scholarly journals D1/D2 Domain of Large-Subunit Ribosomal DNA for Differentiation of Orpinomyces spp.

2011 ◽  
Vol 77 (18) ◽  
pp. 6722-6725 ◽  
Author(s):  
Sumit S. Dagar ◽  
Sanjay Kumar ◽  
Priti Mudgil ◽  
Rameshwar Singh ◽  
Anil K. Puniya
Keyword(s):  
Ribosomal Dna ◽  
Restriction Site ◽  
Fragment Length Polymorphism ◽  
Large Subunit ◽  
Species Level ◽  
Additional Restriction ◽  
Lsu Rdna ◽  
Content Type ◽  
D2 Domain ◽  
Additional Restriction Site

ABSTRACTThis study presents the suitability of D1/D2 domain of large-subunit (LSU) ribosomal DNA (rDNA) for differentiation ofOrpinomyces joyoniiandOrpinomyces intercalarisbased on PCR-restriction fragment length polymorphism (RFLP). A variation of G/T inO. intercalariscreated an additional restriction site for AluI, which was used as an RFLP marker. The results demonstrate adequate heterogeneity in the LSU rDNA for species-level differentiation.

scholarly journals Cryptococcus rajasthanensis sp. nov., an anamorphic yeast species related to Cryptococcus laurentii, isolated from Rajasthan, India

2007 ◽  
Vol 57 (2) ◽  
pp. 414-418 ◽  
Author(s):  
Puja Saluja ◽  
G. S. Prasad
Keyword(s):  
Large Subunit ◽  
Its Region ◽  
Molecular Data ◽  
Lsu Rdna ◽  
Cryptococcus Laurentii ◽  
The Novel ◽  
D2 Domain ◽  
Its Regions ◽  
Anamorphic Yeast ◽  
Physiological Tests

Two novel anamorphic yeast strains (S-15LT and 3-C1) were isolated from the inflorescences of plants collected in two different towns in Rajasthan State, India. Sequencing of the D1/D2 domains of the large-subunit (LSU) rDNA and the internal transcribed spacer (ITS) regions suggested they are strains of the same species. Phenotypic characteristics such as the absence of fermentation, the absence of sexual structures and ballistoconidia, the assimilation of myo-inositol and d-glucuronate, and positive Diazonium blue B and urease reactions indicated that these strains belong to the genus Cryptococcus. The novel strains differed from Cryptococcus laurentii in six physiological tests and differed from other related species in more than six tests. A phylogenetic analysis of the sequences of the D1/D2 domains of the LSU rDNA and the ITS regions placed these strains in the Bulleromyces clade within the order Tremellales, with C. laurentii as their closest described relative. The novel strains showed 1.6 and 7.5 % divergence in the D1/D2 domain of the LSU rDNA and ITS regions, respectively, with respect to C. laurentii. The divergence from other species was more than 3 % for the D1/D2 domain and more than 9 % for the ITS region. On the basis of the phenotypic and molecular data, strains S-15LT and 3-C1 represent a novel species within the genus Cryptococcus, for which the name Cryptococcus rajasthanensis sp. nov. is proposed. The type strain is S-15LT (=MTCC 7075T=CBS 10406T).

scholarly journals Colletotrichum isolates related to Anthracnose of cashew trees in Brazil: morphological and molecular description using LSU rDNA sequences

2010 ◽  
Vol 53 (4) ◽  
pp. 741-752 ◽  
Author(s):  
Ana Maria Queijeiro Lopez ◽  
John Alexander Lucas
Keyword(s):  
Mycelial Growth ◽  
Host Plants ◽  
Large Subunit ◽  
Lsu Rdna ◽  
Rdna Sequences ◽  
D2 Domain ◽  
The One ◽  
High Degree ◽  
Molecular Description ◽  
28S Ribosomal Dna

Thirty six isolates of fungi obtained from anthracnose lesions of cashew and associated host plants in Brazil, were compared by their cultural, morphological and partial sequences of the 28S ribosomal DNA characters. They showed a high degree of cultural variability. The average mycelial growth rate on all tested media ranged from 10.2-13.3 mm/day between the isolates. Most of them produced perithecia (sterile and fertile) and some produced setae (sterile and fertile). All the isolates produced acervuli with predominantly cylindrical conidia (12.4-17.7 µmX 4.8-6.0 µm in width) with round ends, which became septate on germination, and produced unlobed or slightlylobed appressoria. Comparison of the D2 domain of the large subunit (LSU) rDNA sequences with those of other defined species of Colletotrichum and Glomerella grouped 35 of the isolates with known strains of C. gloeosporioides from different hosts (> 98.9% homology). The one exception (LARS 921) was identical to G. cingulata (LARS 238) from Vigna unguiculata.

