title: Genome-wide survey of artificial mutations induced by ethyl methanesulfonate and gamma rays in tomato.
abstract: Genome-wide mutations induced by ethyl methanesulfonate (EMS) and gamma irradiation in the tomato Micro-Tom genome were identified by a whole-genome shotgun sequencing analysis to estimate the spectrum and distribution of whole-genome DNA mutations and the frequency of deleterious mutations. A total of ~370 Gb of paired-end reads for four EMS-induced mutants and three gamma-ray-irradiated lines as well as a wild-type line were obtained by next-generation sequencing technology. Using bioinformatics analyses, we identified 5920 induced single nucleotide variations and insertion/deletion (indel) mutations. The predominant mutations in the EMS mutants were C/G to T/A transitions, while in the gamma-ray mutants, C/G to T/A transitions, A/T to T/A transversions, A/T to G/C transitions and deletion mutations were equally common. Biases in the base composition flanking mutations differed between the mutagenesis types. Regarding the effects of the mutations on gene function, >90% of the mutations were located in intergenic regions, and only 0.2% were deleterious. In addition, we detected 1,140,687 spontaneous single nucleotide polymorphisms and indel polymorphisms in wild-type Micro-Tom lines. We also found copy number variation, deletions and insertions of chromosomal segments in both the mutant and wild-type lines. The results provide helpful information not only for mutation research, but also for mutant screening methodology with reverse-genetic approaches.
authors.affiliation: Kazusa DNA Research Institute, Kisarazu, Japan.
authors.forename: Kenta
authors.initials: K
authors.lastname: Shirasawa
authors.affiliation: Kazusa DNA Research Institute, Kisarazu, Japan.
authors.forename: Hideki
authors.initials: H
authors.lastname: Hirakawa
authors.affiliation: NARO Institute of Vegetable and Tea Sciences, Tsu, Japan.
authors.forename: Tsukasa
authors.initials: T
authors.lastname: Nunome
authors.affiliation: Kazusa DNA Research Institute, Kisarazu, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Tabata
authors.affiliation: Kazusa DNA Research Institute, Kisarazu, Japan.
authors.forename: Sachiko
authors.initials: S
authors.lastname: Isobe
mesh_terms: D001483:Base Sequence; D056915:DNA Copy Number Variations / Q000235:genetics; D005020:Ethyl Methanesulfonate; D005720:Gamma Rays; D017343:Genes, Plant; D018745:Genome, Plant; D054643:INDEL Mutation / Q000235:genetics; D018551:Solanum lycopersicum / Q000235:genetics* / Q000528:radiation effects*; D009154:Mutation / Q000235:genetics*; D030821:Plants, Genetically Modified; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D017422:Sequence Analysis, DNA; D011795:Surveys and Questionnaires
chemical_list: D005020:Ethyl Methanesulfonate
keywords: ethyl methanesulfonate; gamma rays; mutation; tomato (Solanum lycopersicum); whole-genome resequencing