Cargando…
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...
Autores principales: | , , , , , , |
---|---|
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 |
_version_ | 1782365700025745408 |
---|---|
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. |
format | Online Article Text |
id | pubmed-4390572 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Genetics Society of America |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT mohdyusoffnurfatihah scanningtheeffectsofethylmethanesulfonateonthewholegenomeoflotusjaponicususingsecondgenerationsequencinganalysis AT ruperaopradeep scanningtheeffectsofethylmethanesulfonateonthewholegenomeoflotusjaponicususingsecondgenerationsequencinganalysis AT tomoyoshinurainemylia scanningtheeffectsofethylmethanesulfonateonthewholegenomeoflotusjaponicususingsecondgenerationsequencinganalysis AT edwardsdavid scanningtheeffectsofethylmethanesulfonateonthewholegenomeoflotusjaponicususingsecondgenerationsequencinganalysis AT gresshoffpeterm scanningtheeffectsofethylmethanesulfonateonthewholegenomeoflotusjaponicususingsecondgenerationsequencinganalysis AT biswasbandana scanningtheeffectsofethylmethanesulfonateonthewholegenomeoflotusjaponicususingsecondgenerationsequencinganalysis AT batleyjacqueline scanningtheeffectsofethylmethanesulfonateonthewholegenomeoflotusjaponicususingsecondgenerationsequencinganalysis |