scholarly journals Mapping the Distribution of Cysts from the Toxic Dinoflagellate Cochlodinium polykrikoides in Bloom-Prone Estuaries by a Novel FluorescenceIn SituHybridization Assay

2015 ◽  
Vol 82 (4) ◽  
pp. 1114-1125 ◽  
Author(s):  
Theresa K. Hattenrath-Lehmann ◽  
Yu Zhen ◽  
Ryan B. Wallace ◽  
Ying-Zhong Tang ◽  
Christopher J. Gobler
Keyword(s):  
Harmful Algal Blooms ◽  
Algal Blooms ◽  
Large Subunit ◽  
Cross Reactivity ◽  
Epifluorescence Microscopy ◽  
Lsu Rdna ◽  
Cochlodinium Polykrikoides ◽  
Content Type ◽  
Ecosystem Studies ◽  
Resting Cysts

ABSTRACTCochlodinium polykrikoidesis a cosmopolitan dinoflagellate that is notorious for causing fish-killing harmful algal blooms (HABs) across North America and Asia. While recent laboratory and ecosystem studies have definitively demonstrated thatCochlodiniumforms resting cysts that may play a key role in the dynamics of its HABs, uncertainties regarding cyst morphology and detection have prohibited even a rudimentary understanding of the distribution ofC. polykrikoidescysts in coastal ecosystems. Here, we report on the development of a fluorescencein situhybridization (FISH) assay using oligonucleotide probes specific for the large subunit (LSU) ribosomal DNA (rDNA) ofC. polykrikoides. The LSU rDNA-targeted FISH assay was used with epifluorescence microscopy and was iteratively refined to maximize the fluorescent reaction withC. polykrikoidesand minimize cross-reactivity. The final LSU rDNA-targeted FISH assay was found to quantitatively recover cysts made by North American isolates ofC. polykrikoidesbut not cysts formed by other common cyst-forming dinoflagellates. The method was then applied to identify and mapC. polykrikoidescysts across bloom-prone estuaries. Annual cyst and vegetative cell surveys revealed that elevated densities ofC. polykrikoidescysts (>100 cm−3) during the spring of a given year were spatially consistent with regions of dense blooms the prior summer. The identity of cysts in sediments was confirmed via independent amplification ofC. polykrikoidesrDNA. This study mappedC. polykrikoidescysts in a natural marine setting and indicates that the excystment of cysts formed by this harmful alga may play a key role in the development of HABs of this species.

Kodamaea kakaduensisandCandida tolerans, two new ascomycetous yeast species from AustralianHibiscusflowers

1999 ◽  
Vol 45 (2) ◽  
pp. 172-177 ◽  
Author(s):  
Marc-André Lachance ◽  
Jane M Bowles ◽  
William T Starmer ◽  
J Stuart F. Barker
Keyword(s):  
Ribosomal Dna ◽  
Yeast Species ◽  
Large Subunit ◽  
New Yeast Species ◽  
Ascomycetous Yeast ◽  
Carbon And Nitrogen ◽  
D2 Domain ◽  
New Yeast ◽  
Type Strains ◽  
Candida Mogii

Two new yeast species were isolated from flowers of Hibiscus species in Eastern and Northern Australia. Kodamaea kakaduensis is heterothallic, haploid, and similar to other Kodamaea species and to Candida restingae. Buds are often produced on short protuberances, and a true mycelium is formed. The new species differs from others by the assimilation of trehalose, melezitose, and xylitol, and is reproductively isolated. The cells of Candida tolerans are small and a pseudomycelium is formed. The carbon and nitrogen assimilation pattern is reminiscent of that of Zygosaccharomyces rouxii but the two are not closely related. Sequences of the D1/D2 domain of large subunit ribosomal DNA confirm the membership of K. kakaduensis in the genus Kodamaea and indicate that C. tolerans belongs to the Clavispora-Metschnikowia clade, with a moderate relatedness to Candida mogii. The type strains are: K. kakaduensis, UWO(PS)98-119.2 (h+, holotype, CBS 8611) and UWO(PS)98-117.1 (h-, isotype, CBS 8612); and C. tolerans, UWO(PS)98-115.5 (CBS 8613).Key words: Kodamaea, Candida, new yeast species, ribosomal DNA, whole-cell PCR.

scholarly journals A restriction site to differentiate Plasmodium and Haemoproteus infections in birds: on the inefficiency of general primers for detection of mixed infections

Parasitology ◽  
2009 ◽  
Vol 136 (7) ◽  
pp. 713-722 ◽  
Author(s):  
J. MARTÍNEZ ◽  
J. MARTÍNEZ-DE LA PUENTE ◽  
J. HERRERO ◽  
S. DEL CERRO ◽  
E. LOBATO ◽  
...  
Keyword(s):  
Restriction Site ◽  
General Rule ◽  
Dna Amplification ◽  
Additional Restriction ◽  
Mixed Infections ◽  
Specific Primers ◽  
Dna Analyses ◽  
Restriction Sites ◽  
Additional Restriction Site ◽  
Do So

