scholarly journals Phylogenetic Analysis of Astigmatid Mites Sarcoptes scabiei and Dermatophagoides farinae using ITS-2 as a Genetic Marker

2020 ◽  
Vol 1 (2) ◽  
pp. 5
Author(s):  
Shumaila Naz ◽  
Farhana Riaz Chaudhry ◽  
Dilawar Abbas Rizvi ◽  
Muhammad Ismail
Keyword(s):  
Phylogenetic Tree ◽  
Genetic Marker ◽  
Control Strategies ◽  
Sarcoptes Scabiei ◽  
Mite Species ◽  
Pairwise Distance ◽  
Military Hospital ◽  
Dermatophagoides Farinae ◽  
Gene Sequences ◽  
Astigmatid Mites

Objective: The coding of astigmatid mites based on their morphological and developmental characteristics often leads to uncertainty in the results. The ribosomal internal transcribed spacer (ITS-2) region, being highly conserved in eukaryotes is commonly employed as a barcode for identification of mite species. The present study was an attempt to characterize the gene sequences of astigmatid mites i.e. Sarcoptes scabiei (S. scabiei), Dermatophagoides farinae (D. farinae) using ITS-2 as a genetic marker. Place and Duration of Study: The study was conducted at Department of Dermatology, Military Hospital (MH), Rawalpindi from September 2012 to October 2013. Materials and Methods: In order to characterize relationship of astigmatid mites, the ITS-2 marker was successfully amplified and sequenced. The resulting ITS-2 gene sequences were aligned using Clustal W. MEGA 7 was used to construct phylogenetic tree of the aligned sequence. Results: The phylogenetic tree showed an overall genetic distance of 0.53 indicating close genetic relationship among astigmatid mite species. Pairwise distance was calculated for the ITS-2 gene and low genetic diversity values were observed within S. scabiei and D. farinae that range from 0.003-0.008 and 0.006-0.038 respectively. Conclusion: The study supports the view that the ITS-2 region can be used to identify morphologically difficult astigmatid mites but is not useful in characterization of different species based on the geographical distribution. This study has important implication in our understanding of the epidemiology of S. scabiei and D. farinae and development of control strategies in human transmission.

Study on the Relationship Between Microbial Composition and Living Environment in Important Medical Mites Based on Illumina MiSeq Sequencing Technology

2020 ◽  
Vol 57 (4) ◽  
pp. 1049-1056 ◽  
Author(s):  
Yijie Guo ◽  
Ruiling Wang ◽  
Yae Zhao ◽  
Dongling Niu ◽  
Xiaojuan Gong ◽  
...  
Keyword(s):  
Life Stage ◽  
Illumina Miseq ◽  
Blood Feeding ◽  
Sarcoptes Scabiei ◽  
Mite Species ◽  
Living Environment ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
Microbial Composition ◽  
Psoroptes Cuniculi

Abstract The microbiota of mites is closely related to their growth, development, and pathogenicity. Therefore, it is necessary to study the bacteria in mites. Here, for the first time, based on 16s rRNA V3-V4 region, the microbiota of 45 samples of nine species in six families of medically important mites were analyzed using Illumina MiSeq sequencing technique. The results showed that, at the phylum level, Proteobacteria (56.20–86.40%) were the dominant, followed by Firmicutes (6.41–19.43%), Bacteroidetes (5.56–13.38%) and Actinobacteria (1.93–28.07%). But at the genera the microbiota of mites are different, showing four characteristics: 1) The microbiota is related to the parasitic host. Demodex folliculorum (Acariforms: Demodicidae) and D. brevis (Acariforms: Demodicidae), both parasitizing humans, showed similar microbial composition, as did D. canis (Acariforms: Demodicidae) and Sarcoptes scabiei canis (Acariforms: Sarcoptidae) parasitizing dogs, but D. caprae (Acariforms: Demodicidae) parasitizing sheep showed unique microbial community; 2) The microbiota is related to mite’s species. Dermatophagoides farinae and Cheyletus malaccensis (Acariforms: Cheyletidae), both collecting from flour, show respective microbial composition; 3) The microbiota is related to the life stage. There were differences in microbiota between adults and larvae of D. farinae, but no differences observed in Psoroptes cuniculi (Acariforms: Psoroptidae); and 4) The microbiota is related to the blood-feeding state. The microbiota of blood-fed Ornithonyssus bacoti (Parasitiformes: Macronyssidae) adults was significantly higher than that of unfed adults. This indicates that the microbiota of mites is affected by mite species, parasitic host, growth stage and habitat. Therefore, understanding these influencing factors will have a very important guiding significance for the prevention and control of mite-borne diseases.

