scholarly journals Applications of Next-Generation Sequencing for Large-Scale Pathogen Diagnoses in Soybean

Plant Disease ◽  
2019 ◽  
Vol 103 (6) ◽  
pp. 1075-1083 ◽  
Author(s):  
Gustavo A. Díaz-Cruz ◽  
Charlotte M. Smith ◽  
Kiana F. Wiebe ◽  
Sachi M. Villanueva ◽  
Adam R. Klonowski ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Pseudomonas Syringae ◽  
Large Scale ◽  
Fold Increase ◽  
Yellow Mosaic Virus ◽  
Growth Stages ◽  
Sequence Information ◽  
Next Generation ◽  
Leaf Sample ◽  
Generation Sequencing

Soybean (Glycine max) has become an important crop in Manitoba, Canada, with a 10-fold increase in dedicated acreage over the past decade. Given the rapid increase in production, scarce information about foliar diseases present in the province has been recorded. In order to describe the foliar pathogens affecting this legume, we harnessed next-generation sequencing (NGS) to carry out a comprehensive survey across Manitoba in 2016. Fields were sampled during the V2/3 (33 fields) and R6 (70 fields) growth stages, with at least three symptomatic leaves per field collected and subjected to RNA sequencing. We successfully detected several bacteria, fungi, and viruses known to infect soybean, including Pseudomonas savastanoi pv. glycinea, Septoria glycines, and Peronospora manshurica, as well as pathogens not previously identified in the province (e.g., Pseudomonas syringae pv. tabaci, Cercospora sojina, and Bean yellow mosaic virus). For some microorganisms, we were able to disentangle the different pathovars present and/or assemble their genome sequence. Since NGS generates data on the entire flora and fauna occupying a leaf sample, we also identified residual pathogens (i.e., pathogens of crops other than soybean) and multiple species of arthropod pests. Finally, the sequence information produced by NGS allowed for the development of polymerase chain reaction-based diagnostics for some of the most widespread and important pathogens. Although there are many benefits of using NGS for large-scale plant pathogen diagnoses, we also discuss some of the limitations of this technology.

Next-Generation Sequencing: An Emerging Tool for Drug Designing

2019 ◽  
Vol 25 (31) ◽  
pp. 3350-3357 ◽  
Author(s):  
Pooja Tripathi ◽  
Jyotsna Singh ◽  
Jonathan A. Lal ◽  
Vijay Tripathi
Keyword(s):  
Next Generation Sequencing ◽  
High Throughput ◽  
Large Scale ◽  
Massively Parallel Sequencing ◽  
Genomic Research ◽  
Biological Research ◽  
Next Generation ◽  
Human Welfare ◽  
Drug Designing ◽  
Generation Sequencing

Background: With the outbreak of high throughput next-generation sequencing (NGS), the biological research of drug discovery has been directed towards the oncology and infectious disease therapeutic areas, with extensive use in biopharmaceutical development and vaccine production. Method: In this review, an effort was made to address the basic background of NGS technologies, potential applications of NGS in drug designing. Our purpose is also to provide a brief introduction of various Nextgeneration sequencing techniques. Discussions: The high-throughput methods execute Large-scale Unbiased Sequencing (LUS) which comprises of Massively Parallel Sequencing (MPS) or NGS technologies. The Next geneinvolved necessarily executes Largescale Unbiased Sequencing (LUS) which comprises of MPS or NGS technologies. These are related terms that describe a DNA sequencing technology which has revolutionized genomic research. Using NGS, an entire human genome can be sequenced within a single day. Conclusion: Analysis of NGS data unravels important clues in the quest for the treatment of various lifethreatening diseases and other related scientific problems related to human welfare.

scholarly journals NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina) Data

PLoS ONE ◽  
2015 ◽  
Vol 10 (10) ◽  
pp. e0139868 ◽  
Author(s):  
Mohan A. V. S. K. Katta ◽  
Aamir W. Khan ◽  
Dadakhalandar Doddamani ◽  
Mahendar Thudi ◽  
Rajeev K. Varshney
Keyword(s):  
Quality Control ◽  
Next Generation Sequencing ◽  
Large Scale ◽  
Control Analysis ◽  
Next Generation ◽  
Quality Control Analysis ◽  
Illumina Data ◽  
Generation Sequencing

Next generation sequencing reveals past and current widespread occurrence of maize yellow mosaic virus in South Africa

