scholarly journals Genetic diversity within the 18S rRNA and actin locus of Cryptosporidium scrofarum (Apicomplexa: Cryptosporidiidae) infecting domestic pigs (Sus scrofa domesticus) of India

2021 ◽  
Vol 91 (3) ◽  
pp. 269-276
Author(s):  
Devina Sharma ◽  
◽  
Nirbhay K. Singh ◽  
Harkirat Singh ◽  
Shitanshu S. Rath ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sus Scrofa ◽  
18S Rrna ◽  
Pcr Amplification ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Domestic Pigs ◽  
New Genotype ◽  
Sus Scrofa Domesticus ◽  
Genotype Ii

The genetic diversity was studied of Cryptosporidium scrofarum (syn Cryptosporidium pig genotype II) of domestic pigs (Sus scrofa domesticus) from Punjab, India. Nested PCR amplification targeting the 18S rRNA and actin gene loci from Cryptosporidium positive samples was carried out, and the amplicons were sequenced. Phylogenetic comparison of a partial 18S rRNA gene revealed that they were genetically most similar to C. scrofarum isolated from other parts of the world. However, comparison of sequences representing a fragment of the genomic actin locus identified a new genotype conserved within the isolates sampled from India but distinct from other published sequences, suggesting the presence of a different Indian genotype.

scholarly journals Phylogenetic Analysis of the Hypervariable Region of the 18S rRNA Gene of Cryptosporidium Oocysts in Feces of Canada Geese (Branta canadensis): Evidence for Five Novel Genotypes

2004 ◽  
Vol 70 (1) ◽  
pp. 452-458 ◽  
Author(s):  
Kristen L. Jellison ◽  
Daniel L. Distel ◽  
Harold F. Hemond ◽  
David B. Schauer
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
18S Rrna ◽  
Hypervariable Region ◽  
Pcr Amplification ◽  
The United States ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Canada Geese ◽  
Pcr Products

ABSTRACT To assess genetic diversity in Cryptosporidium oocysts from Canada geese, 161 fecal samples from Canada geese in the United States were analyzed. Eleven (6.8%) were positive for Cryptosporidium spp. following nested PCR amplification of the hypervariable region of the 18S rRNA gene. Nine PCR products from geese were cloned and sequenced, and all nine diverged from previously reported Cryptosporidium 18S rRNA gene sequences. Five sequences were very similar or identical to each other but genetically distinct from that of Cryptosporidium baileyi; two were most closely related to, but genetically distinct from, the first five; and two were distinct from any other sequence analyzed. One additional sequence in the hypervariable region of the 18S rRNA gene isolated from a cormorant was identical to that of C. baileyi. Phylogenetic analysis provided evidence for new genotypes of Cryptosporidium species in Canada geese. Results of this study suggest that the taxonomy of Cryptosporidium species in geese is complex and that a more complete understanding of genetic diversity among these parasites will facilitate our understanding of oocyst sources and species in the environment.

Genetic Diversity of Theileria equi from Horses in Different Regions of Brazil Based on the 18S rRNA Gene

10.1645/18-34 ◽  
2019 ◽  
Vol 105 (1) ◽  
pp. 186 ◽  
Author(s):  
Gabriela L. V. Vitari ◽  
Renata L. Costa ◽  
Ana Paula M. Abreu ◽  
Maristela Peckle ◽  
Claudia B. Silva ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Theileria Equi

scholarly journals Analysis of Acanthamoeba genotypes from public freshwater sources in Thailand reveals a new genotype, T23 Acanthamoeba bangkokensis sp. nov.

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chaturong Putaporntip ◽  
Napaporn Kuamsab ◽  
Warisa Nuprasert ◽  
Rattanaporn Rojrung ◽  
Urassaya Pattanawong ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
18S Rrna ◽  
Nucleotide Diversity ◽  
Purifying Selection ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Group Iii ◽  
Subtype B ◽  
New Genotype ◽  
Novel Genotype

