scholarly journals Whole-Genome Deep Sequencing Reveals Host-Driven in-planta Evolution of Columnea Latent Viroid (CLVd) Quasi-Species Populations

2020 ◽  
Vol 21 (9) ◽  
pp. 3262 ◽  
Author(s):  
Parichate Tangkanchanapas ◽  
Annelies Haegeman ◽  
Tom Ruttink ◽  
Monica Höfte ◽  
Kris De Jonghe
Keyword(s):  
Structure Prediction ◽  
Host Plants ◽  
Secondary Structure Prediction ◽  
Infectious Clone ◽  
Amplicon Sequencing ◽  
Nucleotide Polymorphisms ◽  
In Planta ◽  
Single Nucleotide ◽  
Nucleotide Insertions ◽  
Columnea Latent Viroid

Columnea latent viroid (CLVd) is one of the most serious tomato diseases. In general, viroids have high mutation rates. This generates a population of variants (so-called quasi-species) that co-exist in their host and exhibit a huge level of genetic diversity. To study the population of CLVd in individual host plants, we used amplicon sequencing using specific CLVd primers linked with a sample-specific index sequence to amplify libraries. An infectious clone of a CLVd isolate Chaipayon-1 was inoculated on different solanaceous host plants. Six replicates of the amplicon sequencing results showed very high reproducibility. On average, we obtained 133,449 CLVd reads per PCR-replicate and 79 to 561 viroid sequence variants, depending on the plant species. We identified 19 major variants (>1.0% mean relative abundance) in which a total of 16 single-nucleotide polymorphisms (SNPs) and two single nucleotide insertions were observed. All major variants contained a combination of 4 to 6 SNPs. Secondary structure prediction clustered all major variants into a tomato/bolo maka group with four loops (I, II, IV and V), and a chili pepper group with four loops (I, III, IV and V) at the terminal right domain, compared to the CLVd Chaipayon-1 which consists of five loops (I, II, III, IV and V).

scholarly journals Population structure of eulachon Thaleichthys pacificus from Northern California to Alaska using single nucleotide polymorphisms from direct amplicon sequencing

2020 ◽  
Author(s):  
Ben J. G. Sutherland ◽  
John Candy ◽  
Kayla Mohns ◽  
Olivia Cornies ◽  
Kim Jonsen ◽  
...  
Keyword(s):  
Gulf Of Alaska ◽  
Amplicon Sequencing ◽  
Fraser River ◽  
Northern California ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Southeast Alaska ◽  
Southern Us ◽  
Mixed Stock ◽  
Future Work

ABSTRACTEulachon Thaleichthys pacificus, a culturally and ecologically important anadromous smelt (Family Osmeridae), ranges from Northern California to the southeast Bering Sea. In recent decades, some populations have experienced declines. Here we use a contig-level genome assembly combined with previously published RADseq-derived markers to construct an amplicon panel for eulachon. Using this panel, we develop a filtered genetic baseline of 521 variant loci genotyped in 1,989 individuals from 14 populations ranging from Northern California through Central Alaska. Consistent with prior genetic studies, the strongest separation occurs among three main regions: from Northern California up to and including the Fraser River; north of the Fraser River to southeast Alaska; and within the Gulf of Alaska. Separating the Fraser River from southern US populations, and refining additional substructure within the central coast may be possible in mixed-stock analysis; this will be addressed in future work. The amplicon panel outperformed the previous microsatellite panel, and thus will be used in future mixed-stock analyses of eulachon in order to provide new insights for management and conservation of eulachon.

A STRUCTURAL BIOINFORMATICS APPROACH TO THE ANALYSIS OF NONSYNONYMOUS SINGLE NUCLEOTIDE POLYMORPHISMS (nsSNPs) AND THEIR RELATION TO DISEASE

2007 ◽  
Vol 05 (06) ◽  
pp. 1297-1318 ◽  
Author(s):  
CATHERINE L. WORTH ◽  
G. RICHARD J. BICKERTON ◽  
ADRIAN SCHREYER ◽  
JULIA R. FORMAN ◽  
TAMMY M. K. CHENG ◽  
...  
Keyword(s):  
Amino Acid ◽  
Single Nucleotide Polymorphisms ◽  
Structure Prediction ◽  
Three Dimensional ◽  
Comparative Modeling ◽  
Divergent Evolution ◽  
Amino Acid Substitutions ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Human Proteins

