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 and Batley, Jacqueline (2015) Scanning the effects of ethyl methanesulfonate on the whole genome of lotus japonicus using second-generation sequencing analysis. G3-Genes Genomes Genetics, 5 4: 559-567. doi:10.1534/g3.114.014571


Author Mohd-Yusoff, Nur Fatihah
Ruperao, Pradeep
Tomoyoshi, Nurain Emylia
Edwards, David
Gresshoff, Peter M.
Biswas, Bandana
Batley, Jacqueline
Title Scanning the effects of ethyl methanesulfonate on the whole genome of lotus japonicus using second-generation sequencing analysis
Formatted title
Scanning the effects of ethyl methanesulfonate on the whole genome of lotus japonicus using second-generation sequencing analysis
Journal name G3-Genes Genomes Genetics   Check publisher's open access policy
ISSN 2160-1836
Publication date 2015-04
Year available 2015
Sub-type Article (original research)
DOI 10.1534/g3.114.014571
Open Access Status DOI
Volume 5
Issue 4
Start page 559
End page 567
Total pages 9
Place of publication Bethesda, MD, United States
Publisher Genetics Society of America
Collection year 2016
Language eng
Formatted abstract
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.
Keyword Abscisic acid
Lotus japonicus
Mutagenesis
Second-generation sequencing
Single nucleotide polymorphism (SNP)
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Centre for Integrative Legume Research Publications
School of Agriculture and Food Sciences
Official 2016 Collection
 
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