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76 results for “reduced representation sequencing”
epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS-based reduced representation bisulfite sequencing
<p>We present epiGBS2, a laboratory protocol based on epiGBS (Gurp et al., 2016) with a revised and user-friendly bioinformatics pipeline for a wide range of species with or without reference genome. Performance of several critical steps in epiGBS2 was evaluated against baseline data sets from <em>Arabidopsis thaliana</em> and Great tit (<em>Parus major</em>), which confirmed overall good performance of epiGBS2. We provide here the raw bisulfite sequencing data of the epiGBS2 run for <em>Arabidopsis thaliana.</em></p> <p>A detailed description of the laboratory protocol and an extensive manual of the bioinformatics pipeline are publicly accessible on github (<a href="https://github.com/nioo-knaw/epiGBS2">https://github.com/nioo-knaw/epiGBS2)</a> and zenodo (https://doi.org/10.5281/zenodo.4764652).</p> <p>Demultiplexed data were deposited on NCBI under the BioProject ID PRJNA764918</p>
Data and code for "Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR"
<p>This data set provides data files and R code to accompany the article <em>Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR</em> published by F1000Research.</p> <p>The data consists of Reduced Representation BS-seq methylation profiles of epithelial populations from the mouse mammary gland, with n=2 biological replicates for each of three cell populations.</p> <p>RNA-seq expression profiles of luminal and basal mammary epithelial populations are also provided.</p> <p>The R code undertakes an differential methylation analysis of the BS-seq profiles and demonstrates a strong negative correlation between the differential methylation and differential expression results.</p>
Code and data associated with Christiansen et al. 2021 "Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing"
<p>All code and data input and output files (except reference genome and raw sequencing data) needed to reproduce the results of Christiansen et al. 2021 as released on <a href="https://github.com/notothen/radpilot">https://github.com/notothen/radpilot</a> alongside journal publication. See published paper:</p> <p>Christiansen, H., Heindler, F.M., Hellemans, B. <em>et al.</em> Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing. <em>BMC Genomics</em> <strong>22, </strong>625 (2021). <a href="https://doi.org/10.1186/s12864-021-07917-3">https://doi.org/10.1186/s12864-021-07917-3</a></p>
Reduced representation sequencing to understand the evolutionary history of Torrey pine (Pinus torreyana Parry) with implications for rare species conservation
<p>Understanding the contribution of neutral and adaptive evolutionary processes to population differences is often necessary for better-informed management and conservation of rare species. In this study, we focused on <em>Pinus torreyana</em> Parry (Torrey pine), one of the world's rarest pines, endemic to one island and one mainland population in California. Small population size, low genetic diversity, and susceptibility to abiotic and biotic stresses suggest Torrey pine may benefit from inter-population genetic rescue to preserve the species' evolutionary potential. We leveraged reduced representation sequencing to tease apart the respective contributions of stochastic and deterministic evolutionary processes to population differentiation. We applied these data to model spatial and temporal demographic changes in effective population sizes and genetic connectivity, to assess loci possibly under selection, and to evaluate genetic rescue as a potential conservation strategy. Overall, we observed exceedingly low standing variation reflecting consistently low effective population sizes across time and limited genetic differentiation suggesting maintenance of gene flow following divergence. However, genome scans identified more than 2000 candidate SNPs for divergent selection. Combined with previous observations indicating population phenotypic differentiation, this indicates natural selection has likely contributed to the evolution of population genetic differences. Thus, while reduced genetic diversity, small effective population size, and genetic connectivity between populations suggest genetic rescue could mitigate the adverse effects of rarity, divergent selection suggests genetic mixing could disrupt adaptation. Further work evaluating the fitness consequences of inter-population admixture is necessary to empirically evaluate the trade-offs associated with genetic rescue in Torrey pine.</p>
Data from: How "simple" methodological decisions affect interpretation of population structure based on reduced representation library DNA sequencing: a case study using the lake whitefish
Reduced representation (RRL) sequencing approaches (e.g., RADSeq, genotyping by sequencing) require decisions about how much to invest in genome coverage and sequencing depth (library quality), as well as choices of values for adjustable bioinformatics parameters. To empirically explore the importance of these "simple" decisions, we generated two independent sequencing libraries for the same 142 individual lake whitefish (Coregonus clupeaformis) using a nextRAD RRL approach: (1) A small number of loci and low sequencing depth (library A); and (2) more loci and higher sequencing depth (library B). The fish were selected from populations with different levels of expected genetic subdivision. Each library was analyzed using the STACKS pipeline followed by three types of population structure assessment (FST, DAPC and ADMIXTURE) with iterative increases in the stringency of sequencing depth and missing data requirements, as well as more specific a priori population maps. Library B was always able to resolve strong population differentiation in all three types of assessment regardless of the selected parameters. In contrast, library A produced more variable results; increasing the minimum sequencing depth threshold (-m) resulted in a reduced number of retained loci, and therefore lost resolution at high -m values for FST and ADMIXTURE, but not DAPC. FST and DAPC were robust to varying the population map and increasing the stringency of missing data requirements. In contrast, ADMIXTURE was unable to resolve strong population differentiation when increasing these same parameters in library A. Similarly, when examining fine scale population subdivision, library B was robust to changing parameters but library A lost resolution depending on the parameter set. We used library B to examine actual subdivision in our study populations. All three types of analysis found complete subdivision among populations in Lake Huron, ON and Dore Lake, SK, Canada using 10,640 SNP loci. Weak population subdivision was detected in Lake Huron with fish from sites in the north-west, Search Bay, North Point and Hammond Bay, showing slight differentiation. Overall, we show that apparently simple decisions about library quality and bioinformatics parameters can have potentially important impacts on the interpretation of population subdivision. Although costly, the early investment in a high-quality library and more conservative stringency settings on STACKS parameters lead to a final dataset that was more consistent and robust when examining both weak and strong population differentiation.
