scholarly journals First Molecular Characterization of Poxviruses in Cattle, Sheep, and Goats in Botswana

2021 ◽  
Author(s):  
Boitumelo Magret Modise ◽  
Tirumala Bharani Kumar Settypalli ◽  
Tebogo Kgotlele ◽  
Dingrong Xue ◽  
Kebonyemodisa Ntesang ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Clinical Symptoms ◽  
Phylogenetic Analyses ◽  
Small Ruminants ◽  
Virus Diseases ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Lumpy Skin Disease ◽  
Multiple Sequence Alignments

Abstract BackgroundPoxviruses within the Capripoxvirus, Orthopoxvirus, and Parapoxvirus genera can infect livestock, with the two former presenting also zoonotic importance. In addition, they induce similar clinical symptoms in common host species, creating a challenge for diagnosis. Although endemic in the country, poxvirus infections of small ruminants and cattle have received little attention in Botswana, and there was no prior attempt of using molecular tools to diagnose the diseases and characterize the pathogens.MethodsA high-resolution melting (HRM) assay was used to detect and differentiate poxviruses in samples from four cattle (from Mahalapye, Kasane, and Molepolole), one sheep (from Jwaneng), and one goat (from Kasane). Molecular characterization of capripoxviruses and parapoxviruses was undertaken by sequence analysis of RPO30 and GPCR genes.ResultsThe HRM assay revealed lumpy skin disease virus (LSDV) in three cattle samples, pseudocowpox virus (PCPV) in one cattle sample, and orf virus (ORFV) in one goat and one sheep sample. The phylogenetic analyses, based on the RPO30 and GPCR, and the inspection of the multiple sequence alignments showed that the LSDV sequences of Botswana were more like those of common LSDV field isolates encountered in Africa, Asia, and Europe. The Botswana PCPV presented unique features and clustered between camel isolates and cattle isolates of the PCPV group. The Botswana ORFV from goat differed from the ORFV collected in sheep.ConclusionsThis study is the first report on the genetic characterization of pox virus diseases circulating in cattle, goats, and sheep in Botswana. It shows the importance of molecular methods to differentially diagnose pox virus diseases of ruminants.

scholarly journals First molecular characterization of poxviruses in cattle, sheep, and goats in Botswana

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Boitumelo Magret Modise ◽  
Tirumala Bharani Kumar Settypalli ◽  
Tebogo Kgotlele ◽  
Dingrong Xue ◽  
Kebonyemodisa Ntesang ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Clinical Symptoms ◽  
Phylogenetic Analyses ◽  
Small Ruminants ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Lumpy Skin Disease ◽  
Multiple Sequence Alignments ◽  
Prior Use

Abstract Background Poxviruses within the Capripoxvirus, Orthopoxvirus, and Parapoxvirus genera can infect livestock, with the two former having zoonotic importance. In addition, they induce similar clinical symptoms in common host species, creating a challenge for diagnosis. Although endemic in the country, poxvirus infections of small ruminants and cattle have received little attention in Botswana, with no prior use of molecular tools to diagnose and characterize the pathogens. Methods A high-resolution melting (HRM) assay was used to detect and differentiate poxviruses in skin biopsy and skin scab samples from four cattle, one sheep, and one goat. Molecular characterization of capripoxviruses and parapoxviruses was undertaken by sequence analysis of RPO30 and GPCR genes. Results The HRM assay revealed lumpy skin disease virus (LSDV) in three cattle samples, pseudocowpox virus (PCPV) in one cattle sample, and orf virus (ORFV) in one goat and one sheep sample. The phylogenetic analyses, based on the RPO30 and GPCR multiple sequence alignments showed that the LSDV sequences of Botswana were similar to common LSDV field isolates encountered in Africa, Asia, and Europe. The Botswana PCPV presented unique features and clustered between camel and cattle PCPV isolates. The Botswana ORFV sequence isolated from goat differed from the ORFV sequence isolated from sheep. Conclusions This study is the first report on the genetic characterization of poxvirus diseases circulating in cattle, goats, and sheep in Botswana. It shows the importance of molecular methods to differentially diagnose poxvirus diseases of ruminants.

