Scanning the effects of ethyl methanesulfonate on the whole genome of lotus japonicus using second-generation sequencing analysis

N.F. Mohd-Yusoff, Pradeep Ruperao, N.E. Tomoyoshi, Dave Edwards, P.M. Gresshoff, B. Biswas, Jacqueline Batley

    Research output: Contribution to journalArticle

    9 Citations (Scopus)

    Abstract

    © 2015 Mohd-Yusoff et al. 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 highthroughput 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.
    Original languageEnglish
    Pages (from-to)559-567
    JournalG3: Genes, Genomes, Genetics
    Volume5
    Issue number4
    DOIs
    Publication statusPublished - 2015

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