Data from: How “simple” methodological decisions affect interpretation of population structure based on reduced representation library DNA sequencing: a case study using the lake whitefish
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Data from: Reduced representation sequencing detects only subtle regional structure in a heavily exploited and rapidly recolonizing marine mammal species
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Reduced representation sequencing to understand the evolutionary history of Torrey pine (Pinus torreyana Parry) with implications for rare species conservation
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Data from: Reduced-representation sequencing detects trans-Arctic connectivity and local adaptation in polar cod (Boreogadus saida)
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Data from: Reduced representation sequencing reveals weak genetic differentiation between Canadian and European Larus hyperboreus (Glaucous Gull)
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Data from: Inferring speciation history in the Andes with reduced-representation sequence data: an example in the bay-backed antpittas (Aves; Grallariidae; Grallaria hypoleuca s. l.)
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Data from: Reconstructing phylogeny from reduced-representation genome sequencing data without assembly or alignment
Reduced-representation genome sequencing such as RADseq aids the analysis of genomes by reducing the quantity of data, thereby lowering both sequencing costs and computational burdens. RADseq was initially designed for studying genetic variation across genomes at the population level, but has also proved to be suitable for interspecific phylogeny reconstruction. RADseq data pose challenges for standard phylogenomic methods, however, due to incomplete coverage of the genome and large amounts of missing data. Alignment-free methods are both efficient and accurate for phylogenetic reconstructions with whole genomes and are especially practical for non-model organisms; nonetheless, alignment-free methods have not been applied with reduced genome sequencing data. Here, we test a full-genome assembly and alignment-free method, AAF, in application to RADseq data and propose two procedures for reads selection to remove reads from restriction sites that were not found in taxa being compared. We validate these methods using both simulations and real datasets. Reads selection improved the accuracy of phylogenetic construction in every simulated scenario and the two real datasets, making AAF as good or better than a comparable alignment-based method, even though AAF had much lower computational burdens. We also investigated the sources of missing data in RADseq and their effects on phylogeny reconstruction using AAF. The AAF pipeline modified for RADseq or other reduced-representation sequencing data, phyloRAD, is available on github (https://github.com/fanhuan/phyloRAD).
Data from: Degenerate adaptor sequences for detecting PCR duplicates in reduced representation sequencing data improve genotype calling accuracy
RAD-tag is a powerful tool for high-throughput genotyping. It relies on PCR amplification of the starting material, following enzymatic digestion and sequencing adaptor ligation. Amplification introduces duplicate reads into the data, which arise from the same template molecule and are statistically nonindependent, potentially introducing errors into genotype calling. In shotgun sequencing, data duplicates are removed by filtering reads starting at the same position in the alignment. However, restriction enzymes target specific locations within the genome, causing reads to start in the same place, and making it difficult to estimate the extent of PCR duplication. Here, we introduce a slight change to the Illumina sequencing adaptor chemistry, appending a unique four-base tag to the first index read, which allows duplicate discrimination in aligned data. This approach was validated on the Illumina MiSeq platform, using double-digest libraries of ants (Wasmannia auropunctata) and yeast (Saccharomyces cerevisiae) with known genotypes, producing modest though statistically significant gains in the odds of calling a genotype accurately. More importantly, removing duplicates also corrected for strong sample-to-sample variability of genotype calling accuracy seen in the ant samples. For libraries prepared from low-input degraded museum bird samples (Mixornis gularis), which had low complexity, having been generated from relatively few starting molecules, adaptor tags show that virtually all of the genotypes were called with inflated confidence as a result of PCR duplicates. Quantification of library complexity by adaptor tagging does not significantly increase the difficulty of the overall workflow or its cost, but corrects for differences in quality between samples and permits analysis of low-input material.
Data from: Degenerate adaptor sequences for detecting PCR duplicates in reduced representation sequencing data improve genotype calling accuracy
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Data from: "454 sequencing of reduced representation libraries to discover single nucleotide polymorphisms (SNPs) in Megabunus harvestmen" in Genomic Resources Notes accepted 1 December 2013 to 31 January 2014
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Data from: "A reduced representation libraries approach for nuclear marker development via 454 sequencing applied on Tetramorium (Hymenoptera: Formicidae)" in Genomic Resources Notes Accepted 1 February 2015 to 31 March 2015
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Data from: Reconstructing phylogeny from reduced-representation genome sequencing data without assembly or alignment
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Reduced representation bisulfite sequencing (RRBS) profiles of human induced pluripotent stem cells exposed to varied chemicals
GEO Series GSE228658. Homo sapiens. 5 samples. Type: Methylation profiling by high throughput sequencing.
Reduced representation bisulfite sequencing data of mouse genome
GEO Series GSE76238. Mus musculus. 4 samples. Type: Methylation profiling by high throughput sequencing.
Quantitative reduced representation bisulfite sequencing with unique molecular identifiers of single cell
GEO Series GSE76863. Homo sapiens. 2 samples. Type: Methylation profiling by high throughput sequencing.
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