scholarly journals Next-Generation Sequencing and the CRISPR-Cas Nexus: A Molecular Plant Virology Perspective

2021 ◽  
Vol 11 ◽  
Author(s):  
Muhammad Shafiq Shahid ◽  
Muhammad Naeem Sattar ◽  
Zafar Iqbal ◽  
Amir Raza ◽  
Abdullah M. Al-Sadi
Keyword(s):  
Next Generation Sequencing ◽  
Plant Viruses ◽  
Genetically Engineered ◽  
Site Directed Mutagenesis ◽  
Host Susceptibility ◽  
Base Substitution ◽  
Next Generation ◽  
Plant Virology ◽  
Detection Techniques ◽  
Generation Sequencing

In recent years, next-generation sequencing (NGS) and contemporary Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) technologies have revolutionized the life sciences and the field of plant virology. Both these technologies offer an unparalleled platform for sequencing and deciphering viral metagenomes promptly. Over the past two decades, NGS technologies have improved enormously and have impacted plant virology. NGS has enabled the detection of plant viruses that were previously undetectable by conventional approaches, such as quarantine and archeological plant samples, and has helped to track the evolutionary footprints of viral pathogens. The CRISPR-Cas-based genome editing (GE) and detection techniques have enabled the development of effective approaches to virus resistance. Different versions of CRISPR-Cas have been employed to successfully confer resistance against diverse plant viruses by directly targeting the virus genome or indirectly editing certain host susceptibility factors. Applications of CRISPR-Cas systems include targeted insertion and/or deletion, site-directed mutagenesis, induction/expression/repression of the gene(s), epigenome re-modeling, and SNPs detection. The CRISPR-Cas toolbox has been equipped with precision GE tools to engineer the target genome with and without double-stranded (ds) breaks or donor templates. This technique has also enabled the generation of transgene-free genetically engineered plants, DNA repair, base substitution, prime editing, detection of small molecules, and biosensing in plant virology. This review discusses the utilities, advantages, applications, bottlenecks of NGS, and CRISPR-Cas in plant virology.

scholarly journals Detection of genome-wide low-frequency mutations with Paired-End and Complementary Consensus Sequencing (PECC-Seq) revealed end-repair derived artifacts as residual errors

2019 ◽  
Author(s):  
Xinyue You ◽  
Suresh Thiruppathi ◽  
Weiying Liu ◽  
Yiyi Cao ◽  
Mikihiko Naito ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Low Frequency ◽  
Repair Process ◽  
Sequencing Error ◽  
Base Substitution ◽  
Next Generation ◽  
Background Error ◽  
Technical Errors ◽  
Genome Wide ◽  
Generation Sequencing

ABSTRACTTo improve the accuracy and the cost-efficiency of next-generation sequencing in ultralow-frequency mutation detection, we developed the Paired-End and Complementary Consensus Sequencing (PECC-Seq), a PCR-free duplex consensus sequencing approach. PECC-Seq employed shear points as endogenous barcodes to identify consensus sequences from the overlap in the shortened, complementary DNA strands-derived paired-end reads for sequencing error correction. With the high accuracy of PECC-Seq, we identified the characteristic base substitution errors introduced by the end-repair process of mechanical fragmentation-based library preparations, which were prominent at the terminal 6 bp of the library fragments in the 5’-NpCpA-3’ or 5’-NpCpT-3’ trinucleotide context. As demonstrated at the human genome scale (TK6 cells), after removing these potential end-repair artifacts from the terminal 6 bp, PECC-Seq could reduce the sequencing error frequency to mid-10−7 with a relatively low sequencing depth. For TA base pairs, the background error rate could be suppressed to mid-10−8. In mutagen-treated TK6, slight increases in mutagen treatment-related mutant frequencies could be detected, indicating the potential of PECC-Seq in detecting genome-wide ultra-rare mutations. In addition, our finding on the patterns of end-repair artifacts may provide new insights in further reducing technical errors not only for PECC-Seq, but also for other next-generation sequencing techniques.

scholarly journals Next Generation Sequencing Technique and Its Application in Plant Virology

2019 ◽  
Vol 8 (2) ◽  
pp. 77-85
Author(s):  
zohreh Davoodi ◽  
jahangir heydarnejad ◽  
Hossein Masoomi ◽  
◽  
◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Plant Virology ◽  
Sequencing Technique ◽  
Generation Sequencing

scholarly journals Next-Generation Sequencing and Genome Editing in Plant Virology

2016 ◽  
Vol 7 ◽  
Author(s):  
Ahmed Hadidi ◽  
Ricardo Flores ◽  
Thierry Candresse ◽  
Marina Barba
Keyword(s):  
Next Generation Sequencing ◽  
Genome Editing ◽  
Next Generation ◽  
Plant Virology ◽  
Generation Sequencing

TP53 fusions with next-generation sequencing (NGS) in Chinese non-small cell lung cancer (NSCLC): A multicenter study.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e21742-e21742
Author(s):  
Huafei Chen ◽  
Wen xian Wang ◽  
Chunwei Xu ◽  
You-cai Zhu ◽  
Wu Zhuang ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Next Generation Sequencing ◽  
Multicenter Study ◽  
Lung Tumor ◽  
Next Generation ◽  
Entire Cohort ◽  
Detection Techniques ◽  
Nsclc Patients ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

e21742 Background: Currently, with the advances in detection techniques, such as next generation sequencing (NGS), more and more rare or atypical TP53 fusions had been identified. Such as TP53-PSMD14, the importance of EGFR signaling in the pathogenesis of lung cancer and the efficacy of EGFR-TKI treatment had been demonstrated. The aim of this study was to evaluate the prevalence of TP53 fusions in Chinese NSCLC populations, which had not been reported earlier, and to describe targeting potential in Chinese NSCLC populations. Methods: A multicenter study in China was initiated from February 2014, and NSCLC patients have been enrolled as of December 2018. A total of 2743 patients with NSCLC were screened by using next-generation sequencing (NGS)-based 381 genes panel assay for detecting TP53 fusions. Results: Of this entire cohort, just four (0.15%) patients were identified with a TP53 fusion, including DNAH2-TP53 (1), TP53-MPDU1 (1), TP53-FXR2 (1), TP53-VEZF1 (1). Of the TP53 fusion NSCLC patients, 50.00% were detected in female patients. Biopsies were obtained from primary lung tumor (25.00%) and metastatic sites (75.00%). Overall TMB in the TP53 fusion was high, which had more than 20 mut/Mb. Of the TP53 fusion NSCLC, two cases (50.00%) featured EGFR SV alterations. Conclusions: The frequency of TP53 fusions in Chinese populations with NSCLC is extremely rare (0.17%). TP53 fusions may reduce responsiveness to TKIs and worsen prognosis in EGFR-mutated NSCLC patients, mainly those carrying exon 19 deletions or exon 21 L858R.

scholarly journals Ecogenomic survey of plant viruses infecting Tobacco by Next generation sequencing

2016 ◽  
Vol 13 (1) ◽  
Author(s):  
Ibukun A. Akinyemi ◽  
Fang Wang ◽  
Benguo Zhou ◽  
Shuishui Qi ◽  
Qingfa Wu
Keyword(s):  
Next Generation Sequencing ◽  
Plant Viruses ◽  
Next Generation ◽  
Generation Sequencing
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