scholarly journals Characterization of two novel EF-hand proteins identifies a clade of putative Ca2+-binding protein specific to the Ambulacraria

2020 ◽  
Author(s):  
Arisnel Soto-Acabá ◽  
Pablo A. Ortíz-Pineda ◽  
José E. García-Arrarás
Keyword(s):  
Calcium Binding ◽  
Phylogenetic Analyses ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Significant Similarity ◽  
Significant Differential Expression ◽  
Multiple Sequence Alignments ◽  
Ef Hand ◽  
Protein Discovery

AbstractIn recent years, transcriptomic databases have become one of the main sources for protein discovery. In our studies of nervous system and digestive tract regeneration in echinoderms, we have identified several transcripts that have attracted our attention. One of these molecules corresponds to a previously unidentified transcript (Orpin) from the sea cucumber Holothuria glaberrima that appeared to be upregulated during intestinal regeneration. We have now identified a second highly similar sequence and analyzed the predicted proteins using bioinformatics tools. Both sequences have EF-hand motifs characteristic of calcium-binding proteins (CaBPs) and N-terminal signal peptides. Sequence comparison analyses such as multiple sequence alignments and phylogenetic analyses only showed significant similarity to sequences from other echinoderms or from hemichordates. Semi-quantitative RT-PCR analyses revealed that transcripts from these sequences are expressed in various tissues including muscle, haemal system, gonads, and mesentery. However, contrary to previous reports, there was no significant differential expression in regenerating tissues. Nonetheless, the identification of unique features in the predicted proteins suggests that these might comprise a novel subfamily of EF-hand containing proteins specific to the Ambulacraria clade.

scholarly journals Molecular characterization of lumpy skin disease virus (LSDV) emerged in Bangladesh reveals unique genetic features compared to contemporary field strains

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Shukes Chandra Badhy ◽  
Mohammad Golam Azam Chowdhury ◽  
Tirumala Bharani Kumar Settypalli ◽  
Giovanni Cattoli ◽  
Charles Euloge Lamien ◽  
...  
Keyword(s):  
Middle East ◽  
Molecular Characterization ◽  
Disease Virus ◽  
Skin Disease ◽  
Clinical Signs ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Lumpy Skin Disease ◽  
Lumpy Skin Disease Virus

Abstract Background Lumpy skin disease (LSD) is a contagious viral disease of cattle caused by lumpy skin disease virus (LSDV). LSD has recently spread in Asia following outbreaks in the Middle East and Europe. The disease emerged in Bangladesh in July 2019 in the Chattogram district, then rapidly spread throughout the entire country. We investigated six LSD outbreaks in Bangladesh to record the clinical signs and collect samples for diagnostic confirmation. Furthermore, we performed the molecular characterization of Bangladesh isolates, analyzing the full RPO30 and GPCR genes and the partial EEV glycoprotein gene. Results Clinical observations revealed common LSD clinical signs in the affected cattle. PCR and real-time PCR, showed the presence of the LSDV genome in samples from all six districts. Phylogenetic analysis and detailed inspection of multiple sequence alignments revealed that Bangladesh isolates differ from common LSDV field isolates encountered in Africa, the Middle East, and Europe, as well as newly emerged LSDV variants in Russia and China. Instead, they were closely related to LSDV KSGP-0240, LSDV NI2490, and LSDV Kenya. Conclusions These results show the importance of continuous monitoring and characterization of circulating strains and the need to continually refine the strategies for differentiating vaccine strains from field viruses.