AbstractA survey of Acanthamoeba in 100 public freshwater sources in 28 provinces across Thailand has identified 9 genotypes comprising T2/6, T3-T5, T9, T11, T12, T18 and a novel ‘T23’ among 131 isolates. Sequencing of the near complete 18S rRNA gene of Acanthamoeba of all isolates has shown that the most predominant genotype T4 found in 87 isolates (66.4%) contained 4 subtypes, i.e. T4A, T4B, T4C and T4F, while all isolates assigned to genotype T2/6 belonged to subtype B. Among intron-bearing genotypes, most isolates harbouring genotype T3 contained S516 introns, characterised by 3 distinct variants whilst all genotypes T4A and T5 were intronless. Identical 18S rRNA sequences of Acanthamoeba were identified across regions of the country and four isolates in this study shared the same sequences with those from remote nations, suggesting that some strains have reproductive success in diverse ecological niche. Nucleotide diversity of genotypes T2/6B, T3, T4, T9 and T11 in this study was significantly less than that among global isolates outside Thailand, implying that limited sequence diversity occurred within local populations. A remarkably higher level of nucleotide diversity in genotype T11 than those of other genotypes (0.041 vs. 0.012–0.024) could be due to cryptic subtypes. Recombination breakpoints have been detected within genotypes and subtypes as well as within isolates despite no evidence for sexual and parasexual cycles in the genus Acanthamoeba. Tajima’s D, Fu & Li’s D* and F* statistics revealed significantly negative deviation from neutrality across genotypes and subtypes, implying purifying selection in this locus. The 18S rRNA gene of the novel genotype ‘T23’ displayed 7.82% to 28.44% sequence differences in comparison with all known genotypes. Both Bayesian and maximum likelihood phylogenetic trees have placed genotype T23 as sister to the clade comprising genotypes T10, T12 and T14, all of these possess cyst structure belonging to morphological group III. Hence, Acanthamoeba bangkokensis sp. nov. is proposed for this novel genotype. It is likely that more genotypes of Acanthamoeba remain to be discovered while the evolution of the 18S rRNA gene of this pathogenic-free living amoeba seems to be ongoing.

scholarly journals MORPHOLOGICAL AND MOLECULAR VARIATION OF FUSARIUM OXYSPORUM F.SP LYCOPERSICI ISOLATES CAUSING FUSARIUM WILT IN TOMATO

2020 ◽  
Vol 21 (supplement 1) ◽  
Author(s):  
K. Vignesh ◽  
K. Rajamohan ◽  
R. Anandan ◽  
R. Udhayakumar
Keyword(s):  
Fusarium Oxysporum ◽  
Fusarium Wilt ◽  
18S Rrna ◽  
Sequence Similarity ◽  
Fusarium Species ◽  
Critical Role ◽  
Pcr Amplification ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Molecular Variation

Tomato (Solanum lycopersicum L.) is one of the most important, commercial and widely grown vegetable crop in the world. Tomato plays a critical role in nutritional food requirements, income and employment opportunities for the people. However, its production is threatened by the Fusarium wilt caused by Fusarium oxysporum f.sp. lycopersici and productionlossesbetween30%to40%. In the present investigation an attempt has been made to study the morphological and molecular variation of Fusarium oxysporum f.sp lycopersici isolates. Usual identification of Fusarium species based on their micro and macroscopic features and morphological characters alone may lead to incorrect designation. In order to identify the correct species, we amplified the 18S rRNA gene region by PCR, sequenced and analyzed for sequence similarity among the NCBI data through BLAST. Further, PCR amplification of ITS regions was performed using ITS primers. The amplified product of 18S rRNA gene was sequenced and deposited to Gen Bank with the accession numbers.

Host specificity of Trypanosoma (Herpetosoma) species: evidence that bank voles (Clethrionomys glareolus) carry only one T. (H.) evotomys 18S rRNA genotype but wood mice (Apodemus sylvaticus) carry at least two polyphyletic parasites

Parasitology ◽  
2002 ◽  
Vol 124 (2) ◽  
pp. 185-190 ◽  
Author(s):  
H. A. NOYES ◽  
P. AMBROSE ◽  
F. BARKER ◽  
M. BEGON ◽  
M. BENNET ◽  
...  
Keyword(s):  
Host Specificity ◽  
18S Rrna ◽  
Pcr Amplification ◽  
Wood Mouse ◽  
18S Rrna Gene ◽  
Apodemus Sylvaticus ◽  
Clethrionomys Glareolus ◽  
Rrna Gene ◽  
Wood Mice ◽  
Bank Voles

