New insights into sequence variation in the IGS region of 21 cyathostomin species and the implication for molecular identification

Parasitology ◽  
2012 ◽  
Vol 139 (8) ◽  
pp. 1063-1073 ◽  
Author(s):  
K. CWIKLINSKI ◽  
F. N. J. KOOYMAN ◽  
D. C. K. VAN DOORN ◽  
J. B. MATTHEWS ◽  
J. E. HODGKINSON
Keyword(s):  
Comparative Analysis ◽  
Dna Sequences ◽  
Sequence Variation ◽  
Intergenic Spacer ◽  
Parasitic Nematodes ◽  
Sequence Information ◽  
Detailed Knowledge ◽  
Life Cycle Stages ◽  
Third Stage ◽  
Specific Variation

SUMMARYCyathostomins comprise a group of 50 species of parasitic nematodes that infect equids. Ribosomal DNA sequences, in particular the intergenic spacer (IGS) region, have been utilized via several methodologies to identify pre-parasitic stages of the commonest species that affect horses. These methods rely on the availability of accurate sequence information for each species, as well as detailed knowledge of the levels of intra- and inter-specific variation. Here, the IGS DNA region was amplified and sequenced from 10 cyathostomin species for which sequence was not previously available. Also, additional IGS DNA sequences were generated from individual worms of 8 species already studied. Comparative analysis of these sequences revealed a greater range of intra-specific variation than previously reported (up to 23%); whilst the level of inter-specific variation (3–62%) was similar to that identified in earlier studies. The reverse line blot (RLB) method has been used to exploit the cyathostomin IGS DNA region for species identification. Here, we report validation of novel and existing DNA probes for identification of cyathostomins using this method and highlight their application in differentiating life-cycle stages such as third-stage larvae that cannot be identified to species by morphological means†.

Comparison of ITS and IGS1 regions for strain typing of clinical and non-clinical isolates of Pichia anomala

2004 ◽  
Vol 53 (2) ◽  
pp. 119-123 ◽  
Author(s):  
Rajeshwari Sutar ◽  
Joseph K. David ◽  
K. Ganesan ◽  
Anup K. Ghosh ◽  
Sunit Singhi ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Internal Transcribed Spacer ◽  
Sequence Variation ◽  
Intergenic Spacer ◽  
Pichia Anomala ◽  
Clinical Isolates ◽  
Strain Typing ◽  
Nosocomial Pathogen ◽  
Its Regions

Pichia anomala is an emerging nosocomial pathogen and there is a need for methods that distinguish between different P. anomala strains. In the typing of several clinical as well as non-clinical P. anomala strains, the sequence variation of the internal transcribed spacer (ITS) was found to be inadequate for typing purposes. The intergenic spacer 1 (IGS1) region of the rDNA of several P. anomala strains was therefore investigated in detail. The IGS1 region (which varied from 1213 to 1231 bp in length) was interspersed with repeats and had more variation than the ITS regions. Comparative analysis in cases where analysis by the ITS was ambiguous clearly revealed the IGS1 region to be a more discriminatory tool in the typing of P. anomala strains.

scholarly journals DNA-based species delineation in tropical beetles using mitochondrial and nuclear markers

2005 ◽  
Vol 360 (1462) ◽  
pp. 1925-1933 ◽  
Author(s):  
Michael T Monaghan ◽  
Michael Balke ◽  
T. Ryan Gregory ◽  
Alfried P Vogler
Keyword(s):  
Dna Sequences ◽  
Large Scale ◽  
Sequence Variation ◽  
Nuclear Dna ◽  
Sequence Information ◽  
28S Rrna ◽  
Water Beetles ◽  
Species Discovery ◽  
Tropical Water ◽  
Close Relatives

DNA barcoding has been successfully implemented in the identification of previously described species, and in the process has revealed several cryptic species. It has been noted that such methods could also greatly assist in the discovery and delineation of undescribed species in poorly studied groups, although to date the feasibility of such an approach has not been examined explicitly. Here, we investigate the possibility of using short mitochondrial and nuclear DNA sequences to delimit putative species in groups lacking an existing taxonomic framework. We focussed on poorly known tropical water beetles (Coleoptera: Dytiscidae, Hydrophilidae) from Madagascar and dung beetles (Scarabaeidae) in the genus Canthon from the Neotropics. Mitochondrial DNA sequence variation proved to be highly structured, with >95% of the observed variation existing between discrete sets of very closely related genotypes. Sequence variation in nuclear 28S rRNA among the same individuals was lower by at least an order of magnitude, but 16 different genotypes were found in water beetles and 12 genotypes in Canthon , differing from each other by a minimum of two base pairs. The distribution of these 28S rRNA genotypes in individuals exactly matched the distribution of mtDNA clusters, suggesting that mtDNA patterns were not misleading because of introgression. Moreover, in a few cases where sequence information was available in GenBank for morphologically defined species of Canthon , these matched some of the DNA-based clusters. These findings demonstrate that clusters of close relatives can be identified readily in the sequence variation obtained in field collected samples, and that these clusters are likely to correspond to either previously described or unknown species. The results suggest that DNA-assisted taxonomy will not require more than a short fragment of mtDNA to provide a largely accurate picture of species boundaries in these groups. Applied on a large scale, this DNA-based approach could greatly improve the rate of species discovery in the large assemblages of insects that remain undescribed.

