Genetic combinations of symbionts in a vegetatively reproducing lichen,Parmotrema tinctorum, based on ITS rDNA sequences

Like many lichen-forming fungi, species of the genus Rhizoplaca have wide geographical distributions, but studies of their genetic variability are limited. The information about the ITS rDNA sequences of three species of Rhizoplaca from Anatolia was generated and aligned with other species from other countries and also with the data belonging to Lecanora species. The examined species were collected from the volcanic rocks of Mount Erciyes which is located in the middle of Anatolia (Turkey). The sequence data aligned with eight other samples of Rhizoplaca and six different species of Lecanora were obtained from GenBank. The results support the concept maintained by Arup and Grube (2000) that Rhizoplaca may not be a genus separate from Lecanora. According to the phylogenetic tree, Rhizoplaca melanopthalma from Turkey with two different samples of R. melanopthalma from Arizona (AF159929, AF159934) and a sample from Austria formed a group under the same branch. R. peltata and R. chrysoleuca samples from Anatolia located in two other branches of the tree formed sister groups with the samples of the same species from different countries. Although R. peltata remained on the same branch with other samples of the same species from other countries it was placed in a different branch within the group. When the three species from Anatolia were considered alone, it was noticed that Rhizoplaca melanopthalma and Rhizoplaca peltata are phylogenetically closer to each other than Rhizoplaca chrysoleuca; the morphological characteristics also support this result.

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Molecular identification of cyst-forming nematodes (Heteroderidae) from Iran and a phylogeny based on ITS-rDNA sequences

Nematology ◽

10.1163/156854102765216731 ◽

2003 ◽

Vol 5 (1) ◽

pp. 99-111 ◽

Cited By ~ 112

Author(s):

Zahra Tanha Maafi ◽

Sergei Subbotin ◽

Maurice Moens

Keyword(s):

Phylogenetic Analyses ◽

Species Level ◽

Its Rdna ◽

Heterodera Avenae ◽

Published Data ◽

Rdna Sequences ◽

First Time ◽

Group Species ◽

High Support ◽

Different Parts

Abstract RFLP and sequences of ITS-rDNA of 45 populations of cyst-forming nematodes collected from different parts of Iran were analysed and identified as representatives of 21 species. Eight enzymes generated RFLP for all studied populations. Comparison of RFLP profiles and sequences of the ITS regions with published data confirmed the presence of Heterodera avenae, H. filipjevi, H. glycines, H. hordecalis, H. latipons, H. schachtii and H. trifolii in Iran. RFLP patterns and ITS sequences for H. elachista, H. turcomanica, H. mothi and C. cacti were obtained for the first time in this study. Heterodera humuli, H. goettingiana, H. fici, H. elachista, H. turcomanica and Cactodera cacti are recorded for the first time in Iran. These results correspond with morphological and morphometric identification of the populations. Several populations were not identified at the species level and are attributed to Heterodera sp.; some of these may correspond to new species. Twenty-one new sequences from Iranian cyst-forming nematodes and 36 known sequences were used for the phylogenetic analyses. The cyst-forming nematodes formed several clades corresponding to their morphological features. Heterodera mothi and H. elachista clustered with high support with other Cyperi group species and H. turcomanica formed a moderately to highly supported clade with the Humuli group.

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ITS rDNA sequences of Pomphorhynchus laevis (Zoega in Müller, 1776) and P. lucyi Williams & Rogers, 1984 (Acanthocephala: Palaeacanthocephala)

Systematic Parasitology ◽

10.1023/a:1026127219358 ◽

2003 ◽

Vol 56 (2) ◽

pp. 141-145 ◽

Cited By ~ 27

Author(s):

Iva Král'ová-Hromadová ◽

David F. Tietz ◽

Andrew P. Shinn ◽

Marta Špakulová

Keyword(s):

Its Rdna ◽

Pomphorhynchus Laevis ◽

Rdna Sequences

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Veluticeps fasciculata sp. nov. (Gloeophyllaceae, Basidiomycota), a close relative to V. berkeleyi

Phytotaxa ◽

10.11646/phytotaxa.243.2.6 ◽

2016 ◽

Vol 243 (2) ◽

pp. 163 ◽

Cited By ~ 3

Author(s):

Jiao Yang ◽

Karen K. Nakasone ◽

Shuang-Hui He

Keyword(s):

Southern China ◽

Brown Rot ◽

Distinct Species ◽

Fungal Species ◽

Its Rdna ◽

Close Relative ◽

Rdna Sequences ◽

First Time

A new brown-rot fungal species, Veluticeps fasciculata, is described from southern China. It is characterized by perennial effused basidiocarps with smooth or tuberculose hymenophore, nodose-septate generative hyphae, fasciculate cystidia (as hyphal pegs in hymenophore) and relatively small basidiospores. It occurs on wood of Cunninghamia and Cryptomeria. Although similar to Veluticeps berkeleyi, morphological and molecular (ITS rDNA sequences) data show that V. fasciculata is a distinct species. Complete description and illustrations are provided for the V. fasciculata. In addition, V. fimbriata is reported from China for the first time.