The prediction of the effects of nonsynonymous single nucleotide polymorphisms (nsSNPs) on function depends critically on exploiting all information available on the three-dimensional structures of proteins. We describe software and databases for the analysis of nsSNPs that allow a user to move from SNP to sequence to structure to function. In both structure prediction and the analysis of the effects of nsSNPs, we exploit information about protein evolution, in particular, that derived from investigations on the relation of sequence to structure gained from the study of amino acid substitutions in divergent evolution. The techniques developed in our laboratory have allowed fast and automated sequence-structure homology recognition to identify templates and to perform comparative modeling; as well as simple, robust, and generally applicable algorithms to assess the likely impact of amino acid substitutions on structure and interactions. We describe our strategy for approaching the relationship between SNPs and disease, and the results of benchmarking our approach — human proteins of known structure and recognized mutation.

scholarly journals Population structure of eulachon (Thaleichthys pacificus) from Northern California to Alaska using single nucleotide polymorphisms from direct amplicon sequencing

2021 ◽  
Vol 78 (1) ◽  
pp. 78-89
Author(s):  
Ben J.G. Sutherland ◽  
John Candy ◽  
Kayla Mohns ◽  
Olivia Cornies ◽  
Kim Jonsen ◽  
...  
Keyword(s):  
Gulf Of Alaska ◽  
Amplicon Sequencing ◽  
Fraser River ◽  
Northern California ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Southeast Alaska ◽  
Southern Us ◽  
Mixed Stock ◽  
Future Work

Eulachon (Thaleichthys pacificus), a culturally and ecologically important anadromous smelt (Family Osmeridae), ranges from Northern California to the southeast Bering Sea. In recent decades, some populations have experienced declines. Here we use a contig-level genome assembly combined with previously published restriction site-associated DNA sequencing (RADseq)-derived markers to construct an amplicon panel for eulachon. Using this panel, we develop a filtered genetic baseline of 521 variant loci genotyped in 1989 individuals from 14 populations ranging from Northern California through central Alaska. Consistent with prior genetic studies, the strongest separation occurs among three main regions: from Northern California up to and including the Fraser River; north of the Fraser River to southeast Alaska; and within the Gulf of Alaska. Separating the Fraser River from southern US populations and refining additional substructure within the central coast may be possible in mixed-stock analysis; this will be addressed in future work. The amplicon panel outperformed the previous microsatellite panel and thus will be used in future mixed-stock analyses of eulachon to provide new insights for management and conservation of eulachon.

scholarly journals Predicting the effects of the single nucleotide polymorphism A122V on CXC chemokine receptor type 1 of Bos taurus (Artiodactyla: Bovidae) cattle by in silico analyses

Biotemas ◽  
2017 ◽  
Vol 30 (4) ◽  
pp. 1-6 ◽  
Author(s):  
Anete Ferraz Guzzi ◽  
Felipe Santos de Luna Oliveira ◽  
Márcia Maria de Souza Amaro ◽  
Paulo Fernando Tavares Filho ◽  
Jane Eyre Gabriel
Keyword(s):  
In Silico ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Bos Taurus ◽  
Protein Secondary Structure ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Cxc Chemokine ◽  
In Silico Analyses

Este estudo objetivou predizer bioquimicamente as estruturas primárias e secundárias da proteína receptora de quimiocina CXCR1 bovina não polimórfica e polimórfica carreando o polimorfismo A122V por análises in silico. Duas sequências da proteína CXCR1 de bovino Bos taurus foram selecionadas a partir da base de dados de sequências de proteínas UniProtKB/Swiss-Prot: a) uma sequência não polimórfica (A7KWG0), contendo o aminoácido alanina (A) na posição 122, e b) uma sequência polimórfica, apresentando o aminoácido valina (V) na mesma posição. As estruturas primárias e secundárias da proteína foram preditas empregando os programas ProtParam e Chou & Fasman Protein Secondary Structure Prediction CFSSP. Diferenças nos parâmetros físicos e químicos não foram previstas a partir da estrutura primária de ambas as proteínas analisadas. A presença de um domínio helicoidal, situado nas posições 100 e 150, foi exclusivamente encontrada na proteína CXCR1 não polimórfica. Resíduos de aminoácidos de propriedades bioquímicas variáveis foram detectados na posição 122 na proteína CXCR1 dos ruminantes e humana, sugerindo que esse peptídeo é altamente polimórfico em vertebrados. Os resultados aqui descritos predizem diferenças no padrão da estrutura secundária da proteína CXCR1 bovina não polimórfica e polimórfica A122V empregando ferramentas de Bioinformática. 

scholarly journals Prediction and analysis of functional RNA structures within the integrative genomics viewer

2022 ◽  
Vol 4 (1) ◽  
Author(s):  
Warren B Rouse ◽  
Ryan J Andrews ◽  
Nicholas J Booher ◽  
Jibo Wang ◽  
Michael E Woodman ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Structure Prediction ◽  
Rna Secondary Structure ◽  
Drug Targets ◽  
Rna Binding ◽  
Secondary Structure Prediction ◽  
Rna Binding Proteins ◽  
Published Data ◽  
Nucleotide Polymorphisms ◽  
Integrative Genomics

