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

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.

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Molecular phylogenetic relationships inAveneae (Poaceae) species and other grasses as inferred from ITS1 and ITS2 rDNA sequences

Plant Systematics and Evolution ◽

10.1007/bf00985203 ◽

1998 ◽

Vol 213 (3-4) ◽

pp. 233-250 ◽

Cited By ~ 44

Author(s):

B. Grebenstein ◽

M. R�ser ◽

W. Sauer ◽

V. Hemleben

Keyword(s):

Phylogenetic Relationships ◽

Its2 Rdna ◽

Rdna Sequences ◽

Molecular Phylogenetic ◽

Its1 And Its2 Rdna ◽

Its1 And Its2

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

Fungal Ecology ◽

10.1016/j.funeco.2012.09.003 ◽

2013 ◽

Vol 6 (1) ◽

pp. 102-109 ◽

Cited By ~ 78

Author(s):

Anna L. Bazzicalupo ◽

Miklós Bálint ◽

Imke Schmitt

Keyword(s):

454 Sequencing ◽

Fungal Communities ◽

Its2 Rdna ◽

Its1 And Its2 Rdna ◽

Its1 And Its2

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

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2009.07.032 ◽

2009 ◽

Vol 53 (3) ◽

pp. 749-757 ◽

Cited By ~ 9

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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Phylogenetic relationships of Mediterranean black corals (Cnidaria : Anthozoa : Hexacorallia) and implications for classification within the order Antipatharia

Invertebrate Systematics ◽

10.1071/is17043 ◽

2018 ◽

Vol 32 (5) ◽

pp. 1102 ◽

Cited By ~ 10

Author(s):

M. Bo ◽

M. Barucca ◽

M. A. Biscotti ◽

M. R. Brugler ◽

A. Canapa ◽

...

Keyword(s):

Type Species ◽

Sequence Data ◽

Coral Fauna ◽

Black Coral ◽

Phylogenetic Studies ◽

Black Corals ◽

The Family ◽

The Mediterranean ◽

Its1 And Its2 Rdna ◽

Its1 And Its2

The Mediterranean black coral fauna includes type species of four antipatharian genera belonging to four different families, therefore phylogenetic studies hold great potential for enhancing systematics within the order. The analysis of six Mediterranean antipatharian species by means of nuclear sequence data of internal transcribed spacer (ITS1 and ITS2) rDNA confirms the separation into different families, as was previously noted on a morphological basis, with a clear distinction of the family Leiopathidae, whose position is supported by a unique number of mesenteries and lack of spines on thicker ramifications. The position of a newly recorded black coral species for the Mediterranean basin belonging to the genus Phanopathes is discussed. Antipathes dichotoma, the type species of the genus Antipathes, on which the order Antipatharia was based, does not group with other members of the family Antipathidae. Supporting a recent finding based on mitochondrial markers, this suggests a critical need for revision of the families that will be impacted by reassignment of this nomenclaturally important taxon.

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Life cycles, molecular phylogeny and historical biogeography of the ‘pygmaeus’ microphallids (Digenea: Microphallidae): widespread parasites of marine and coastal birds in the Holarctic

Parasitology ◽

10.1017/s0031182012000583 ◽

2012 ◽

Vol 139 (10) ◽

pp. 1346-1360 ◽

Cited By ~ 30

Author(s):

KIRILL V. GALAKTIONOV ◽

ISABEL BLASCO-COSTA ◽

PETER D. OLSON

Keyword(s):

Life Cycles ◽

The Arctic ◽

Host Switching ◽

Glacial Cycles ◽

Related Group ◽

Coastal Birds ◽

Host Life ◽

Host Parasite ◽

Its1 And Its2 Rdna ◽

Its1 And Its2

SUMMARYThe ‘pygmaeus’ microphallids (MPG) are a closely related group of 6 digenean (Platyhelminthes: Trematoda) Microphallus species that share a derived 2-host life cycle in which metacercariae develop inside daughter sporocysts in the intermediate host (intertidal and subtidal gastropods, mostly of the genus Littorina) and are infective to marine birds (ducks, gulls and waders). Here we investigate MPG transmission patterns in coastal ecosystems and their diversification with respect to historical events, host switching and host-parasite co-evolution. Species phylogenies and phylogeographical reconstructions are estimated on the basis of 28S, ITS1 and ITS2 rDNA data and we use a combination of analyses to test the robustness and stability of the results, and the likelihood of alternative biogeographical scenarios. Results demonstrate that speciation within the MPG was not associated with co-speciation with either the first intermediate or final hosts, but rather by host-switching events coincident with glacial cycles in the Northern Hemisphere during the late Pliocene/Pleistocene. These resulted in the expansion of Pacific biota into the Arctic-North Atlantic and periodic isolation of Atlantic and Pacific populations. Thus we hypothesize that contemporary species of MPG and their host associations resulted from fragmentation of populations in regional refugia during stadials, and their subsequent range expansion from refugial centres during interstadials.

