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133 results for “Amplicon sequencing”
Data from: Unraveling independent origins of two tetraploid Achillea species by amplicon sequencing
<p>Allopolyploidy is a significant mechanism of plant speciation, and many allopolyploid species have arisen recurrently. However, the probability that allopolyploidization between the same two parental species may lead to the origin of different taxa has received little attention. Here we used a new progenitor-specific amplicon sequencing method to demonstrate the independent origins of two yarrow species, <i>Achillea alpina</i> and <i>A. wilsoniana</i>, via allotetraploidy from the same diploid progenitor species pair, <i>A. acuminata</i> and <i>A. asiatica</i>. Based on the sequences of 17 nuclear genes from 21 wild populations of the four <i>Achillea </i>species investigated, a clear view of genetic structure and demographic history was obtained with each species. Significant genetic differentiation was evident between the two tetraploid species. Two genetically distinguishable groups were detected within one of the progenitor, <i>A. acuminata</i>, and ancestors belonging to those two groups contributed to the two tetraploid species, respectively. Excluding fixed heterozygosity, we detected extremely low genetic diversity in many populations of both tetraploid species. Approximate Bayesian computation indicated that both tetraploid species originated before the Last Glacial Maximum, and nearly all diploid lineages went through population declines after the allopolyploidization events. Our study demonstrates that independent allopolyploidization events between the same <i>Achillea</i> parental species have generated two genetically and ecologically distinct taxa.</p>
STAMINA project 883441 related raw sequencing data of RTPCR positive SARS-CoV-2 amplicons
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Supplementary Information of Amplicon-based nanopore sequencing of patients with COVID-19 omicron (B.1.1.529) variant from India
<p><strong>We report sequencing of omicron variants from SARS-CoV-2 in 75 patients, using Nanopore long-read sequencing chemistry. We highlight the nature of mutations in spike glycoprotein that are unique and common to other populations.</strong></p> <p> </p>
Amplicon_sorter: a tool for reference-free amplicon sorting based on sequence similarity and for building consensus sequences
<p>Oxford Nanopore Technologies (ONT) is a third-generation sequencing technology that is gaining popularity in ecological research for its portable and low-cost sequencing possibilities. Although the technology excels at long-read sequencing, it can also be applied to sequence amplicons. The downside of ONT is the low quality of the raw reads. Hence, generating a high-quality consensus sequence is still a challenge. We present Amplicon_sorter, a tool for reference-free sorting of ONT sequenced amplicons based on their similarity in sequence and length and for building solid consensus sequences.</p>
16S Amplicon sequence variants (ASVs) data of NEREA Augmented Observatory
<p><strong>Metabarcoding - 16S ASV generation and taxonomic assignment</strong>. Raw 16S paired-end sequences were subjected to a data quality control step and subsequently imported into the QIIME2 pipeline v.2022.2.0. Leftover primers and adapter sequences were removed through cutadapt. The amplicon sequence variants (ASV) table, which represent true biological sequences within each sample, was generated using the denoised-paired method including truncation, denoising, dereplication, merging, and chimera filtering of the DADA2 (Divisive Amplicon Denoising Algorithm 2) plugin inside QIIME2. Default parameters were used with the exception of the forward and reverse sequence length (--p-trunc-len-f and --p-trunc-len-r), that were set to 220 and 180, respectively. Processed reads that passed all these filters were used for taxonomy classification. The V4-V5 regions were extracted from the pre-formatted reference sequences and taxonomy file built on the SILVA 138 99% OTUs database and the vsearch v.2.6.2 global alignment implemented in QIIME2 was used.</p>
Data from: Digital fragment analysis of short tandem repeats by high-throughput amplicon sequencing
High-throughput sequencing has been proposed as a method to genotype microsatellites and overcome the four main technical drawbacks of capillary electrophoresis: amplification artifacts, imprecise sizing, length homoplasy, and limited multiplex capability. The objective of this project was to test a high-throughput amplicon sequencing approach to fragment analysis of short tandem repeats and characterize its advantages and disadvantages against traditional capillary electrophoresis. We amplified and sequenced 12 muskrat microsatellite loci from 180 muskrat specimens and analyzed the sequencing data for precision of allele calling, propensity for amplification or sequencing artifacts, and for evidence of length homoplasy. Of the 294 total alleles, we detected by sequencing, only 164 alleles would have been detected by capillary electrophoresis as the remaining 130 alleles (44%) would have been hidden by length homoplasy. The ability to detect a greater number of unique alleles resulted in the ability to resolve greater population genetic structure. The primary advantages of fragment analysis by sequencing are the ability to precisely size fragments, resolve length homoplasy, multiplex many individuals and many loci into a single high-throughput run, and compare data across projects and across laboratories (present and future) with minimal technical calibration. A significant disadvantage of fragment analysis by sequencing is that the method is only practical and cost-effective when performed on batches of several hundred samples with multiple loci. Future work is needed to optimize throughput while minimizing costs and to update existing microsatellite allele calling and analysis programs to accommodate sequence-aware microsatellite data.
KTU: K-mer Taxonomic Units improve the biological relevance of amplicon sequence variant microbiota data
<p>Testing datasets and files for the KTU algorithm</p>
16s rRNA sequences, R code used for amplicon analysis and example code for NMGS analysis
<p>This submission contains the following data presented in: "Selection processes of Arctic seasonal glacier snowpack bacterial communities" by Keuschnig et al.</p> <p>the R code used to analyze the 16S rRNA amplicon data</p> <p>the script used for NMGS analysis</p> <p>the sequences obtained from snow samples</p>
Data from: Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex
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Data from: Species tree estimation of North American chorus frogs (Hylidae: Pseudacris) with parallel tagged amplicon sequencing
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Data from: Parallel tagged amplicon sequencing of transcriptome-based genetic markers for Triturus newts with the Ion Torrent next-generation sequencing platform
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Data from: Digital fragment analysis of short tandem repeats by high-throughput amplicon sequencing
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Data from: Allele discovery of ten candidate drought-response genes in Austrian oak using a systematically informatics approach based on 454 amplicon sequencing
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Coregonus spp. opsin amplicon sequence alignments
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Data from: Deep sequencing of amplicons reveals widespread intraspecific hybridization and multiple origins of polyploidy in big sagebrush (Artemisia tridentata)
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Data from: 16S rRNA amplicon sequencing for epidemiological surveys of bacteria in wildlife
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Data from: High-throughput amplicon sequencing of rRNA genes requires a copy number correction to accurately reflect the effects of management practices on soil nematode community structure
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Data from: Unraveling independent origins of two tetraploid Achillea species by amplicon sequencing
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Data from: The QRS (Quantification of Representative Sequences) pipeline for amplicon sequencing: case study on within-population ITS1 sequence variation in a microparasite infecting Daphnia
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Data from: Within-host competition between Borrelia afzelii ospC strains in wild hosts as revealed by massively parallel amplicon sequencing
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