scholarly journals Host Range of Cyclospora Species: Zoonotic Implication

2021 ◽  
Vol 60 ◽  
pp. 13-20
Author(s):  
Piotr Solarczyk
Keyword(s):  
Molecular Markers ◽  
Next Generation Sequencing ◽  
Convincing Evidence ◽  
Human Infection ◽  
Molecular Tools ◽  
Gastrointestinal Parasite ◽  
Genome Heterogeneity ◽  
Experimental Use ◽  
Animal Reservoirs ◽  
Generation Sequencing

Cyclospora is an intracellular, gastrointestinal parasite found in birds and mammals worldwide. Limited accessibility of the protozoan for experimental use, scarcity, genome heterogeneity of the isolates and narrow panel of molecular markers hamper zoonotic investigations. One of the significant limitation in zoonotic studies is the lack of precise molecular tools that would be useful in linking animal vectors as a source of human infection. Strong and convincing evidence of zoonotic features will be achieved through proper typing of Cyclospora spp. taxonomic units (e.g. species or genotypes) in animal reservoirs. The most promising method that can be employ for zoonotic surveys is next-generation sequencing.

Molecular marker information from de novo assembled transcriptomes of chilli pepper (Capsicum annuum L.) varieties based on next-generation sequencing technology

2014 ◽  
Vol 12 (S1) ◽  
pp. S83-S86 ◽  
Author(s):  
Yul-Kyun Ahn ◽  
Swati Tripathi ◽  
Young-Il Cho ◽  
Jeong-Ho Kim ◽  
Hye-Eun Lee ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Next Generation Sequencing ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Sequence Variant ◽  
Nucleotide Polymorphisms ◽  
Next Generation ◽  
Chilli Pepper ◽  
Next Generation Sequencing Technology ◽  
Generation Sequencing

Next-generation sequencing technique has been known as a useful tool for de novo transcriptome assembly, functional annotation of genes and identification of molecular markers. This study was carried out to mine molecular markers from de novo assembled transcriptomes of four chilli pepper varieties, the highly pungent ‘Saengryeg 211’ and non-pungent ‘Saengryeg 213’ and variably pigmented ‘Mandarin’ and ‘Blackcluster’. Pyrosequencing of the complementary DNA library resulted in 361,671, 274,269, 279,221, and 316,357 raw reads, which were assembled in 23,607, 19,894, 18,340 and 20,357 contigs, for the four varieties, respectively. Detailed sequence variant analysis identified numerous potential single-nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) for all the varieties for which the primers were designed. The transcriptome information and SNP/SSR markers generated in this study provide valuable resources for high-density molecular genetic mapping in chilli pepper and Quantitative trait loci analysis related to fruit qualities. These markers for pepper will be highly valuable for marker-assisted breeding and other genetic studies.

scholarly journals Developing molecular tools and insights into the Penstemon genome using genomic reduction and next-generation sequencing

BMC Genetics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 66 ◽  
Author(s):  
Rhyan B Dockter ◽  
David B Elzinga ◽  
Brad Geary ◽  
P Maughan ◽  
Leigh A Johnson ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Molecular Tools ◽  
Generation Sequencing

Development of soybean aphid genomic SSR markers using next generation sequencing

Genome ◽  
2011 ◽  
Vol 54 (5) ◽  
pp. 360-367 ◽  
Author(s):  
Tae-Hwan Jun ◽  
Andrew P. Michel ◽  
M.A. Rouf Mian
Keyword(s):  
Molecular Markers ◽  
Next Generation Sequencing ◽  
Ssr Markers ◽  
The United States ◽  
Soybean Aphid ◽  
Genomic Sequences ◽  
Next Generation ◽  
Soybean Aphids ◽  
Genomic Ssr ◽  
Generation Sequencing

Simple sequence repeats (SSRs) or microsatellites are very useful molecular markers, owing to their locus-specific codominant and multiallelic nature, high abundance in the genome, and high rates of transferability across species. The soybean aphid ( Aphis glycines Matsumura) has become the most damaging insect pest of soybean ( Glycine max (L.) Merr.) in North America, since it was first found in the Midwest of the United States in 2000. Biotypes of the soybean aphid capable of colonizing newly developed aphid-resistant soybean cultivars have been recently discovered. Genetic resources, including molecular markers, to study soybean aphids are severely lacking. Recently developed next generation sequencing platforms offer opportunities for high-throughput and inexpensive genome sequencing and rapid marker development. The objectives of this study were (i) to develop and characterize genomic SSR markers from soybean aphid genomic sequences generated by next generation sequencing technology and (ii) to evaluate the utility of the SSRs for genetic diversity or relationship analyses. In total 128 SSR primer pairs were designed from sequences generated by Illumina GAII from a reduced representation library of A. glycines. Nearly 94% (120) of the primer pairs amplified SSR alleles of expected size and 24 SSR loci were polymorphic among three aphid samples from three populations. The polymorphic SSRs were successfully used to differentiate among 24 soybean aphids from Ohio and South Dakota. Sequencing of PCR products of two SSR markers from four aphid samples revealed that the allelic polymorphism was due to variation in the SSR repeats among the aphids. These markers should be particularly useful for genetic differentiation among aphids collected from soybean fields at different localities and regions. These SSR markers provide the soybean aphid research community with the first set of PCR-based codominant markers developed from the genomic sequences of A. glycines.

scholarly journals Exogene: A performant workflow for detecting viral integrations from paired-end next-generation sequencing data

2021 ◽  
Author(s):  
Jean-Pierre Kocher ◽  
Zachary Stephens ◽  
Daniel O'Brien ◽  
Mrunal Dehankar ◽  
Lewis Roberts ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Sequence Data ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Long Read ◽  
Breakpoint Detection ◽  
Targeted Capture ◽  
Genome Heterogeneity ◽  
Generation Sequencing