scholarly journals Susceptible trichostrongyloid species mask presence of benzimidazole-resistant Haemonchus contortus in cattle

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Khalid M. Mohammedsalih ◽  
Jürgen Krücken ◽  
Ahmed Bashar ◽  
Fathel-Rahman Juma ◽  
Abdalhakaim A. H. Abdalmalaik ◽  
...  
Keyword(s):  
Haemonchus Contortus ◽  
Epidemiological Data ◽  
Nematode Species ◽  
Parasitic Nematodes ◽  
Molecular Approaches ◽  
Tubulin Genes ◽  
Faecal Egg Count ◽  
Third Stage ◽  
Before And After ◽  
Β Tubulin

Abstract Background Benzimidazole (BZ) anthelmintics are widely used to control infections with parasitic nematodes, but BZ resistance is an emerging threat among several nematode species infecting humans and animals. In Sudan, BZ-resistant Haemonchus contortus populations were recently reported in goats in South Darfur State. The objective of this study was to collect data regarding the situation of BZ resistance in cattle parasitic nematodes in South Darfur using phenotypic and molecular approaches, besides providing some epidemiological data on nematodes in cattle. Methods The faecal egg count reduction test and the egg hatch test (EHT) were used to evaluate benzimidazole efficacy in cattle nematodes in five South Darfur study areas: Beleil, Kass, Nyala, Rehed Al-Birdi and Tulus. Genomic DNA was extracted from pools of third-stage larvae (L3) (n = 40) during trials, before and after treatment, and pools of adult male Haemonchus spp. (n = 18) from abattoirs. The polymorphisms F167Y, E198A and F200Y in isotype 1 β-tubulin genes of H. contortus and H. placei were analysed using Sanger and pyrosequencing. Results Prevalence of gastro-intestinal helminths in cattle was 71% (313/443). Reduced albendazole faecal egg count reduction efficacy was detected in three study areas: Nyala (93.7%), Rehed Al-Birdi (89.7%) and Tulus (88.2%). In the EHT, EC50 values of these study areas ranged between 0.032 and 0.037 µg/ml thiabendazole. Genus-specific PCRs detected the genera Haemonchus, Trichostrongylus and Cooperia in L3 samples collected after albendazole treatment. Sanger sequencing followed by pyrosequencing assays did not detect elevated frequencies of known BZ resistance-associated alleles in codon F167Y, E198A and F200Y in isotype 1 β-tubulin gene of H. placei (≤ 11.38%). However, polymorphisms were detected in H. contortus and in samples with mixed infections with H. contortus and H. placei at codon 198, including E198L (16/58), E198V (2/58) and potentially E198Stop (1/58). All pooled L3 samples post-albendazole treatment (n = 13) were identified as H. contortus with an E198L substitution at codon 198. Conclusions To the knowledge of the authors, this is the first report of reduced albendazole efficacy in cattle in Sudan and is the first study describing an E198L substitution in phenotypically BZ-resistant nematodes collected from cattle.

ITS sequence variation supports the hybrid origin of Malus toringoides Hughes

2007 ◽  
Vol 85 (7) ◽  
pp. 659-666 ◽  
Author(s):  
Ting-Ting Feng ◽  
Zhi-Qin Zhou ◽  
Jian-Min Tang ◽  
Ming-Hao Cheng ◽  
Shi-Liang Zhou
Keyword(s):  
Sequence Variation ◽  
Gene Tree ◽  
Natural Populations ◽  
Its Sequences ◽  
Nuclear Ribosomal Dna ◽  
Hybrid Origin ◽  
Putative Hybrid ◽  
Molecular Evidence ◽  
Sequence Information ◽  
Aflp Data

