Discovery of mutations in Chenopodium quinoa Willd through EMS mutagenesis and mutation screening using pre-selection phenotypic data and next-generation sequencing

AbstractQuinoa (Chenopodium quinoaWilld) is a dicotyledonous annual species belonging to the family Amaranthaceae, which is nutritionally well balanced in terms of its oil, protein and carbohydrate content. Targeting-induced local lesions in genomes (the TILLING strategy) was employed to find mutations in acetolactate synthase (AHAS) genes in a mutant quinoa population. TheAHASgenes were targeted because they are common enzyme target sites for five herbicide groups. Ethyl methane sulfonate (EMS) was used to induce mutations in theAHASgenes; it was found that 2% EMS allowed a mutation frequency of one mutation every 203 kilobases to be established. In the mutant population created, a screening strategy using pre-selection phenotypic data and next-generation sequencing (NGS) allowed identification of a mutation that alters the amino acid composition of this species (nucleotide 1231 codon GTT→ATT, Val→Ile); however, this mutation did not result in herbicide resistance. The current work shows that TILLING combined with the high-throughput of NGS technologies and an overlapping pool design provides an efficient and economical method for detecting induced mutations in pools of individuals.

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Determining the Mutation Bias of Favipiravir in Influenza Using Next-generation Sequencing

10.1101/375378 ◽

2018 ◽

Cited By ~ 1

Author(s):

Daniel H. Goldhill ◽

Pinky Langat ◽

Hongyao Xie ◽

Monica Galiano ◽

Shahjahan Miah ◽

...

Keyword(s):

Next Generation Sequencing ◽

Broad Spectrum ◽

Influenza Pandemic ◽

Antiviral Drug ◽

Sequence Information ◽

Next Generation ◽

Induced Mutations ◽

Mutation Bias ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

AbstractFavipiravir is a broad spectrum antiviral drug that may be used to treat influenza. Previous research has identified that favipiravir likely acts as a mutagen but the precise mutation bias that favipiravir induces in influenza virus RNAs has not been described. Here, we use next-generation sequencing (NGS) with barcoding of individual RNA molecules to accurately and quantitatively detect favipiravir-induced mutations and to sample orders of magnitude more mutations than would be possible through Sanger sequencing. We demonstrate that favipiravir causes mutations and show that favipiravir primarily acts as a guanine analogue and secondarily as an adenine analogue resulting in the accumulation of transition mutations. We also use a standard NGS pipeline to show that the mutagenic effect of favipiravir can be measured by whole genome sequencing of virus.ImportanceNew antiviral drugs are needed as a first line of defence in the event of a novel influenza pandemic. Favipiravir is a broad-spectrum antiviral which is effective against influenza. The exact mechanism of how favipiravir works to inhibit influenza is still unclear. We used next-generation sequencing (NGS) to demonstrate that favipiravir causes mutations in influenza RNA. The greater depth of NGS sequence information over traditional sequencing methods allowed us to precisely determine the bias of particular mutations caused by favipiravir. NGS can also be used in a standard diagnostic pipeline to show that favipiravir is acting on the virus by revealing the mutation bias pattern typical to the drug. Our work will aid in testing whether viruses are resistant to favipiravir and may help demonstrate the effect of favipiravir on viruses in a clinical setting. This will be important if favipiravir is used during a future influenza pandemic.

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Next-generation sequencing (NGS)-based identification of induced mutations in a doubly mutagenized tomato (Solanum lycopersicum ) population

The Plant Journal ◽

10.1111/tpj.13654 ◽

2017 ◽

Vol 92 (3) ◽

pp. 495-508 ◽

Cited By ~ 9

Author(s):

Prateek Gupta ◽

Bodanapu Reddaiah ◽

Hymavathi Salava ◽

Pallawi Upadhyaya ◽

Kamal Tyagi ◽

...

Keyword(s):

Next Generation Sequencing ◽

Solanum Lycopersicum ◽

Next Generation ◽

Induced Mutations ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

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Procedure for phenotypic data collection as an important stage of predictive studies

Issues of Forensic Science ◽

10.34836/pk.2017.295.3 ◽

2017 ◽

Vol 295 ◽

pp. 64-69

Author(s):

Magdalena Zubańska ◽

◽

Przemysław Knut ◽

Keyword(s):

Next Generation Sequencing ◽

Data Collection ◽

Social Perception ◽

Questionnaire Survey ◽

Dna Analysis ◽

Predictive Analysis ◽

Next Generation ◽

Phenotypic Data ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

The article addresses the issues related to phenotypic data collection at the stage of acquiring research sample and indicates the importance of this stage for studies on DNA-based predictive analysis. It presents the assumptions and the execution of a task carried out as part of the project entitled: “A genetic portrait of the offender and the victim – developing a system to determine human physical appearance and biogeographical origin, based on DNA analysis, involving Next Generation Sequencing (NGS)” – the acronym NEXT. In addition, the results of a questionnaire survey administered to a group of people who have taken part in the above project as sample donors, are discussed. The purpose of the study was to determine the motivation for participation in a scientific undertaking related to genetics. Based on the respondents’ answers, the general conclusion can be formulated that this type of research enjoys positive social perception.

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