2020 ◽  
Vol 158 (1) ◽  
pp. 237-249
Author(s):  
Tanya Welgemoed ◽  
Rian Pierneef ◽  
David A. Read ◽  
Susanna E. Schulze ◽  
Gerhard Pietersen ◽  
...  
Keyword(s):  
South Africa ◽  
Next Generation Sequencing ◽  
Mosaic Virus ◽  
Yellow Mosaic Virus ◽  
Next Generation ◽  
Widespread Occurrence ◽  
Generation Sequencing

scholarly journals Validation of variants using cost effective highresolution melting (HRM) analysis predicted from target re-sequencing in Eucalyptus

2020 ◽  
Vol 79 (2) ◽  
pp. 105-113
Author(s):  
Abdul Bari Muneera Parveen ◽  
Divya Lakshmanan ◽  
Modhumita Ghosh Dasgupta
Keyword(s):  
Next Generation Sequencing ◽  
Large Scale ◽  
Sequence Data ◽  
Cost Effective ◽  
Nucleotide Polymorphisms ◽  
Next Generation ◽  
Time Saving ◽  
Hrm Analysis ◽  
The Cost ◽  
Generation Sequencing

The advent of next-generation sequencing has facilitated large-scale discovery and mapping of genomic variants for high-throughput genotyping. Several research groups working in tree species are presently employing next generation sequencing (NGS) platforms for marker discovery, since it is a cost effective and time saving strategy. However, most trees lack a chromosome level genome map and validation of variants for downstream application becomes obligatory. The cost associated with identifying potential variants from the enormous amount of sequence data is a major limitation. In the present study, high resolution melting (HRM) analysis was optimized for rapid validation of single nucleotide polymorphisms (SNPs), insertions or deletions (InDels) and simple sequence repeats (SSRs) predicted from exome sequencing of parents and hybrids of Eucalyptus tereticornis Sm. ? Eucalyptus grandis Hill ex Maiden generated from controlled hybridization. The cost per data point was less than 0.5 USD, providing great flexibility in terms of cost and sensitivity, when compared to other validation methods. The sensitivity of this technology in variant detection can be extended to other applications including Bar-HRM for species authentication and TILLING for detection of mutants.

Sampling the Waterhemp (Amaranthus tuberculatus) Genome Using Pyrosequencing Technology

Weed Science ◽  
2009 ◽  
Vol 57 (5) ◽  
pp. 463-469 ◽  
Author(s):  
Ryan M. Lee ◽  
Jyothi Thimmapuram ◽  
Kate A. Thinglum ◽  
George Gong ◽  
Alvaro G. Hernandez ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Large Scale ◽  
Ecological Model ◽  
Average Length ◽  
Science Research ◽  
Complete Sequence ◽  
Next Generation ◽  
Next Generation Sequencing Technology ◽  
Sequencing Technologies ◽  
Generation Sequencing

Recent advances in sequencing technologies (next-generation sequencing) offer dramatically increased sequencing throughput at a lower cost than traditional Sanger sequencing. This technology is changing genomics research by allowing large scale sequencing experiments in nonmodel systems. Waterhemp is an important weed in the midwestern United States with characteristics that makes it an interesting ecological model. However, very few genomic resources are available for this species. One half of a 70 by 75 picotiter plate of 454-pyrosequencing was performed on total DNA isolated from waterhemp, generating 158,015 reads of an average length of 271 bp, or a total of nearly 43 Mbp of sequence. Included in this sequence was a nearly complete sequence of the chloroplast genome, sequences of several important herbicide resistance genes, leads for simple sequence repeat (SSR) markers, and a sampling of the repeated elements (e.g., transposons) present in this species. Here we present the waterhemp genomic data gleaned from this sequencing experiment and illustrate the value of next-generation sequencing technology to weed science research.

scholarly journals Next-Generation Sequencing Technologies in Blood Group Typing

2019 ◽  
Vol 47 (1) ◽  
pp. 4-13 ◽  
Author(s):  
Daniel Fürst ◽  
Chrysanthi Tsamadou ◽  
Christine Neuchel ◽  
Hubert Schrezenmeier ◽  
Joannis Mytilineos ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Blood Group ◽  
Large Scale ◽  
Cost Effective ◽  
Molecular Testing ◽  
Blood Group Antigens ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Blood Group Typing ◽  
Generation Sequencing

Sequencing of the human genome has led to the definition of the genes for most of the relevant blood group systems, and the polymorphisms responsible for most of the clinically relevant blood group antigens are characterized. Molecular blood group typing is used in situations where erythrocytes are not available or where serological testing was inconclusive or not possible due to the lack of antisera. Also, molecular testing may be more cost-effective in certain situations. Molecular typing approaches are mostly based on either PCR with specific primers, DNA hybridization, or DNA sequencing. Particularly the transition of sequencing techniques from Sanger-based sequencing to next-generation sequencing (NGS) technologies has led to exciting new possibilities in blood group genotyping. We describe briefly the currently available NGS platforms and their specifications, depict the genetic background of blood group polymorphisms, and discuss applications for NGS approaches in immunohematology. As an example, we delineate a protocol for large-scale donor blood group screening established and in use at our institution. Furthermore, we discuss technical challenges and limitations as well as the prospect for future developments, including long-read sequencing technologies.