scholarly journals Streptococcus suis Serotypes Characterized by Analysis of Chaperonin 60 Gene Sequences

2001 ◽  
Vol 67 (10) ◽  
pp. 4828-4833 ◽  
Author(s):  
Ronald Brousseau ◽  
Janet E. Hill ◽  
Gabrielle Préfontaine ◽  
Swee-Han Goh ◽  
Josée Harel ◽  
...  
Keyword(s):  
16S Rrna ◽  
Distance Matrix ◽  
Streptococcus Suis ◽  
Pairwise Distance ◽  
Likelihood Method ◽  
Gene Sequences ◽  
16S Rna ◽  
Chaperonin 60 ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT Streptococcus suis is an important pathogen of swine which occasionally infects humans as well. There are 35 serotypes known for this organism, and it would be desirable to develop rapid methods methods to identify and differentiate the strains of this species. To that effect, partial chaperonin 60 gene sequences were determined for the 35 serotype reference strains of S. suis. Analysis of a pairwise distance matrix showed that the distances ranged from 0 to 0.275 when values were calculated by the maximum-likelihood method. For five of the strains the distances from serotype 1 were greater than 0.1, and for two of these strains the distances were were more than 0.25, suggesting that they belong to a different species. Most of the nucleotide differences were silent; alignment of protein sequences showed that there were only 11 distinct sequences for the 35 strains under study. The chaperonin 60 gene phylogenetic tree was similar to the previously published tree based on 16S rRNA sequences, and it was also observed that strains with identical chaperonin 60 gene sequences tended to have identical 16S rRNA sequences. The chaperonin 60 gene sequences provided a higher level of discrimination between serotypes than the 16S RNA sequences provided and could form the basis for a diagnostic protocol.

scholarly journals Legume Symbiotic Nitrogen Fixation byβ-Proteobacteria Is Widespread inNature

2003 ◽  
Vol 185 (24) ◽  
pp. 7266-7272 ◽  
Author(s):  
Wen-Ming Chen ◽  
Lionel Moulin ◽  
Cyril Bontemps ◽  
Peter Vandamme ◽  
Gilles Béna ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Nitrogen Fixation ◽  
Phylogenetic Tree ◽  
Phylogenetic Diversity ◽  
Symbiotic Nitrogen Fixation ◽  
The Other ◽  
Gene Sequences ◽  
Free Living ◽  
Initial Discovery ◽  
Different Strains

ABSTRACT Following the initial discovery of two legume-nodulating Burkholderia strains (L. Moulin, A. Munive, B. Dreyfus, and C. Boivin-Masson, Nature 411:948-950, 2001), we identified as nitrogen-fixing legume symbionts at least 50 different strains of Burkholderia caribensis and Ralstonia taiwanensis, all belonging to the β-subclass of proteobacteria, thus extending the phylogenetic diversity of the rhizobia. R. taiwanensis was found to represent 93% of the Mimosa isolates in Taiwan, indicating thatβ -proteobacteria can be the specific symbionts of a legume. The nod genes of rhizobial β-proteobacteria (β-rhizobia) are very similar to those of rhizobia from theα -subclass (α-rhizobia), strongly supporting the hypothesis of the unique origin of common nod genes. Theβ -rhizobial nod genes are located on a 0.5-Mb plasmid, together with the nifH gene, in R. taiwanensis and Burkholderia phymatum. Phylogenetic analysis of available nodA gene sequences clustered β-rhizobial sequences in two nodA lineages intertwined with α-rhizobial sequences. On the other hand, theβ -rhizobia were grouped with free-living nitrogen-fixingβ -proteobacteria on the basis of the nifH phylogenetic tree. These findings suggest that β-rhizobia evolved from diazotrophs through multiple lateral nod gene transfers.

