Genome?￠????wide survey of artificial mutations induced by ethyl methanesulfonate and gamma rays in tomato

摘要

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.