The integration of viruses into the human genome is known to be associated with tumorigenesis in many cancers, but the accurate detection of integration breakpoints from short read sequencing data is made difficult by human-viral homologies, viral genome heterogeneity, coverage limitations, and other factors. To address this, we present Exogene, a sensitive and efficient workflow for detecting viral integrations from paired-end next generation sequencing data. Exogene's read filtering and breakpoint detection strategies yield integration coordinates that are highly concordant with those found in long read validation sets. We demonstrate this concordance across 6 TCGA Hepatocellular carcinoma (HCC) tumor samples, identifying integrations of hepatitis B virus that are validated by long reads. Additionally, we applied Exogene to targeted capture data from 426 previously studied HCC samples, achieving 98.9% concordance with existing methods and identifying 238 high-confidence integrations that were not previously reported. Exogene is applicable to multiple types of paired-end sequence data, including genome, exome, RNA-Seq or targeted capture.

scholarly journals Development of molecular markers tightly linked to Pvr4 gene in pepper using next-generation sequencing

2015 ◽  
Vol 35 (4) ◽  
Author(s):  
Zübeyir Devran ◽  
Erdem Kahveci ◽  
Ercan Özkaynak ◽  
David J. Studholme ◽  
Mahmut Tör
Keyword(s):  
Molecular Markers ◽  
Next Generation Sequencing ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Next-generation sequencing: a powerful tool for the discovery of molecular markers in breast ductal carcinomain situ

2013 ◽  
Vol 13 (2) ◽  
pp. 151-165 ◽  
Author(s):  
Hitchintan Kaur ◽  
Shihong Mao ◽  
Seema Shah ◽  
David H Gorski ◽  
Stephen A Krawetz ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Next Generation Sequencing ◽  
Next Generation ◽  
Ductal Carcinomain Situ ◽  
Carcinomain Situ ◽  
Generation Sequencing

scholarly journals Exogene: A performant workflow for detecting viral integrations from paired-end next-generation sequencing data

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0250915
Author(s):  
Zachary Stephens ◽  
Daniel O’Brien ◽  
Mrunal Dehankar ◽  
Lewis R. Roberts ◽  
Ravishankar K. Iyer ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Sequence Data ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Long Read ◽  
Breakpoint Detection ◽  
Targeted Capture ◽  
Genome Heterogeneity ◽  
Generation Sequencing

The integration of viruses into the human genome is known to be associated with tumorigenesis in many cancers, but the accurate detection of integration breakpoints from short read sequencing data is made difficult by human-viral homologies, viral genome heterogeneity, coverage limitations, and other factors. To address this, we present Exogene, a sensitive and efficient workflow for detecting viral integrations from paired-end next generation sequencing data. Exogene’s read filtering and breakpoint detection strategies yield integration coordinates that are highly concordant with long read validation. We demonstrate this concordance across 6 TCGA Hepatocellular carcinoma (HCC) tumor samples, identifying integrations of hepatitis B virus that are also supported by long reads. Additionally, we applied Exogene to targeted capture data from 426 previously studied HCC samples, achieving 98.9% concordance with existing methods and identifying 238 high-confidence integrations that were not previously reported. Exogene is applicable to multiple types of paired-end sequence data, including genome, exome, RNA-Seq and targeted capture.

scholarly journals Diagnosis and analysis of unexplained cases of childhood encephalitis in Australia using metagenomic next-generation sequencing

2021 ◽  
Author(s):  
Ci-Xiu Li ◽  
Rebecca Burrell ◽  
Russell C Dale ◽  
Alison Kesson ◽  
Christopher C Blyth ◽  
...  
Keyword(s):  
Cerebrospinal Fluid ◽  
Next Generation Sequencing ◽  
Rna Sequencing ◽  
Diagnostic Yield ◽  
Human Infection ◽  
Clinical Samples ◽  
Next Generation ◽  
Dna Viruses ◽  
Immune Mediated ◽  
Generation Sequencing

Encephalitis is most often caused by a variety of infectious agents, the identity of which is commonly determined through diagnostic tests utilising cerebrospinal fluid (CSF). Immune-mediated disorders are also a differential in encephalitis cases. We investigated the clinical characteristics and potential aetiological agents of unexplained encephalitis through metagenomic next-generation sequencing of residual clinical samples of multiple tissue types and independent clinical review. A total of 43 specimens, from both sterile and non-sterile sites, were collected from 18 encephalitis cases with no cause identified by the Australian Childhood Encephalitis study. Samples were subjected to total RNA sequencing to determine the presence and abundance of potential pathogens, to reveal mixed infections, pathogen genotypes, and epidemiological origins, and to describe the possible aetiologies of unexplained encephalitis. From this, we identified five RNA and two DNA viruses associated with human infection from both non-sterile (nasopharyngeal aspirates, nose/throat swabs, urine, stool rectal swab) and sterile (cerebrospinal fluid, blood) sites. These comprised two human rhinoviruses, two human seasonal coronaviruses, two polyomaviruses and one picobirnavirus. With the exception of picobirnavirus all have been previously associated with respiratory disease. Human rhinovirus and seasonal coronaviruses may be responsible for five of the encephalitis cases reported here. Immune-mediated encephalitis was considered clinically likely in six cases and RNA sequencing did not identify a possible pathogen in these cases. The aetiology remained unknown in nine cases. Our study emphasises the importance of respiratory viruses in the aetiology of unexplained child encephalitis and suggests that the routine inclusion of non-CNS sampling in encephalitis clinical guidelines/protocols could improve the diagnostic yield.

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