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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Main Authors:	Mohd-Yusoff, Nur Fatihah, Ruperao, Pradeep, Tomoyoshi, Nurain Emylia, Edwards, David, Gresshoff, Peter M., Biswas, Bandana, Batley, Jacqueline
Format:	Online
Language:	English
Published:	Genetics Society of America 2015
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4390572/

id	pubmed-4390572
recordtype	oai_dc
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 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.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Mohd-Yusoff, Nur Fatihah Ruperao, Pradeep Tomoyoshi, Nurain Emylia Edwards, David Gresshoff, Peter M. Biswas, Bandana Batley, Jacqueline
spellingShingle	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
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
title	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_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_sort	scanning the effects of ethyl methanesulfonate on the whole genome of lotus japonicus using second-generation sequencing analysis
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.
publisher	Genetics Society of America
publishDate	2015
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4390572/
_version_	1613209316913840128

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

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