scholarly journals Rapid identification of non-human sequences in high-throughput sequencing datasets

2012 ◽  
Vol 28 (8) ◽  
pp. 1174-1175 ◽  
Author(s):  
Aparna Bhaduri ◽  
Kun Qu ◽  
Carolyn S. Lee ◽  
Alexander Ungewickell ◽  
Paul A. Khavari
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Rapid Identification

scholarly journals Technological advancements and their importance for nematode identification

SOIL ◽  
2016 ◽  
Vol 2 (2) ◽  
pp. 257-270 ◽  
Author(s):  
Mohammed Ahmed ◽  
Melanie Sapp ◽  
Thomas Prior ◽  
Gerrit Karssen ◽  
Matthew Alan Back
Keyword(s):  
High Throughput ◽  
Crop Production ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Biological Indicators ◽  
Rapid Identification ◽  
Community Studies ◽  
Terrestrial Environments ◽  
Traditional Taxonomy ◽  
Sequencing Platforms

Abstract. Nematodes represent a species-rich and morphologically diverse group of metazoans known to inhabit both aquatic and terrestrial environments. Their role as biological indicators and as key players in nutrient cycling has been well documented. Some plant-parasitic species are also known to cause significant losses to crop production. In spite of this, there still exists a huge gap in our knowledge of their diversity due to the enormity of time and expertise often involved in characterising species using phenotypic features. Molecular methodology provides useful means of complementing the limited number of reliable diagnostic characters available for morphology-based identification. We discuss herein some of the limitations of traditional taxonomy and how molecular methodologies, especially the use of high-throughput sequencing, have assisted in carrying out large-scale nematode community studies and characterisation of phytonematodes through rapid identification of multiple taxa. We also provide brief descriptions of some the current and almost-outdated high-throughput sequencing platforms and their applications in both plant nematology and soil ecology.

scholarly journals sppIDer: a species identification tool to investigate hybrid genomes with high-throughput sequencing

2018 ◽  
Author(s):  
Quinn K. Langdon ◽  
David Peris ◽  
Brian Kyle ◽  
Chris Todd Hittinger
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Rapid Identification ◽  
Sequencing Data ◽  
Pure Species ◽  
High Throughput Sequencing Data ◽  
Interspecies Hybrids ◽  
Evolutionary Trajectories ◽  
Low Coverage ◽  
Reference Genomes

AbstractThe genomics era has expanded our knowledge about the diversity of the living world, yet harnessing high-throughput sequencing data to investigate alternative evolutionary trajectories, such as hybridization, is still challenging. Here we present sppIDer, a pipeline for the characterization of interspecies hybrids and pure species,that illuminates the complete composition of genomes. sppIDer maps short-read sequencing data to a combination genome built from reference genomes of several species of interest and assesses the genomic contribution and relative ploidy of each parental species, producing a series of colorful graphical outputs ready for publication. As a proof-of-concept, we use the genus Saccharomyces to detect and visualize both interspecies hybrids and pure strains, even with missing parental reference genomes. Through simulation, we show that sppIDer is robust to variable reference genome qualities and performs well with low-coverage data. We further demonstrate the power of this approach in plants, animals, and other fungi. sppIDer is robust to many different inputs and provides visually intuitive insight into genome composition that enables the rapid identification of species and their interspecies hybrids. sppIDer exists as a Docker image, which is a reusable, reproducible, transparent, and simple-to-run package that automates the pipeline and installation of the required dependencies (https://github.com/GLBRC/sppIDer).

scholarly journals Rapid identification of unknown pathogens in environmental samples using a high-throughput sequencing-based approach

Heliyon ◽  
2019 ◽  
Vol 5 (5) ◽  
pp. e01793 ◽  
Author(s):  
Ofir Israeli ◽  
Inbar Cohen-Gihon ◽  
Anat Zvi ◽  
Shirley Lazar ◽  
Ohad Shifman ◽  
...  
Keyword(s):  
High Throughput ◽  
Environmental Samples ◽  
High Throughput Sequencing ◽  
Rapid Identification

scholarly journals Auxiliary rapid identification of pathogenic and antagonistic microorganisms associated with Coptis chinensis root rot by high-throughput sequencing

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hailang Liao ◽  
Ling Huang ◽  
Na Li ◽  
Wenjia Ke ◽  
Yiqing Xiang ◽  
...  
Keyword(s):  
High Throughput ◽  
Root Rot ◽  
High Throughput Sequencing ◽  
Microbial Community Composition ◽  
Rapid Identification ◽  
Suppression Effect ◽  
Medical Quality ◽  
Antagonistic Microorganisms ◽  
Animal Pathogens ◽  
And Function