ABSTRACT In recent years, interest in RNA secondary structure has exploded due to its implications in almost all biological functions and its newly appreciated capacity as a therapeutic agent/target. This surge of interest has driven the development and adaptation of many computational and biochemical methods to discover novel, functional structures across the genome/transcriptome. To further enhance efforts to study RNA secondary structure, we have integrated the functional secondary structure prediction tool ScanFold, into IGV. This allows users to directly perform structure predictions and visualize results—in conjunction with probing data and other annotations—in one program. We illustrate the utility of this new tool by mapping the secondary structural landscape of the human MYC precursor mRNA. We leverage the power of vast ‘omics’ resources by comparing individually predicted structures with published data including: biochemical structure probing, RNA binding proteins, microRNA binding sites, RNA modifications, single nucleotide polymorphisms, and others that allow functional inferences to be made and aid in the discovery of potential drug targets. This new tool offers the RNA community an easy to use tool to find, analyze, and characterize RNA secondary structures in the context of all available data, in order to find those worthy of further analyses.

scholarly journals Multiple Drug Resistance in the canine hookworm Ancylostoma caninum: an Emerging Threat

2019 ◽  
Author(s):  
Pablo D. Jimenez Castro ◽  
Sue Howell ◽  
John. J. Schaefer ◽  
Russell. W. Avramenko ◽  
John. S. Gilleard ◽  
...  
Keyword(s):  
Anthelmintic Resistance ◽  
Multiple Drug Resistance ◽  
Scale Up ◽  
Amplicon Sequencing ◽  
The United States ◽  
Multiple Drug ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Ancylostoma Caninum ◽  
Health Community

AbstractIn the past few years, diagnoses by veterinarians of recurrent canine hookworm infections have dramatically increased, suggesting that anthelmintic resistance (AR) may have evolved in the parasite Ancylostoma caninum. To investigate this, we established three “suspected-resistant” and two susceptible A. caninum isolates in research dogs for further study. The egg hatch assay (EHA) and the larval development assay (LDA) were used for detecting resistance to benzimidazoles, and macrocyclic lactones, respectively. Resistance ratios ranged from 6.0 to >100 and 5.5-69.8 for the EHA and LDA, respectively. Following treatments with fenbendazole, pyrantel and milbemycin oxime, reduction in faecal egg counts ranged from 64–86%, 0–72% and 58–92%, respectively. Deep amplicon sequencing of the isotype-1 β tubulin gene identified a high frequency of resistance-associated single nucleotide polymorphisms at codon 167 in the resistant isolates and clinical cases.. These data conclusively demonstrate multiple anthelmintic resistance in A. caninum, and provide pivotal evidence that this is an emerging problem in the United States. Consequently, these findings should provide some concern to the global health community, as the scale-up of mass drug administration for soil-transmitted helminths (STH) is now placing similar selection pressures for benzimidazole resistance in human hookworms.

Carboxylesterase 1 genes: systematic review and evaluation of existing genotyping procedures

2018 ◽  
Vol 33 (1) ◽  
pp. 3-14 ◽  
Author(s):  
Henrik Berg Rasmussen ◽  
Majbritt Busk Madsen
Keyword(s):  
Amplicon Sequencing ◽  
Enzyme Treatment ◽  
Sequence Information ◽  
Segmental Duplications ◽  
Gene Exchange ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Specific Amplification ◽  
Carboxylesterase 1 ◽  
Hybrid Genes

AbstractThe carboxylesterase 1 gene (CES1) encodes a hydrolase that metabolizes commonly used drugs. TheCES1-related pseudogene, carboxylesterase 1 pseudogene 1 (CES1P1), has been implicated in gene exchange withCES1and in the formation of hybrid genes including the carboxylesterase 1A2 gene (CES1A2). Hence, theCES1region is complex. Usingin silicoPCR and alignment, we assessed the specificity of PCR-assisted procedures for genotypingCES1,CES1A2andCES1P1in studies identified in PubMed. We identified 33 such studies and excluded those that were not the first to use a procedure or lacked sequence information. After this 17 studies remained. Ten of these used haplotype-specific amplification, restriction enzyme treatment or amplicon sequencing, and included five that were predicted to lack specificity. All procedures for genotyping of single nucleotide polymorphisms in eight studies lacked specificity. One of these studies also used amplicon sequencing, thus being present in the group above. Some primers and their intended targets were mismatched. We provide experimental evidence that one of the procedures lacked specificity. Additionally, a complex pattern of segmental duplications in theCES1region was revealed. In conclusion, many procedures forCES1,CES1A2andCES1P1genotyping appear to lack specificity. Knowledge about the segmental duplications may improve the typing of these genes.

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