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.

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 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 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.

scholarly journals Impact of metal oxide nanoparticles on in vitro DNA amplification

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7228 ◽  
Author(s):  
Chun-Hui Gao ◽  
Monika Mortimer ◽  
Ming Zhang ◽  
Patricia A. Holden ◽  
Peng Cai ◽  
...  
Keyword(s):  
Metal Oxide ◽  
Dna Polymerase ◽  
Metal Oxide Nanoparticles ◽  
Pcr Amplification ◽  
Dna Amplification ◽  
Amplicon Sequencing ◽  
High Fidelity ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

Polymerase chain reaction (PCR) is used as an in vitro model system of DNA replication to assess the genotoxicity of nanoparticles (NPs). Prior results showed that several types of NPs inhibited PCR efficiency and increased amplicon error frequency. In this study, we examined the effects of various metal oxide NPs on inhibiting PCR, using high- vs. low-fidelity DNA polymerases; we also examined NP-induced DNA mutation bias at the single nucleotide level. The effects of seven major types of metal oxide NPs (Fe2O3, ZnO, CeO2, Fe3O4, Al2O3, CuO, and TiO2) on PCR replication via a low-fidelity DNA polymerase (Ex Taq) and a high-fidelity DNA polymerase (Phusion) were tested. The successfully amplified PCR products were subsequently sequenced using high-throughput amplicon sequencing. Using consistent proportions of NPs and DNA, we found that the effects of NPs on PCR yield differed depending on the DNA polymerase. Specifically, the efficiency of the high-fidelity DNA polymerase (Phusion) was significantly inhibited by NPs during PCR; such inhibition was not evident in reactions with Ex Taq. Amplicon sequencing showed that the overall error rate of NP-amended PCR was not significantly different from that of PCR without NPs (p > 0.05), and NPs did not introduce single nucleotide polymorphisms during PCR. Thus, overall, NPs inhibited PCR amplification in a DNA polymerase-specific manner, but mutations were not introduced in the process.

scholarly journals Development of a workflow for identification of nuclear genotyping markers for Cyclospora cayetanensis

Parasite ◽  
2020 ◽  
Vol 27 ◽  
pp. 24 ◽  
Author(s):  
Katelyn A. Houghton ◽  
Alexandre Lomsadze ◽  
Subin Park ◽  
Fernanda S. Nascimento ◽  
Joel Barratt ◽  
...  
Keyword(s):  
Sanger Sequencing ◽  
Intestinal Parasite ◽  
Epidemiological Data ◽  
Amplicon Sequencing ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Molecular Genotyping ◽  
Cyclospora Cayetanensis ◽  
Outbreak Investigations ◽  
Stool Specimens

Cyclospora cayetanensis is an intestinal parasite responsible for the diarrheal illness, cyclosporiasis. Molecular genotyping, using targeted amplicon sequencing, provides a complementary tool for outbreak investigations, especially when epidemiological data are insufficient for linking cases and identifying clusters. The goal of this study was to identify candidate genotyping markers using a novel workflow for detection of segregating single nucleotide polymorphisms (SNPs) in C. cayetanensis genomes. Four whole C. cayetanensis genomes were compared using this workflow and four candidate markers were selected for evaluation of their genotyping utility by PCR and Sanger sequencing. These four markers covered 13 SNPs and resolved parasites from 57 stool specimens, differentiating C. cayetanensis into 19 new unique genotypes.

scholarly journals Genomic consequences of multiple speciation processes in a stick insect

2012 ◽  
Vol 279 (1749) ◽  
pp. 5058-5065 ◽  
Author(s):  
Patrik Nosil ◽  
Zach Gompert ◽  
Timothy E. Farkas ◽  
Aaron A. Comeault ◽  
Jeffrey L. Feder ◽  
...  
Keyword(s):  
Spatial Information ◽  
Stick Insect ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Outlier Loci ◽  
Stick Insects ◽  
Genomic Divergence ◽  
Host Plant Use ◽  
Future Work

Diverse geographical modes and mechanisms of speciation are known, and individual speciation genes have now been identified. Despite this progress, genome-wide outcomes of different evolutionary processes during speciation are less understood. Here, we integrate ecological and spatial information, mating trials, transplantation data and analysis of 86 130 single nucleotide polymorphisms (SNPs) in eight populations (28 pairwise comparisons) of Timema cristinae stick insects to test the effects of different factors on genomic divergence in a system undergoing ecological speciation. We find patterns consistent with effects of numerous factors, including geographical distance, gene flow, divergence in host plant use and climate, and selection against maladaptive hybridization (i.e. reinforcement). For example, the number of highly differentiated ‘outlier loci’, allele-frequency clines and the overall distribution of genomic differentiation were recognizably affected by these factors. Although host use has strong effects on phenotypic divergence and reproductive isolation, its effects on genomic divergence were subtler and other factors had pronounced effects. The results demonstrate how genomic data can provide new insights into speciation and how genomic divergence can be complex, yet predictable. Future work could adopt experimental, mapping and functional approaches to directly test which genetic regions are affected by selection and determine their physical location in the genome.

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