The strongest evidence for host specificity of mammalian trypanosomes comes from parasites of the subgenus Trypanosoma (Herpetosoma). Laboratory studies have shown that T. (Herpetosoma) species will not infect an alternative host. However, this has not been demonstrated in wild populations. We screened 560 bank voles (Clethrionomys glareolus) and 148 wood mice (Apodemus sylvaticus) for trypanosomes by PCR amplification of the 18S rRNA gene. In total, 109 (19%) bank voles and 12 (8%) wood mice were infected. A HaeIII restriction site was discovered that could be used to discriminate between T. (H.) evotomys of the bank vole and T. (H.) grosi of the wood mouse. All the parasites in the bank voles were identified as T. (Herpetosoma) evotomys by RFLP-PCR. Out of the 12 wood mouse infections 10 were due to T. grosi. Two of the wood mice were infected with parasites with a novel genotype that was most similar to those of T. evotomys and T. microti of voles. Fifty-six fleas collected from the rodents were also screened for trypanosomes; 9 were infected with T. evotomys and 1 with T. grosi. One of the fleas infected with T. evotomys was collected from a wood mouse.

scholarly journals Development of a Dinoflagellate-Oriented PCR Primer Set Leads to Detection of Picoplanktonic Dinoflagellates from Long Island Sound

2006 ◽  
Vol 72 (8) ◽  
pp. 5626-5630 ◽  
Author(s):  
Senjie Lin ◽  
Huan Zhang ◽  
Yubo Hou ◽  
Lilibeth Miranda ◽  
Debashish Bhattacharya
Keyword(s):  
18S Rrna ◽  
Long Island ◽  
Pcr Amplification ◽  
Long Island Sound ◽  
Systematic Investigation ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Island Sound ◽  
Pcr Primer

ABSTRACT We developed dinoflagellate-specific 18S rRNA gene primers. PCR amplification using these oligonucleotides for a picoplanktonic DNA sample from Long Island Sound yielded 24 clones, and all but one of these clones were dinoflagellates primarily belonging to undescribed and Amoebophrya-like lineages. These results highlight the need for a systematic investigation of picodinoflagellate diversity in both coastal and oceanic ecosystems.

scholarly journals A Versatile qPCR for Diagnosis of Leporid Gammaherpesvirus 5 Using Evagreen® or Taqman® Technologies

Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 715
Author(s):  
Fábio A. Abade dos Santos ◽  
Carina L. Carvalho ◽  
Maria C. Peleteiro ◽  
Francisco Parra ◽  
Margarida D. Duarte
Keyword(s):  
Sensitivity And Specificity ◽  
Internal Control ◽  
18S Rrna ◽  
Pcr Amplification ◽  
18S Rrna Gene ◽  
Myxoma Virus ◽  
Rrna Gene ◽  
Molecular Method ◽  
The Real ◽  
Iberian Hare

In late 2019, the first herpesvirus in the genus Lepus, named leporid gammaherpesvirus 5 (LeHV-5) was described. At the time, herpetic typical lesions were observed in hares infected by the myxoma virus, which is known to induce immunosuppression. Though the real impact of LeHV-5 is still poorly understood, since it affects reproduction, it poses an additional threat to the already fragile populations of Iberian hare, demanding prevalence investigations. In this article, we describe the first quantitative molecular method for LeHV-5 detection, using either Taqman or the EvaGreen systems. This method has excellent sensitivity and specificity, it is able to detect 2.1 copies of LeHV-5 DNA and was validated with an internal control targeting the 18S rRNA gene, allowing monitoring extraction and PCR amplification efficiencies.

scholarly journals Molecular characterization of Cryptosporidium xiaoi in goat kids in Bangladesh by nested PCR amplification of 18S rRNA gene

2015 ◽  
Vol 5 (3) ◽  
pp. 202-207 ◽  
Author(s):  
AMAM Zonaed Siddiki ◽  
Sohana Akter Mina ◽  
Zinat Farzana ◽  
Bibi Ayesa ◽  
Rasel Das ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Nested Pcr ◽  
18S Rrna ◽  
Pcr Amplification ◽  
18S Rrna Gene ◽  
Rrna Gene
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