Malus toringoides (Rehd.) Hughes was suggested to have originated from hybridization between Malus transitoria Schneid. and Malus kansuensis Rehd., followed by repeated backcrossing to one of the putative parents. In the present study, the sequence information of the internal transcribed spacer (ITS) of nuclear ribosomal DNA (nrDNA) was used to re-examine the origin of this species. A total of 69 accessions from three natural populations (Maerkang, Xiaba and Kehe, Aba Autonomous Region, Sichuan, China) of M. toringoides and 10 accessions of its putative parents were analyzed. Using Malus angustifolia (Ait.) Michx., Malus ioensis (Wood) Britt. and Malus doumeri Chev. as outgroups, our phylogenetic analysis of the ITS sequences of M. toringoides and its putative parents showed that M. toringoides was not monophyletic, and two different types of ITS sequences which were obtained from each of the six accessions of M. toringoides were found to have clustered separately with those of the two putative parent species on the gene tree. A comparison of the sequence variation between M. toringoides and its putative parents revealed an additive variation pattern of ITS sequences in the putative hybrid species. These results are consistent with the previous morphological and amplified fragment length polymorphism (AFLP) data which suggested that M. toringoides was of hybrid origin. Our ITS data provide new molecular evidence for the hybrid origin hypothesis of M. toringoides and these results are of great importance for future study on hybridization, polyploid speciation and evolution of the genus Malus Miller.

Highly Condensed Potato Pericentromeric Heterochromatin Contains rDNA-Related Tandem Repeats

Genetics ◽  
2002 ◽  
Vol 162 (3) ◽  
pp. 1435-1444 ◽  
Author(s):  
Robert M Stupar ◽  
Junqi Song ◽  
Ahmet L Tek ◽  
Zhukuan Cheng ◽  
Fenggao Dong ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Intergenic Spacer ◽  
Pericentromeric Heterochromatin ◽  
Dna Repeats ◽  
Solanum Bulbocastanum ◽  
Origin And Evolution ◽  
Potato Genome ◽  
Dna Elements

Abstract The heterochromatin in eukaryotic genomes represents gene-poor regions and contains highly repetitive DNA sequences. The origin and evolution of DNA sequences in the heterochromatic regions are poorly understood. Here we report a unique class of pericentromeric heterochromatin consisting of DNA sequences highly homologous to the intergenic spacer (IGS) of the 18S•25S ribosomal RNA genes in potato. A 5.9-kb tandem repeat, named 2D8, was isolated from a diploid potato species Solanum bulbocastanum. Sequence analysis indicates that the 2D8 repeat is related to the IGS of potato rDNA. This repeat is associated with highly condensed pericentromeric heterochromatin at several hemizygous loci. The 2D8 repeat is highly variable in structure and copy number throughout the Solanum genus, suggesting that it is evolutionarily dynamic. Additional IGS-related repetitive DNA elements were also identified in the potato genome. The possible mechanism of the origin and evolution of the IGS-related repeats is discussed. We demonstrate that potato serves as an interesting model for studying repetitive DNA families because it is propagated vegetatively, thus minimizing the meiotic mechanisms that can remove novel DNA repeats.

scholarly journals Comparative Analysis of Mycobacterium tuberculosis pe and ppe Genes Reveals High Sequence Variation and an Apparent Absence of Selective Constraints

PLoS ONE ◽  
2012 ◽  
Vol 7 (4) ◽  
pp. e30593 ◽  
Author(s):  
Christopher R. E. McEvoy ◽  
Ruben Cloete ◽  
Borna Müller ◽  
Anita C. Schürch ◽  
Paul D. van Helden ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Comparative Analysis ◽  
Sequence Variation ◽  
Apparent Absence ◽  
Selective Constraints ◽  
High Sequence Variation

An updated look at the uneven distribution of cryptic diversity among parasitic helminths

2017 ◽  
Vol 92 (2) ◽  
pp. 197-202 ◽  
Author(s):  
G. Pérez-Ponce de León ◽  
R. Poulin
Keyword(s):  
Cryptic Species ◽  
Dna Sequences ◽  
Meta Analysis ◽  
Parasitic Nematodes ◽  
Trematode Species ◽  
Sampling Effort ◽  
Separate Analysis ◽  
Cryptic Diversity ◽  
Parasite Diversity ◽  
Parasitic Helminths

