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 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).

Single nucleotide polymorphisms, putatively neutral DNA markers and population genetic parameters in Indian Plasmodium vivax isolates

Parasitology ◽  
2010 ◽  
Vol 137 (12) ◽  
pp. 1721-1730 ◽  
Author(s):  
BHAVNA GUPTA ◽  
ADITYA P. DASH ◽  
NALINI SHRIVASTAVA ◽  
APARUP DAS
Keyword(s):  
Population Genetics ◽  
Single Nucleotide Polymorphisms ◽  
Plasmodium Vivax ◽  
Population Genetic ◽  
Syntenic Region ◽  
Sequence Information ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Intergenic Regions ◽  
Neutral Markers

SUMMARYWith a view to developing putatively neutral markers based on Single Nucleotide Polymorphisms (SNPs) in the human malaria parasite, Plasmodium vivax, we utilized the published whole genome sequence information of P. falciparum and P. vivax to find a ~200 kb conserved syntenic region between these two species. We have selected 27 non-coding DNA fragments (in introns and intergenic regions) of variable length (300–750 bp) in P. vivax in this syntenic region. PCR of P. vivax isolates of a population sample from India could successfully amplify 17 fragments. Subsequently, DNA sequencing and sequence analysis confirmed the polymorphic status of only 11 fragments. Altogether, 18 SNPs were detected and 2 different measures of nucleotide diversity showed variable patterns across different fragments; in general, introns were less variable than the intergenic regions. All 11 polymorphic fragments were found to be evolving according to a neutral equilibrium model and thus could be utilized as putatively neutral markers for population genetic studies in P. vivax. Different molecular population genetics parameters were also estimated, providing initial insight into the population genetics of Indian P. vivax.

Continuous Exchange of Sequence Information Between Dispersed Tc1 Transposons in the Caenorhabditis elegans Genome

Genetics ◽  
2003 ◽  
Vol 164 (1) ◽  
pp. 127-134
Author(s):  
Sylvia E J Fischer ◽  
Erno Wienholds ◽  
Ronald H A Plasterk
Keyword(s):  
Caenorhabditis Elegans ◽  
Strand Break ◽  
Sequence Information ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
C Elegans ◽  
Genome Wide ◽  
A Genome ◽  
Endogenous Genes ◽  
Caenorhabditis Elegans Genome

Abstract In a genome-wide analysis of the active transposons in Caenorhabditis elegans we determined the localization and sequence of all copies of each of the six active transposon families. Most copies of the most active transposons, Tc1 and Tc3, are intact but individually have a unique sequence, because of unique patterns of single-nucleotide polymorphisms. The sequence of each of the 32 Tc1 elements is invariant in the C. elegans strain N2, which has no germline transposition. However, at the same 32 Tc1 loci in strains with germline transposition, Tc1 elements can acquire the sequence of Tc1 elements elsewhere in the N2 genome or a chimeric sequence derived from two dispersed Tc1 elements. We hypothesize that during double-strand-break repair after Tc1 excision, the template for repair can switch from the Tc1 element on the sister chromatid or homologous chromosome to a Tc1 copy elsewhere in the genome. Thus, the population of active transposable elements in C. elegans is highly dynamic because of a continuous exchange of sequence information between individual copies, potentially allowing a higher evolution rate than that found in endogenous genes.

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.

scholarly journals Identification of the Genetic Variation and Gene Exchange between Citrus Trifoliata and Citrus Clementina

Biomolecules ◽  
2018 ◽  
Vol 8 (4) ◽  
pp. 182
Author(s):  
Tian-Jia Liu ◽  
Jing-Jing Zhou ◽  
Fa-Yi Chen ◽  
Zhi-Meng Gan ◽  
Yong-Ping Li ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genetic Basis ◽  
Reference Genome ◽  
Gene Exchange ◽  
Nucleotide Polymorphisms ◽  
Citrus Species ◽  
Genome Resequencing ◽  
Single Nucleotide ◽  
Citrus Clementina ◽  
Fundamental Information

To identify the genetic variation between Citrus trifoliata and Citrus clementina, we performed genome resequencing on the two citrus species. Compared with the citrus reference genome, a total of 9,449,204 single-nucleotide polymorphisms (SNPs) and 846,615 insertion/deletion polymorphisms (InDels) were identified in the two citrus species, while 1,868,115 (19.77%) of the SNPs and 190,199 (22.47%) of the InDels from the two citrus species were located in the genic regions. Meanwhile, a total of 8,091,407 specific SNPs and 692,654 specific InDels were identified in the two citrus genotypes, yielding an average of 27.32 SNPs/kb and 2.34 InDels/kb. We identified and characterized the patterns of gene exchanges in the grafted citrus plants by using specific genetic variation from genome resequencing. A total of 4396 transporting genes across graft junctions was identified. Some specific genetic variation and mobile genes was also confirmed by Sanger sequencing. Furthermore, these mobile genes could move directionally or bidirectionally between the scions and the rootstocks. In addition, a total of 1581 and 2577 differentially expressed genes were found in the scions and the rootstocks after grafting compared with the control, respectively. These genetic variations provide fundamental information on the genetic basis of important traits between C. trifoliata and C. clementina, as the transport of genes would be applicable to horticulture crops.

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