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Scanning the Effects of Ethyl Methanesulfonate on the Whole Genome of Lotus japonicus Using Second-Generation Sequencing Analysis

Genetic structure can be altered by chemical mutagenesis, which is a common method applied in molecular biology and genetics. Second-generation sequencing provides a platform to reveal base alterations occurring in the whole genome due to mutagenesis. A model legume, Lotus japonicus ecotype Miyakoji...

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Autores principales: Mohd-Yusoff, Nur Fatihah, Ruperao, Pradeep, Tomoyoshi, Nurain Emylia, Edwards, David, Gresshoff, Peter M., Biswas, Bandana, Batley, Jacqueline
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Genetics Society of America 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4390572/
https://www.ncbi.nlm.nih.gov/pubmed/25660167
http://dx.doi.org/10.1534/g3.114.014571
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author Mohd-Yusoff, Nur Fatihah
Ruperao, Pradeep
Tomoyoshi, Nurain Emylia
Edwards, David
Gresshoff, Peter M.
Biswas, Bandana
Batley, Jacqueline
author_facet Mohd-Yusoff, Nur Fatihah
Ruperao, Pradeep
Tomoyoshi, Nurain Emylia
Edwards, David
Gresshoff, Peter M.
Biswas, Bandana
Batley, Jacqueline
author_sort Mohd-Yusoff, Nur Fatihah
collection PubMed
description Genetic structure can be altered by chemical mutagenesis, which is a common method applied in molecular biology and genetics. Second-generation sequencing provides a platform to reveal base alterations occurring in the whole genome due to mutagenesis. A model legume, Lotus japonicus ecotype Miyakojima, was chemically mutated with alkylating ethyl methanesulfonate (EMS) for the scanning of DNA lesions throughout the genome. Using second-generation sequencing, two individually mutated third-generation progeny (M3, named AM and AS) were sequenced and analyzed to identify single nucleotide polymorphisms and reveal the effects of EMS on nucleotide sequences in these mutant genomes. Single-nucleotide polymorphisms were found in every 208 kb (AS) and 202 kb (AM) with a bias mutation of G/C-to-A/T changes at low percentage. Most mutations were intergenic. The mutation spectrum of the genomes was comparable in their individual chromosomes; however, each mutated genome has unique alterations, which are useful to identify causal mutations for their phenotypic changes. The data obtained demonstrate that whole genomic sequencing is applicable as a high-throughput tool to investigate genomic changes due to mutagenesis. The identification of these single-point mutations will facilitate the identification of phenotypically causative mutations in EMS-mutated germplasm.
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spelling pubmed-43905722015-04-10 Scanning the Effects of Ethyl Methanesulfonate on the Whole Genome of Lotus japonicus Using Second-Generation Sequencing Analysis Mohd-Yusoff, Nur Fatihah Ruperao, Pradeep Tomoyoshi, Nurain Emylia Edwards, David Gresshoff, Peter M. Biswas, Bandana Batley, Jacqueline G3 (Bethesda) Investigations Genetic structure can be altered by chemical mutagenesis, which is a common method applied in molecular biology and genetics. Second-generation sequencing provides a platform to reveal base alterations occurring in the whole genome due to mutagenesis. A model legume, Lotus japonicus ecotype Miyakojima, was chemically mutated with alkylating ethyl methanesulfonate (EMS) for the scanning of DNA lesions throughout the genome. Using second-generation sequencing, two individually mutated third-generation progeny (M3, named AM and AS) were sequenced and analyzed to identify single nucleotide polymorphisms and reveal the effects of EMS on nucleotide sequences in these mutant genomes. Single-nucleotide polymorphisms were found in every 208 kb (AS) and 202 kb (AM) with a bias mutation of G/C-to-A/T changes at low percentage. Most mutations were intergenic. The mutation spectrum of the genomes was comparable in their individual chromosomes; however, each mutated genome has unique alterations, which are useful to identify causal mutations for their phenotypic changes. The data obtained demonstrate that whole genomic sequencing is applicable as a high-throughput tool to investigate genomic changes due to mutagenesis. The identification of these single-point mutations will facilitate the identification of phenotypically causative mutations in EMS-mutated germplasm. Genetics Society of America 2015-02-06 /pmc/articles/PMC4390572/ /pubmed/25660167 http://dx.doi.org/10.1534/g3.114.014571 Text en Copyright © 2015 Mohd-Yusoff et al. http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution Unported License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Investigations
Mohd-Yusoff, Nur Fatihah
Ruperao, Pradeep
Tomoyoshi, Nurain Emylia
Edwards, David
Gresshoff, Peter M.
Biswas, Bandana
Batley, Jacqueline
Scanning the Effects of Ethyl Methanesulfonate on the Whole Genome of Lotus japonicus Using Second-Generation Sequencing Analysis
title Scanning the Effects of Ethyl Methanesulfonate on the Whole Genome of Lotus japonicus Using Second-Generation Sequencing Analysis
title_full Scanning the Effects of Ethyl Methanesulfonate on the Whole Genome of Lotus japonicus Using Second-Generation Sequencing Analysis
title_fullStr Scanning the Effects of Ethyl Methanesulfonate on the Whole Genome of Lotus japonicus Using Second-Generation Sequencing Analysis
title_full_unstemmed Scanning the Effects of Ethyl Methanesulfonate on the Whole Genome of Lotus japonicus Using Second-Generation Sequencing Analysis
title_short Scanning the Effects of Ethyl Methanesulfonate on the Whole Genome of Lotus japonicus Using Second-Generation Sequencing Analysis
title_sort scanning the effects of ethyl methanesulfonate on the whole genome of lotus japonicus using second-generation sequencing analysis
topic Investigations
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4390572/
https://www.ncbi.nlm.nih.gov/pubmed/25660167
http://dx.doi.org/10.1534/g3.114.014571
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