AbstractCryptic parasite diversity is a major issue for taxonomy and systematics, and for attempts to control diseases of humans, domestic animals and wildlife. Here, we re-examine an earlier report that, after correcting for sampling effort, more cryptic species of trematodes are found per published study than for other helminth taxa. We performed a meta-analysis of 110 studies that used DNA sequences to search for cryptic species in parasitic helminth taxa. After correcting for study effort and accounting for the biogeographical region of origins, we found that more cryptic species tend to be uncovered among trematodes, and fewer among cestodes and animal-parasitic nematodes, than in other helminth groups. However, this pattern was only apparent when we included only studies using nuclear markers in the analysis; it was not seen in a separate analysis based only on mitochondrial markers. We propose that the greater occurrence of cryptic diversity among trematodes may be due to some of their unique features, such as their mode of reproduction or frequent lack of hard morphological structures, or to the way in which trematode species are described. Whatever the reason, the high frequency of cryptic species among trematodes has huge implications for estimates of parasite diversity and for future taxonomic research.

scholarly journals Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland's permafrost

2021 ◽  
Author(s):  
Gilda Varliero ◽  
Muhammad Rafiq ◽  
Swati Singh ◽  
Annabel Summerfield ◽  
Fotis Sgouridis ◽  
...  
Keyword(s):  
Active Layer ◽  
Sequence Variation ◽  
Gene Clusters ◽  
Taxonomic Composition ◽  
Sequence Information ◽  
Biosynthetic Gene Clusters ◽  
Medical Settings ◽  
Cold Adapted ◽  
Database Construction ◽  
Medium Quality

Abstract Permafrost represents a reservoir for the biodiscovery of cold-adapted proteins which are advantageous in industrial and medical settings. Comparisons between different thermo-adapted proteins can give important information for cold-adaptation bioengineering. We collected permafrost active layer samples from 34 points along a proglacial transect in southwest Greenland. We obtained a deep read coverage assembly (>164x) from nanopore and Illumina sequences for the purposes of i) analysing metagenomic and metatranscriptomic trends of the microbial community of this area, and ii) creating the Cold-Adapted Predicted Protein (CAPP) database. The community showed a similar taxonomic composition in all samples along the transect, with a solid permafrost-shaped community, rather than microbial trends typical of proglacial systems. We retrieved 69 high- and medium-quality metagenome-assembled clusters, 213 complete biosynthetic gene clusters and more than three million predicted proteins. The latter constitute the CAPP database that can provide cold-adapted protein sequence information for protein- and taxon-focused amino acid sequence modifications for the future bioengineering of cold-adapted enzymes. As an example, we focused on the enzyme polyphenol oxidase, and demonstrated how sequence variation information could inform its protein engineering.

scholarly journals Molecular analysis of the hot spot region related to length mutations in wheat chloroplast DNAs. I. Nucleotide divergence of genes and intergenic spacer regions located in the hot spot region.

Genetics ◽  
1991 ◽  
Vol 129 (3) ◽  
pp. 873-884 ◽  
Author(s):  
Y Ogihara ◽  
T Terachi ◽  
T Sasakuma
Keyword(s):  
Dna Sequences ◽  
Gene Evolution ◽  
Hot Spot ◽  
Intergenic Spacer ◽  
Open Reading Frames ◽  
Coding Region ◽  
Nucleotide Substitutions ◽  
Plant Groups ◽  
Nucleotide Divergence ◽  
Chloroplast Dnas

Abstract The nucleotide divergence of chloroplast DNAs around the hot spot region related to length mutation in Triticum (wheat) and Aegilops was analyzed. DNA sequences (ca. 4.5 kbp) of three chloroplast genome types of wheat complex were compared with one another and with the corresponding region of other grasses. The sequences region contained rbcL and psaI, two open reading frames, and a pseudogene, rpl23' (pseudogene for ribosomal protein L23) disrupted by AT-rich intergic spacer regions. The evolution of these genes in the closely related wheat complex is characterized by nonbiased nucleotide substitutions in terms of being synonymous/nonsynonymous, having A-T pressure transitions over transversions, and frequent changes at the third codon position, in contrast with the gene evolution among more distant plant groups where biased nucleotide substitutions have frequently occurred. The sequences of these genes had diverged almost in proportion to taxonomic distance. The sequence of the pseudogene rpl23' changed approximately two times faster than that of the coding region. Sequence comparison between the pseudogene and its protein-coding counterpart revealed different degrees of nucleotide homology in wheat, rice and maize, suggesting that the transposition timing of the pseudogene differed and/or that different rates of gene conversion operated on the pseudogene in the cpDNA of the three plant groups in Gramineae. The intergenic spacer regions diverged approximately ten times faster than the genes. The divergence of wheat from barley, and that from rice are estimated based on the nucleotide similarity to be 1.5, 10 and 40 million years, respectively.

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