scholarly journals Genetic characterization and risk factors for feline hemoplasma infection in semi-domesticated cats in Bangkok, Thailand

2020 ◽  
Vol 13 (5) ◽  
pp. 975-980 ◽  
Author(s):  
Thom Do ◽  
Ketsarin Kamyingkird ◽  
Linh Khanh Bui ◽  
Tawin Inpankaew
Keyword(s):  
Risk Factors ◽  
Phylogenetic Tree ◽  
Genetic Characterization ◽  
Control Strategies ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Chi Square ◽  
Effective Prevention ◽  
Stray Cats ◽  
Vector Borne

Background and Aim: Stray cats are a reservoir for various zoonotic diseases relevant to public health in Thailand. The vector-borne infection, hemoplasmosis, also known as infectious anemia, is one such disease carried by domestic and wild felids. This study focuses on molecular characterization and phylogenetic analysis of hemoplasma in semi-domesticated cats in Bangkok, Thailand. Materials and Methods: In total, 473 blood samples were collected from 53 temple communities in 34 metropolitan districts and assayed using polymerase chain reaction (PCR) to amplify partial 16S rRNA genes for hemoplasma detection. Risk factors for hemoplasma infection (gender, age, free-roaming, and ectoparasite exposure) were analyzed using Chi-square tests, logistic regression, and odds ratios (OR) with 95% confidence intervals (95% CI) using R software (version 3.6.1). A phylogenetic tree was established from genetic characterization of hemoplasmas. Results: In total, 180 samples (38.05%) were positive for hemoplasma. Of half of the positive sequenced samples, 83.33% were infected with Candidatus Mycoplasma haemominutum (CMhm), 13.33% with Mycoplasma haemofelis (Mhf), and 3.33% with Candidatus Mycoplasma turicensis (CMt). Cats over 5 years old were more likely to be infected than younger cats (p<0.005, OR=3.8, 95% CI=1.64-4.78). Cats were diagnosed as positive based on PCR assays in 97% (33/34) of districts surveyed. The phylogenetic tree showed two majority clusters with three clades of feline hemotropic mycoplasma. Conclusion: Overall, the survey shows the prevalence (38.05%) and distribution of feline hemoplasma in semi-domesticated cats. This information will contribute to effective prevention and control strategies to minimize infections by feline vector-borne pathogens in Thailand.

scholarly journals StrainHub: A phylogenetic tool to construct pathogen transmission networks

2019 ◽  
Author(s):  
Adriano de Bernardi Schneider ◽  
Colby T. Ford ◽  
Reilly Hostager ◽  
John Williams ◽  
Michael Cioce ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Control Strategies ◽  
Pathogen Transmission ◽  
Character State ◽  
Transmission Networks ◽  
Web Based ◽  
Centrality Metrics ◽  
Alternative Approach ◽  
Arbitrary Space ◽  
State Changes

SummaryIn exploring the epidemiology of infectious diseases, networks have been used to reconstruct contacts among individuals and/or populations. Summarizing networks using pathogen metadata (e.g., host species and place of isolation) and a phylogenetic tree is a nascent, alternative approach. In this paper, we introduce a tool for reconstructing transmission networks in arbitrary space from phylogenetic information and metadata. Our goals are to provide a means of deriving new insights and infection control strategies based on the dynamics of the pathogen lineages derived from networks and centrality metrics. We created a web-based application, called StrainHub, in which a user can input a phylogenetic tree based on genetic or other data along with characters derived from metadata using their preferred tree search method. StrainHub generates a transmission network based on character state changes in meta-data, such as place or source of isolation, mapped on the phylogenetic tree. The user has the option to calculate centrality metrics on the nodes including betweenness, closeness, degree, and a new metric, the source/hub ratio. The outputs include the network with values for metrics on its nodes and the tree with characters reconstructed. All of these results can be exported for further analysis.Availabilityhttps://github.com/abschneider/StrainHub and strainhub.io

scholarly journals Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses

2015 ◽  
Author(s):  
Jennifer Fouquier ◽  
Jai R Rideout ◽  
Evan Bolyen ◽  
John H Chase ◽  
Arron Shiffer ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Genetic Marker ◽  
Phylogenetic Trees ◽  
Phylogenetic Diversity ◽  
Sequence Data ◽  
Fungal Species ◽  
Bioinformatics Tool ◽  
Hybrid Gene ◽  
Fungal Database ◽  
Taxonomic Groups

