found in China, based on morphological characters of both female and first-stage juvenile, is provided.

scholarly journals Molecular phylogenetic analyses of tissue coccidia (sarcocystidae; apicomplexa) based on nuclear 18s RDNA and mitochondrial COI sequences confirms the paraphyly of the genus Hammondia

2016 ◽  
Vol 2 ◽  
Author(s):  
MOSUN E. OGEDENGBE ◽  
JOSEPH D. OGEDENGBE ◽  
JULIA C. WHALE ◽  
KRISTIN ELLIOT ◽  
MARCO A. JUÁREZ-ESTRADA ◽  
...  
Keyword(s):  
18S Rdna ◽  
Neospora Caninum ◽  
Phylogenetic Analyses ◽  
Mitochondrial Coi ◽  
Rdna Sequences ◽  
Molecular Phylogenetic ◽  
18S Rdna Sequences ◽  
Phylogenetic Hypotheses ◽  
Coi Sequences ◽  
Sarcocystis Rileyi

SUMMARYPartial mitochondrial cytochromecoxidase subunit I (mt COI) sequences were generated from:Toxoplasma gondii(strains CTG, GTI, MAS, ME49, PTG, TgCatBr5, TgCat, Br64, TgCgCal, TgToucan);Neospora caninum(Strain NC1);Hammondia hammondi(Strain H.H–20);H. heydorni; H. cf.triffittae; Cystoisospora felis; C. suis; C. canis; C. rivolta; C. cf.ohioensis; Caryospora bigenetica; Sarcocystis rileyi; andS. neurona. Nuclear 18S rDNA sequences were generated forH. heydorni, H. hammondi, C. suis, C. canis, C. felis, C. rivolta, C. cf.ohioensis, S. neurona, andS. rileyi. Aligned, concatenated 18S rDNA and COI sequences were Bayesian analysed using partitioned nucleotide substitution models [HKY + I + G for 18S; GTR + I + G codon (code = metmt) for COI]. Phylogenetic hypotheses supported a monophyletic Sarcocystidae and its subfamilie with two major clades within the Toxoplasmatinae: (1) a monophyletic clade ofCystoisosporaspp. withNephroisospora eptesici; and (2) a clade ofToxoplasma, NeosporaandHammondia. Within the latter,Hammondiawas shown to be paraphyletic;H. heydorniandH. triffittaewere monophyletic withN. caninum[canine definitive hosts (DHs)], whereasH. hammondiwas monophyletic withT. gondii(feline DHs). A new genus is erected to resolve the paraphyly of the genusHammondiaconfirmed using mt COI and combined 18S/COI sequence datasets.

Sequence variability in internal transcribed spacers of nuclear ribosomal DNA among isolates of the oxyurid nematodes Syphacia obvelata and Aspiculuris tetraptera from mice reared in laboratories in China

2015 ◽  
Vol 90 (1) ◽  
pp. 81-85 ◽  
Author(s):  
J.H. Qiu ◽  
Y. Lou ◽  
Y. Zhang ◽  
Q.C. Chang ◽  
Z.X. Liu ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Its2 Rdna ◽  
Sequence Variability ◽  
Rdna Sequences ◽  
Syphacia Muris ◽  
Syphacia Obvelata ◽  
Aspiculuris Tetraptera ◽  
Its1 And Its2

AbstractThis study examined sequence variability in internal transcribed spacers (ITS) of nuclear ribosomal DNA among Syphacia obvelata and Aspiculuris tetraptera isolates from laboratory mice from different geographical locations in China. ITS1, 5.8S and ITS2 rDNA were amplified separately from adult S. obvelata and A. tetraptera individuals by polymerase chain reaction (PCR), and the amplicons were subjected to sequencing from both directions. The lengths of the sequences of ITS1, 5.8S and ITS2 rDNA from both nematodes were 314 bp and 456 bp, 157 bp, and 273 bp and 419 bp, respectively. The intraspecific sequence variations in S. obvelata ITS1 were 0–0.3%. For A. tetraptera they were 0–0.7% in ITS1 and 0–1.0% in ITS2. However, the interspecific sequence differences among members of the infraorder Oxyuridomorpha were significantly higher, being 54.0–65.5% for ITS1 and 55.3–64.1% for ITS2. Phylogenetic analysis based on the combined partial sequences of ITS1 and ITS2 using three inference methods – Bayesian inference, maximum likelihood and maximum parsimony – revealed that all the S. obvelata and A. tetraptera samples formed independent monophyletic groups. Syphacia obvelata was closer to Syphacia muris than to A. tetraptera, consistent with morphological classification. These results demonstrate that ITS1 and ITS2 rDNA sequences are useful markers for population genetic studies of oxyurid nematodes.

Generalized structure and evolution of ITS1 and ITS2 rDNA in black flies (Diptera: Simuliidae)

2009 ◽  
Vol 53 (3) ◽  
pp. 749-757 ◽  
Author(s):  
Bernard LaRue ◽  
Christine Gaudreau ◽  
Hubert O. Bagre ◽  
Guy Charpentier
Keyword(s):  
Black Flies ◽  
Its2 Rdna ◽  
Its1 And Its2 Rdna ◽  
Its1 And Its2
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