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Exploring cryptic diversity in publicly available strains of the model diatom Thalassiosira pseudonana (Bacillariophyceae)

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315415000120 ◽

2015 ◽

Vol 95 (6) ◽

pp. 1081-1090 ◽

Cited By ~ 5

Author(s):

Cecilia Rad-Menéndez ◽

Michele Stanley ◽

David H. Green ◽

Eileen J. Cox ◽

John G. Day

Keyword(s):

Morphological Analysis ◽

Fragment Length Polymorphism ◽

Temporal Distribution ◽

Single Species ◽

Thalassiosira Pseudonana ◽

Salinity Range ◽

Culture Collections ◽

Geographic Origins ◽

Its1 And Its2 Rdna ◽

Its1 And Its2

The model diatom Thalassiosira pseudonana is believed to be a single species with a global distribution, but it has not been confirmed previously whether isolates from different environmental and geographic origins are genotypically and phenotypically identical. In the present study, a polyphasic approach was employed to characterize nine clonal isolates, plus an additional replicate of one of the isolates, of the diatom T. pseudonana from culture collections to investigate whether there was any cryptic speciation in the publicly available strains of this species. Morphological analysis using scanning electron microscopy concluded that the strains were indistinguishable. Furthermore, conventional DNA barcoding genes (SSU rDNA, ITS1 and ITS2 rDNA and rbcL), revealed no nucleotide variation among the strains tested. On employing a whole genome fingerprinting technique, Amplified Fragment Length Polymorphism (AFLP), three clusters were revealed, although the level of variation between the clusters was surprisingly low. These findings indicate a low level of diversity among these cultured T. pseudonana strains, despite their wide spatial and temporal distribution and the salinity range of their original habitats. Based on the limited number of available strains, this suggests that T. pseudonana is a highly conserved diatom that nevertheless has an ability to tolerate wide ranges of salinity and populate varied geographic locations.

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Morphological and molecular characterisation of Longidorus juglans sp. nov. and a sister species L. fangi Xu & Cheng, 1991 (Nematoda: Longidoridae) from China

Nematology ◽

10.1163/15685411-00003099 ◽

2017 ◽

Vol 19 (8) ◽

pp. 951-970 ◽

Cited By ~ 4

Author(s):

Yumei Xu ◽

Kai Guo ◽

Weimin Ye ◽

Jianming Wang ◽

Jingwu Zheng ◽

...

Keyword(s):

Dna Sequences ◽

Shanxi Province ◽

Lsu Rdna ◽

Molecular Characterisation ◽

Juvenile Stages ◽

Using Data ◽

Amphidial Fovea ◽

Guide Ring ◽

Its1 And Its2 Rdna ◽

Its1 And Its2

Longidorus juglanssp. nov. is a new needle nematode detected from the rhizosphere of a walnut tree in Shanxi Province, P.R. China. It was distinguished by female body length of 3.9-5.2 mm; lip region 14-18 μm wide, rounded and continuous, amphidial fovea pocket-shaped without distinct basal lobes; moderately long odontostyle (125-140 μm); guide ring at mid-odontostyle and situated 69-78 μm from anterior end; short and blunt conoid tail (30-41 μm long, c = 118-147, c′ = 0.6-0.9), bearing 2-3 caudal pores on each side. The male ofL. juglanssp. nov. is 5.1 mm long, with 13 ventro-median supplements, a short and blunt conoid tail bearing 3-4 caudal pores on each side, and spicules 73 μm long. Three developmental juvenile stages were recognised. This new species is very similar to another Chinese speciesL. fangiin general morphology, but can be distinguished by the number of juvenile stages and DNA sequences of SSU, ITS1, ITS2 and D2-D3 of LSU rDNA. Morphological and molecular characterisation was provided forL. fangirepresenting two new geographical records. The phylogenetic relationships among these species were analysed using data from SSU, D2-D3 of LSU, ITS1 and ITS2 rDNA, which revealed thatL. juglanssp. nov. andL. fangiwere clustered together withL. diadecturus,L. litchiiandL. jonesiwhose guide ring is located at mid-odontostyle level.

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Phylogenetic Information Content of Copepoda Ribosomal DNA Repeat Units: ITS1 and ITS2 Impact

BioMed Research International ◽

10.1155/2014/926342 ◽

2014 ◽

Vol 2014 ◽

pp. 1-15 ◽

Cited By ~ 8

Author(s):

Maxim V. Zagoskin ◽

Valentina I. Lazareva ◽

Andrey K. Grishanin ◽

Dmitry V. Mukha

Keyword(s):

Ribosomal Dna ◽

Phylogenetic Trees ◽

Repeat Unit ◽

Its2 Rdna ◽

Minimum Evolution ◽

Nucleotide Substitutions ◽

Repeat Units ◽

Dna Repeat ◽

Ribosomal Repeat ◽

Its1 And Its2

The utility of various regions of the ribosomal repeat unit for phylogenetic analysis was examined in 16 species representing four families, nine genera, and two orders of the subclass Copepoda (Crustacea). Fragments approximately 2000 bp in length containing the ribosomal DNA (rDNA) 18S and 28S gene fragments, the 5.8S gene, and the internal transcribed spacer regions I and II (ITS1 and ITS2) were amplified and analyzed. The DAMBE (Data Analysis in Molecular Biology and Evolution) software was used to analyze the saturation of nucleotide substitutions; this test revealed the suitability of both the 28S gene fragment and the ITS1/ITS2 rDNA regions for the reconstruction of phylogenetic trees. Distance (minimum evolution) and probabilistic (maximum likelihood, Bayesian) analyses of the data revealed that the 28S rDNA and the ITS1 and ITS2 regions are informative markers for inferring phylogenetic relationships among families of copepods and within the Cyclopidae family and associated genera. Split-graph analysis of concatenated ITS1/ITS2 rDNA regions of cyclopoid copepods suggested that theMesocyclops,Thermocyclops,andMacrocyclopsgenera share complex evolutionary relationships. This study revealed that the ITS1 and ITS2 regions potentially represent different phylogenetic signals.

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