Ghost-tree is a bioinformatics tool that integrates sequence data from two genetic markers into a single phylogenetic tree that can be used for diversity analyses. Our approach uses one genetic marker whose sequences can be aligned across organisms spanning divergent taxonomic groups (e.g., fungal families) as a “foundation” phylogeny. A second, more rapidly evolving genetic marker is then used to build “extension” phylogenies for more closely related organisms (e.g., fungal species or strains) that are then grafted on to the foundation tree by mapping taxonomic names. We apply ghost-tree to graft fungal extension phylogenies derived from ITS sequences onto a foundation phylogeny derived from fungal 18S sequences. The result is a phylogenetic tree, compatible with the commonly used UNITE fungal database, that supports phylogenetic diversity analysis (e.g., UniFrac) of fungal communities profiled using ITS markers. Availability: ghost-tree is pip-installable. All source code, documentation, and test code are available under the BSD license at https://github.com/JTFouquier/ghost-tree.

scholarly journals Analysis SARS-CoV-2 Genomes of G20 Areas on Phylogeny Tree, t-SNE based on Machine Learning

2020 ◽  
Author(s):  
Renyang Liu ◽  
Mu Qiao ◽  
Alima ◽  
Jeffrey Zheng ◽  
Wei Zhou
Keyword(s):  
Public Health ◽  
Machine Learning ◽  
Phylogenetic Tree ◽  
Treatment Strategies ◽  
Gene Sequences ◽  
Effective Prevention ◽  
Multiple Resources ◽  
The World ◽  
Prevention And Treatment ◽  
Epidemiological Characteristics

Abstract The new coronavirus disease (COVID-19) broke out earlier in Wuhan, and the plague spread rapidly from multiple resources of different countries. COVID-19 has caused millions of diagnosed people worldwide, causing many deaths and posing a severe threat to public health in countries around the world. Facing this urgent situation, in-depth research on the emerging SARS-CoV-2 to understand the related pathogenic mechanism and epidemiological characteristics is urgent. This type of activity would be useful to determine its origin to formulate effective prevention and treatment strategies for affected patients.This paper adopts t-SNE based on machine learning to draw a phylogenetic tree from collected genomic sequences to analyze G20 countries’ samples. The phylogenetic tree of the generating mechanism was described, and intermediate results were illustrated. The results of this research showed that viruses in many countries have similar or similar relationships among the gene sequences.

scholarly journals Ribosomal protein gene-based phylogeny for finer differentiation and classification of phytoplasmas

2007 ◽  
Vol 57 (9) ◽  
pp. 2037-2051 ◽  
Author(s):  
M. Martini ◽  
I.-M. Lee ◽  
K. D. Bottner ◽  
Y. Zhao ◽  
S. Botti ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Tree ◽  
Ribosomal Protein ◽  
Phylogenetic Analyses ◽  
Rflp Analysis ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Gram Positive ◽  
The 16S Rrna Gene