AbstractRoot rot reduces the yield and medical quality of C. chinensis (Cc). Previous studies of Coptis root rot focused on the identification of pathogens and the rhizosphere microbial community composition. The present study aimed to identify potential pathogenic and antagonistic microorganisms associated with root rot based on a high-throughput sequencing technique to prevent this disease. Healthy and diseased Cc in the endosphere and rhizosphere from the same field were collected to investigate the differences in microbiome composition and function. The results showed that the composition and function of microbes were different. The numbers of animal pathogens, soil saprotrophs, plant saprotrophs, and wood saprotrophs in the endosphere of diseased Cc were higher than those in the healthy endosphere and were dominated by Phaeosphaeriaceae, Cladorrhinum, Fusarium, Exophiala, and Melanommataceae. Fusarium, Volutella, Cladorrhinum, Cylindrocarpon, and Exophiala were significantly enriched in the endosphere of the diseased plants. Co-occurrence network analysis showed that Bacillus was negatively correlated with Fusarium, Volutella, and Cylindrocarpon, indicating that Bacillus may be antagonistic microorganisms. To verify the sequencing results, F. solani and F. avenaceum were isolated and verified as pathogens, and 14 Bacillus strains were isolated, which displayed an apparent suppression effect against the two pathogens on PDA medium and detached roots. The strategy of high-throughput sequencing has the potential for the comprehensive identification of pathogenic and antagonistic microorganisms for plant disease. These results provide research ideas and microbial resources for future studies on mitigating or preventing root rot damage to Cc.

scholarly journals The rise and fall of SARS-CoV-2 variants and the mutational profile of Omicron

2021 ◽  
Author(s):  
Tanner Roy Wiegand ◽  
Aidan McVey ◽  
Anna Nemudraia ◽  
Artem Nemudryi ◽  
Blake Wiedenheft
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Viral Proteins ◽  
Rapid Identification ◽  
Etiological Agent ◽  
Spike Protein ◽  
Mutation Rates ◽  
Selective Pressures ◽  
Sequencing Technologies ◽  
Over Time

In late December of 2019, high throughput sequencing technologies enabled rapid identification of SARS-CoV-2 as the etiological agent of COVID-19, and global sequencing efforts are now a critical tool for monitoring the ongoing spread and evolution of this virus. Here, we analyze a subset (n=87,032) of all publicly available SARS-CoV-2 genomes (n=~5.6 million) that were randomly selected, but equally distributed over the course of the pandemic. We plot the appearance of new variants of concern (VOCs) over time and show that the mutation rates in Omicron viruses are significantly greater than those in previously identified SARS-CoV-2 variants. Mutations in Omicron are primarily restricted to the spike protein, while 25 other viral proteins—including those involved in SARS-CoV-2 replication—are highly conserved. Collectively, this suggests that the genetic distinction of Omicron primarily arose from selective pressures on the spike, and that the fidelity of replication of this variant has not been altered.

scholarly journals Microcoding: the second step in DNA barcoding

2005 ◽  
Vol 360 (1462) ◽  
pp. 1897-1903 ◽  
Author(s):  
R.C Summerbell ◽  
C.A Lévesque ◽  
K.A Seifert ◽  
M Bovers ◽  
J.W Fell ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Cost Effective ◽  
Rapid Identification ◽  
Second Step ◽  
Base Pairs ◽  
Software Analysis ◽  
Fungal Identification

After the process of DNA barcoding has become well advanced in a group of organisms, as it has in the economically important fungi, the question then arises as to whether shorter and literally more barcode-like DNA segments should be utilized to facilitate rapid identification and, where applicable, detection. Through appropriate software analysis of typical full-length barcodes (generally over 500 base pairs long), uniquely distinctive oligonucleotide ‘microcodes’ of less than 25 bp can be found that allow rapid identification of circa 100–200 species on various array-like platforms. Microarrays can in principle fulfill the function of microcode-based species identification but, because of their high cost and low level of reusability, they tend to be less cost-effective. Two alternative platforms in current use in fungal identification are reusable nylon-based macroarrays and the Luminex system of specific, colour-coded DNA detection beads analysed by means of a flow cytometer. When the most efficient means of rapid barcode-based species identification is sought, a choice can be made either for one of these methodologies or for basic high-throughput sequencing, depending on the strategic outlook of the investigator and on current costs. Arrays and functionally similar platforms may have a particular advantage when a biologically complex material such as soil or a human respiratory secretion sample is analysed to give a census of relevant species present.

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