Morphological redescription and molecular characterization of Trichodina matsu Basson & Van As, 1994 (Ciliophora, Mobilida, Trichodinidae) infecting Tachysurus fulvidraco (Richardson, 1846) from Chongqing, China

Zootaxa ◽  
2021 ◽  
Vol 4995 (2) ◽  
pp. 334-344
Author(s):  
QIAN ZHOU ◽  
FAHUI TANG ◽  
YUANJUN ZHAO
Keyword(s):  
Phylogenetic Analyses ◽  
Molecular Data ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Similar Species ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Morphological And Molecular Data ◽  
Tachysurus Fulvidraco

During a survey of parasitic ciliates in Chongqing, China, Trichodina matsu Basson & Van As, 1994 was isolated from gills of Tachysurus fulvidraco. Furthermore, the 18S rRNA gene and ITS-5.8S rRNA region of T. matsu were sequenced for the first time and applied for the species identification and comparison with similar species in the present study. Based on the morphological and molecular comparisons, the results indicate that T. matsu is an ectoparasite specific for the Siluriformes catfish. Based on the analyses of genetic distance, multiple sequence alignments, and phylogenetic analyses, no obvious differentiation within populations of T. matsu was found. In addition, the ‘Trichodina hyperparasitis’ (KX904933) in GenBank is a misidentification and appears to be conspecific with T. matsu according to the comparison of morphological and molecular data.  

scholarly journals SequenceBouncer: A method to remove outlier entries from a multiple sequence alignment

2020 ◽  
Author(s):  
Cory D. Dunn
Keyword(s):  
Nucleic Acid ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Phylogenetic Analyses ◽  
Protein Sequences ◽  
Mitochondrial Genomes ◽  
Dna Barcodes ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments

AbstractPhylogenetic analyses can take advantage of multiple sequence alignments as input. These alignments typically consist of homologous nucleic acid or protein sequences, and the inclusion of outlier or aberrant sequences can compromise downstream analyses. Here, I describe a program, SequenceBouncer, that uses the Shannon entropy values of alignment columns to identify outlier alignment sequences in a manner responsive to overall alignment context. I demonstrate the utility of this software using alignments of available mammalian mitochondrial genomes, bird cytochrome c oxidase-derived DNA barcodes, and COVID-19 sequences.

Phylogenetics of scolopendromorph centipedes: can denser taxon sampling improve an artificial classification?

2013 ◽  
Vol 27 (5) ◽  
pp. 578 ◽  
Author(s):  
Varpu Vahtera ◽  
Gregory D. Edgecombe ◽  
Gonzalo Giribet
Keyword(s):  
Bayesian Inference ◽  
New World ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Taxon Sampling ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Artificial Classification

Previous phylogenetic analyses of the centipede order Scolopendromorpha indicated a fundamental division into blind and ocellate clades. These analyses corroborated the monophyly of most families and tribes but suggested that several species-rich, cosmopolitan genera in traditional and current classifications are polyphyletic. Denser taxon sampling is applied to a dataset of 122 morphological characters and sequences for four nuclear and mitochondrial loci. Phylogenetic analyses including 98 species and subspecies of Scolopendromorpha employ parsimony under dynamic and static homology schemes as well as maximum likelihood and Bayesian inference of multiple sequence alignments. The monotypic Australian genera Notiasemus and Kanparka nest within Cormocephalus and Scolopendra, respectively, and the New Caledonian Campylostigmus is likewise a clade within Cormocephalus. New World Scolopendra are more closely related to Hemiscolopendra and Arthrorhabdus than to Scolopendra s.s., which is instead closely allied to Asanada; the tribe Asanadini nests within Scolopendrini for molecular and combined datasets. The generic classification of Otostigmini has a poor fit to phylogenetic relationships, although nodal support within this tribe is weak. New synonymies are proposed for Ectonocryptopinae Shelley & Mercurio, 2005 (= Newportiinae Pocock, 1896), Asanadini Verhoeff, 1907 (= Scolopendrini Leach, 1814), and Kanparka Waldock & Edgecombe, 2012 (= Scolopendra Linnaeus, 1758). Scolopendrid systematics largely depicts incongruence between phylogeny and classification rather than between morphology and molecules.

scholarly journals Relative model selection can be sensitive to multiple sequence alignment uncertainty

2021 ◽  
Author(s):  
Stephanie J Spielman ◽  
Molly Miraglia
Keyword(s):  
Model Selection ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Selection Procedure ◽  
Evolutionary Model ◽  
Ancestral State ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Nucleotide Data