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Identification of Photobionts from the lichen family Physciaceae using algal-specific ITS rDNA sequencing

The Lichenologist ◽

10.1006/lich.2000.0298 ◽

2001 ◽

Vol 33 (1) ◽

pp. 73-86 ◽

Cited By ~ 116

Author(s):

Gert Helms ◽

Thomas Friedl ◽

Gerhard Rambold ◽

Helmut Mayrhofer

Keyword(s):

Phylogenetic Analyses ◽

Pcr Primers ◽

Its Rdna ◽

Generic Level ◽

Sequence Comparisons ◽

Its Phylogeny ◽

Specific Pcr ◽

Rdna Sequences ◽

Rdna Sequencing ◽

Geographical Regions

AbstractThe identity of photobionts from 20 species of the Physciaceae from different habitats and geographical regions has been determined by ITS rDNA sequence comparisons in order to estimate the diversity of photobionts within that lichen group, to detect patterns of specificity of mycobionts towards their photobionts and as a part of an ongoing study to investigate possible parallel cladogenesis of both symbionts. Algal-specific PCR primers have been used to determine the ITS rDNA sequences from DNA extractions of dried lichens that were up to 5 years old. Direct comparisons and phylogenetic analyses allowed the assignment of Physciaceae photobionts to four distinct clades in the photobiont ITS rDNA phylogeny. The results indicate a diversity within the genus Trebouxia Puymaly and Physciaceae photobionts that is higher than expected on the basis morphology alone. Physciaceae photobionts belonged to 12 different ITS lineages of which nine could unambiguously be assigned to six morphospecies of Trebouxia. The identity of the remaining three sequences was not clarified; they may represent new species. Specificity at the generic level was low as a whole range of photobiont species were found within a genus of Physciaceae and different ranges were detected. The photobionts of Physcia (Schreb.) Michaux were closely related and represented one morphospecies of Trebouxia, whereas the algal partners of Buellia De Not and Rinodina (Ach.) Gray were in distant lineages of the ITS phylogeny and from several Trebouxia morphospecies. Photobiont variation within a genus of Physciaceae may be due to phylogeny, geographical distance or because photobionts from neighbouring lichens were taken (“algal sharing“). At the species level Physciaceae mycobionts seem to be rather selective and contained photobionts that were very closely related within one morphospecies of Trebouxia.

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

Journal of Helminthology ◽

10.1017/s0022149x12000740 ◽

2012 ◽

Vol 88 (1) ◽

pp. 64-68 ◽

Cited By ~ 18

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.

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A new entomopathogenic nematode, Steinernema colombiense n. sp. (Nematoda: Steinernematidae), from Colombia

Nematology ◽

10.1163/156854108784513879 ◽

2008 ◽

Vol 10 (4) ◽

pp. 561-574 ◽

Cited By ~ 10

Author(s):

Juan Carlos López-Núñez ◽

Kathryn Plichta ◽

Carmenza E. Góngora-Botero ◽

S. Patricia Stock

Keyword(s):

Excretory Pore ◽

Sequence Data ◽

Entomopathogenic Nematode ◽

Tail Length ◽

Rdna Sequence ◽

Its Rdna ◽

Infective Juvenile ◽

Diagnostic Features ◽

Rdna Sequences ◽

Rdna Sequence Data

Abstract A new entomopathogenic nematode, Steinernema colombiense n. sp., is described from Colombia. Morphological, molecular (28S and ITS rDNA sequence data) and cross-hybridisation studies were used for diagnostics and identification purposes. In addition, 28S and ITS rDNA sequence data were used to assess evolutionary relationships of the new species with other Steinernema spp. Morphological diagnostic features for S. colombiense n. sp. include morphometric features of the third-stage infective juvenile, including body length of 636 (549-732) μm, narrow body diam. (31 (22-36) μm), position of the excretory pore (35 (31-40) μm), tail length (41 (32-53) μm), D% = 29 (25-33) and E% = 205 (138-284). In addition, males of first and second generations are characterised by the morphology of the spicules and gubernaculum, the number and arrangement of the genital papillae and the excretory pore position (at 67 (56-76) and 54 (46-63) μm, for first and second generations, respectively). In addition to these traits, 28S and ITS rDNA sequences analyses both showed this species to be a distinct and unique entity.

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