SUMMARYAvian Plasmodium and Haemoproteus parasites are easily detected by DNA analyses of infected samples but only correctly assigned to each genus by sequencing and use of a phylogenetic approach. Here, we present a restriction site to differentiate between both parasite genera avoiding the use of those analyses. Alignments of 820 sequences currently listed in GenBank encoding a particular cytochrome B region of avian Plasmodium and Haemoproteus show a shared restriction site for both genera using the endonuclease Hpy CH4III. An additional restriction site is present in Plasmodium sequences that would initially allow differentiation of both genera by differential migration of digested products on gels. Overall 9 out of 326 sequences containing both potential restriction sites do not fit to the general rule. We used this differentiation of parasite genera based on Hpy CH4III restriction sites to evaluate the efficacy of 2 sets of general primers in detecting mixed infections. To do so, we used samples from hosts infected by parasites of both genera. The use of general primers was only able to detect 25% or less of the mixed infections. Therefore, parasite DNA amplification using general primers to determine the species composition of haemosporidian infections in individual hosts is not recommended. Specific primers for each species and study area should be designed until a new method can efficiently discriminate both parasites.

scholarly journals Phylogeny of Opisthokonta and the evolution of multicellularity and complexity in Fungi and Metazoa

2003 ◽  
Vol 2 (3) ◽  
pp. 203-211 ◽  
Author(s):  
Mónica Medina ◽  
Allen G. Collins ◽  
John W. Taylor ◽  
James W. Valentine ◽  
Jere H. Lipps ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Special Interest ◽  
Sequence Data ◽  
Large Subunit ◽  
Sister Group ◽  
Ssu Rdna ◽  
Lsu Rdna ◽  
Evolutionary Transitions ◽  
Stephanoeca Diplocostata ◽  
Paraphyletic Assemblage

While early eukaryotic life must have been unicellular, multicellular lifeforms evolved multiple times from protistan ancestors in diverse eukaryotic lineages. The origins of multicellularity are of special interest because they require evolutionary transitions towards increased levels of complexity. We have generated new sequence data from the nuclear large subunit ribosomal DNA gene (LSU rDNA) and the SSU rDNA gene of several unicellular opisthokont protists – a nucleariid amoeba (Nuclearia simplex) and four choanoflagellates (Codosiga gracilis, Choanoeca perplexa, Proterospongia choanojuncta and Stephanoeca diplocostata) to provide the basis for re-examining relationships among several unicellular lineages and their multicellular relatives (animals and fungi). Our data indicate that: (1) choanoflagellates are a monophyletic rather than a paraphyletic assemblage that independently gave rise to animals and fungi as suggested by some authors and (2) the nucleariid filose amoebae are the likely sister group to Fungi. We also review published information regarding the origin of multicellularity in the opisthokonts.

A Re-Examination of Generic Concepts of Baeomycetoid Lichens Based on Phylogenetic Analyses of Nuclear ssu and Lsu Ribosomal Dna

1999 ◽  
Vol 31 (5) ◽  
pp. 409-418 ◽  
Author(s):  
Jamie L. Platt ◽  
Joseph W. Spatafora
Keyword(s):  
Ribosomal Dna ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Small Subunit ◽  
Lsu Rdna ◽  
Character State ◽  
Nucleotide Sequence Data ◽  
Lichen Symbiosis ◽  
Data Support

AbstractThe lichen symbiosis has evolved several times within the fungal kingdom, although the total number of lichenization events leading to extant taxa is still unclear. Two lichenized families, the Icmadophilaceae and Baeomycetaceae have been classified in the Helotiales. Because the Helotiales are predominantly nonlichenized, this suggests that these families represent independent evolutionary episodes of lichenization from the Lecanorales. As a first step towards understanding the evolution of the lichen symbiosis within this order, we tested recent hypotheses concerning the segregation of lichen genera between the two lichen families. Specifically, we used phylogenetic analyses of nucleotide sequence data from nuclear small-subunit and large-subunit ribosomal DNA to test the morphology-based hypotheses that Dibaeis is a distinct genus from Baeomyces and that Dibaeis is a member of the Icmadophilaceae rather than the Baeomycetaceae. Phylogenetic analyses of nuclear SSU rDNA and combined SSU and LSU rDNA data support the hypothesis that Dibaeis is more closely related to IcmadophUa than it is to Baeomyces. Therefore, these data support the resurrection of Dibaeis from its previous synonymy with Baeomyces based on the characters of ascocarp colour and ascus morphology. The recognition of two distinct genera is also consistent with character state distribution of unique lichen acids.

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