Multiple sequence alignments (MSAs) represent the fundamental unit of data inputted to most comparative sequence analyses. In phylogenetic analyses in particular, errors in MSA construction have the potential to induce further errors in downstream analyses such as phylogenetic reconstruction itself, ancestral state reconstruction, and divergence estimation. In addition to providing phylogenetic methods with an MSA to analyze, researchers must also specify a suitable evolutionary model for the given analysis. Most commonly, researchers apply relative model selection to select a model from candidate set and then provide both the MSA and the selected model as input to subsequent analyses. While the influence of MSA errors has been explored for most stages of phylogenetics pipelines, the potential effects of MSA uncertainty on the relative model selection procedure itself have not been explored. In this study, we assessed the consistency of relative model selection when presented with multiple perturbed versions of a given MSA. We find that while relative model selection is mostly robust to MSA uncertainty, in a substantial proportion of circumstances, relative model selection identifies distinct best-fitting models from different MSAs created from the same set of sequences. We find that this issue is more pervasive for nucleotide data compared to amino-acid data. However, we also find that it is challenging to predict whether relative model selection will be robust or sensitive to uncertainty in a given MSA. We find that that MSA uncertainty can affect virtually all steps of phylogenetic analysis pipelines to a greater extent than has previously been recognized, including relative model selection.

scholarly journals QMaker: Fast and accurate method to estimate empirical models of protein evolution

2020 ◽  
Author(s):  
Bui Quang Minh ◽  
Cuong Cao Dang ◽  
Le Sy Vinh ◽  
Robert Lanfear
Keyword(s):  
Amino Acid ◽  
Amino Acid Substitution ◽  
Search Algorithm ◽  
Phylogenetic Analyses ◽  
Accurate Method ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Substitution Models ◽  
Protein Alignments

AbstractAmino acid substitution models play a crucial role in phylogenetic analyses. Maximum likelihood (ML) methods have been proposed to estimate amino acid substitution models, however, they are typically complicated and slow. In this paper, we propose QMaker, a new ML method to estimate a general time-reversible Q matrix from a large protein dataset consisting of multiple sequence alignments. QMaker combines an efficient ML tree search algorithm, a model selection for handling the model heterogeneity among alignments, and the consideration of rate mixture models among sites. We provide QMaker as a user-friendly function in the IQ-TREE software package (http://www.iqtree.org) supporting the use of multiple CPU cores so that biologists can easily estimate amino acid substitution models from their own protein alignments. We used QMaker to estimate new empirical general amino acid substitution models from the current Pfam database as well as five clade-specific models for mammals, birds, insects, yeasts, and plants. Our results show that the new models considerably improve the fit between model and data and in some cases influence the inference of phylogenetic tree topologies.

scholarly journals Molecular Characterization of a Novel Fusarivirus Infecting the Plant-pathogenic Fungus Alternaria Solani

2021 ◽  
Author(s):  
Jie Wei Gong ◽  
Hong Liu ◽  
Fei Xiao Zhu ◽  
Yun Shi Zhao ◽  
Le Jia Cheng ◽  
...  
Keyword(s):  
Amino Acids ◽  
Pathogenic Fungus ◽  
Alternaria Solani ◽  
Open Reading Frames ◽  
Phytopathogenic Fungus ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Putative Protein

Abstract A novel mycovirus belonging to the proposed family "Fusariviridae" was discovered in Alternaria Solani by sequencing a double-stranded RNA extracted from this phytopathogenic fungus. The virus was tentatively named “Alternaria solani fusarivirus 1” (AsFV1). AsFV1 has a single-stranded positive-sense (+ssRNA) genome of 6,845 nucleotides containing three open reading frames (ORFs) and a poly(A) tail. The largest ORF, ORF1 encodes a large polypeptide of 1,556 amino acids (aa) with conserved RNA-dependent RNA polymerase and helicase domains. The ORF2 and ORF3 have overlapping regions, encoding a putative protein of 522 amino acids (aa) and a putative protein of 105 amino acids (aa) respectively, for which function is unknown now. Multiple sequence alignments and phylogenetic analysis revealed AsFV1 belonging to Fusariviridae. This is the first report of the full-length nucleotide sequence of a fusarivirus infected with Alternaria solani.

Sign in / Sign up

Export Citation Format

Share Document