Extensive phylogenetic analyses were performed based on sequences of the 16S rRNA gene and two ribosomal protein (rp) genes, rplV (rpl22) and rpsC (rps3), from 46 phytoplasma strains representing 12 phytoplasma 16Sr groups, 16 other mollicutes and 28 Gram-positive walled bacteria. The phylogenetic tree inferred from rp genes had a similar overall topology to that inferred from the 16S rRNA gene. However, the rp gene-based tree gave a more defined phylogenetic interrelationship among mollicutes and Gram-positive walled bacteria. Both phylogenies indicated that mollicutes formed a monophyletic group. Phytoplasmas clustered with Acholeplasma species and formed one clade paraphyletic with a clade consisting of the remaining mollicutes. The closest relatives of mollicutes were low-G+C-content Gram-positive bacteria. Comparative phylogenetic analyses using the 16S rRNA gene and rp genes were performed to evaluate their efficacy in resolving distinct phytoplasma strains. A phylogenetic tree was constructed based on analysis of rp gene sequences from 87 phytoplasma strains belonging to 12 16Sr phytoplasma groups. The phylogenetic relationships among phytoplasmas were generally in agreement with those obtained on the basis of the 16S rRNA gene in the present and previous works. However, the rp gene-based phylogeny allowed for finer resolution of distinct lineages within the phytoplasma 16Sr groups. RFLP analysis of rp gene sequences permitted finer differentiation of phytoplasma strains in a given 16Sr group. In this study, we also designed several semi-universal and 16Sr group-specific rp gene-based primers that allow for the amplification of 11 16Sr group phytoplasmas.

Morphological descriptions and DNA barcodes of Oziella viscida n. sp. (Eriophyoidea, Phytoptidae) and two infrequently reported Trisetacus species (Nalepellidae) from Crimea

2021 ◽  
Author(s):  
Philipp E. Chetverikov ◽  
Denis S. Fedorov ◽  
Anna E. Romanovich ◽  
Jacqueline V. Sarratt
Keyword(s):  
Phylogenetic Analyses ◽  
Pinus Nigra ◽  
Mite Species ◽  
Dna Barcodes ◽  
Gene Sequences ◽  
Prodorsal Shield ◽  
Viscous Material ◽  
Pinus Brutia ◽  
Blast Search ◽  
Juncus Maritimus

We report on a new phytoptid mite species, Oziella viscida n. sp., collected in Western Crimea from sea rush, Juncus maritimus (Juncaceae), and give supplementary descriptions of two rarely encountered nalepellid species of the genus Trisetacus from pines: T. confusus Livshits & Vasilieva, 1982 (in Vasilieva et al. 1982) from needle sheaths of Pinus nigra ssp. pallasiana (Pinaceae), an endemic subspecies restricted to Crimea, and T. brevisetus Livshits & Sekerskaya, 1982 (in Vasilieva et al. 1982) from needle sheaths of Pinus brutia ssp. pityusa (Steven) Silba, a relatively isolated subspecies of Turkish pine (P. brutia Tenore) growing in Georgia, Caucasus and Crimea. Oziella viscida n. sp. is remarkable in that most specimens were found inhabiting the basal part of leaves and stems of J. maritimus, an area covered by a transparent, sticky exudate apparently secreted by the plant epidermis. The mites were completely embedded in this substance and, rather than crawling with their legs, were observed moving through the viscous material while bending their opisthosoma in a serpentine or wormlike manner—an adaptation that appears to be currently unreported in eriophyoids and possibly reminiscent of locomotion of ancestral “protoeriophyoids” associated with soil. In comparison to females, males of O. viscida n. sp. and T. confusus have a more distinct prodorsal shield pattern consisting of a larger number of longer lines. Three new barcode gene sequences were obtained: MZ220550 (Cox1, O. viscida n. sp., 1159 bp), MZ224497 (18S, 2012 bp, T. brevisetus), and MZ224498 (18S, 2013 bp T. confusus). A BLAST search of the 18S sequences of T. brevisetus and T. confusus shows them as slightly closer to other 18S sequences of Trisetacus from Pinaceae (95.5%–96.3% identity) than to Trisetacus from Cupressaceae (93.6%–94.0% identity). Comparison of sequences of nalepellids currently present in GenBank suggest that a complete 18S sequence KJ841938.1 (2252 bp) from China belongs to an identified Trisetacus from Pinaceae rather than to Setoptus koraiensis as labelled, highlighting the necessity to review carefully the sequences of Eriophyoidea prior to using them in phylogenetic analyses, as well as the need to recollect and resequence S. koraiensis to clarify the nature of the problematic data from GenBank assigned to this species.  

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