The NK Cell MicroRNA Transcriptome Defined by Next-Generation Sequencing Identifies IL-15-Signaled Alterations In Mature MiR-223 Expression, and MiR-223 as a Potential Regulator of Murine Granzyme B

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 104-104
Author(s):  
Todd A Fehniger ◽  
Todd Wylie ◽  
Elizabeth Germino ◽  
Jeffrey W Leong ◽  
Vincent J Magrini ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Nk Cells ◽  
Real Time ◽  
Nk Cell ◽  
Granzyme B ◽  
Mrna Translation ◽  
Fold Increase ◽  
Next Generation ◽  
Altered Expression ◽  
Generation Sequencing

Abstract Abstract 104 Natural killer (NK) cells are innate lymphocytes important for early host defense against infectious pathogens and surveillance against malignant transformation. Resting murine NK cells regulate the translation of effector molecule mRNAs (e.g. granzyme B, GzmB) through unclear molecular mechanisms. MicroRNAs (miRNAs) are small non-coding RNAs that post-transcriptionally regulate the translation of their mRNA targets, and are therefore candidates mediating this control process. While the expression and importance of miRNAs in T and B lymphocytes has been established, little is known about miRNAs in NK cells. Here, we utilized two next-generation sequencing platforms, Illumina GA and SOLiD, to define the miRNA transcriptomes of resting and IL-15-activated primary murine NK cells. Using Illumina GA sequencing, we identified expression of 297 mature miRNA and 64 miRNA* sequences in NK cells at read counts of 1 to 507,369. The 5 miRNAs with the highest abundance (percent normalized read count) in resting NK cells were miR-21 (31.6%), miR-16 (8.3%), miR-142-5p (6.5%), miR-142-3p (3.8%), miR-24 (3.7%). Detection of known miRNA was similar using SOLiD sequencing in both resting (r2=0.79) and IL-15-activated (r2=0.75) NK cells, with most of the discordant detection arising in miRNAs with low expression (1-10 read counts). These results were further validated using real-time RT-qPCR and microarray profiling. A bioinformatics pipeline was developed that identified 37 novel miRNA genes that encoded 26 novel mature miRNA sequences, including miRNAs processed from snoRNAs. Of 84 miRNAs with significantly altered expression levels (Illumina, normalized read counts) following IL-15-activation, miR-223 demonstrated the greatest fold decrease (2.3, P=1.03E-10). The decrease in mature miR-223 following 24 hours of IL-15 activation was confirmed in SOLiD sequencing (7.7 fold-decrease, P=1.0E-10), qPCR (2.5 fold-decrease, P=0.01), and microarrays (4.6 fold-decrease, P=0.003). IL-15 induced reduction in mature miR-223 was time-dependent with fold decreases of 1.5 (NS) at 8 hours, 2.2 (P=0.003) at 24 hours, and 8.1 (P=0.012) at 48 hours, assessed by real-time qPCR. Decreases in mature miR-223 expression early following activation likely occur via regulation of the miRNA processing machinery, since primary and precursor miR-223 transcripts exhibited increased expression after 8 hours (2.1±0.3 fold increase, P=0.03) and 24 hours (2.5±0.3 fold increase, P=0.03) of IL-15-activation. MiR-223 is computationally predicted to bind to the murine GzmB 3'UTR sequence, and we therefore evaluated the ability of miR-223 to target the murine GzmB 3'UTR in vitro. Overexpression of miR-223 in 293T cells decreased luciferase protein signal controlled by the GzmB 3'UTR by 44±2% (P=0.002) without affecting negative controls (perforin 3'UTR or no 3'UTR). Moreover, mutating the miR-223 predicted binding site within the murine GzmB 3'UTR abrogated miR-223 mediated regulation. These data suggest that miR-223 directly targets the murine GzmB 3'UTR, and thereby contributes to tonic suppression of GzmB mRNA translation in resting NK cells. Thus, the sequenced and validated miRNA transcriptome provides a valuable framework for further elucidation of miRNA expression and function in NK cell biology. Disclosures: No relevant conflicts of interest to declare.

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