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

Mohd-Yusoff NF, Ruperao P, Tomoyoshi NE, Edwards D, Gresshoff PM, Biswas B, Batley J - G3 (Bethesda) (2015)

Bottom Line: 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.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 identification of these single-point mutations will facilitate the identification of phenotypically causative mutations in EMS-mutated germplasm.

View Article: PubMed Central - PubMed

Affiliation: Centre of Integrative Legume Research, School of Agriculture and Food Science, The University of Queensland, St Lucia, Brisbane QLD 4072, Australia Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.

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Mutation effects on codon sequences by type and region in our mutant genomes. Single-nucleotide polymorphisms were observed highly located in intergenic regions, upstream, and downstream parts of the annotated genes. Only a small percentage of nonsynonymous changes was predicted.
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fig3: Mutation effects on codon sequences by type and region in our mutant genomes. Single-nucleotide polymorphisms were observed highly located in intergenic regions, upstream, and downstream parts of the annotated genes. Only a small percentage of nonsynonymous changes was predicted.

Mentions: Here, we used SnpEff to predict the effect of mutations on coding regions of annotated genes of L. japonicus for both mutants, as shown in Figure 3. Our results showed that the greatest number of SNPs (34%) was predicted to be located in intergenic regions, followed by downstream and upstream regions of predicted genes (27% each). Only 7% and 3% of SNPs were located in exon and intron sequences, respectively. Intragenic regions also were predicted to have low EMS effect. The mutation percentage was very low at splice site donor and acceptors. In our mutagenized genomes, EMS effects did not contribute to a high fraction of nonsynonymous and synonymous changes (5% and 2%, respectively).


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

Mohd-Yusoff NF, Ruperao P, Tomoyoshi NE, Edwards D, Gresshoff PM, Biswas B, Batley J - G3 (Bethesda) (2015)

Mutation effects on codon sequences by type and region in our mutant genomes. Single-nucleotide polymorphisms were observed highly located in intergenic regions, upstream, and downstream parts of the annotated genes. Only a small percentage of nonsynonymous changes was predicted.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4390572&req=5

fig3: Mutation effects on codon sequences by type and region in our mutant genomes. Single-nucleotide polymorphisms were observed highly located in intergenic regions, upstream, and downstream parts of the annotated genes. Only a small percentage of nonsynonymous changes was predicted.
Mentions: Here, we used SnpEff to predict the effect of mutations on coding regions of annotated genes of L. japonicus for both mutants, as shown in Figure 3. Our results showed that the greatest number of SNPs (34%) was predicted to be located in intergenic regions, followed by downstream and upstream regions of predicted genes (27% each). Only 7% and 3% of SNPs were located in exon and intron sequences, respectively. Intragenic regions also were predicted to have low EMS effect. The mutation percentage was very low at splice site donor and acceptors. In our mutagenized genomes, EMS effects did not contribute to a high fraction of nonsynonymous and synonymous changes (5% and 2%, respectively).

Bottom Line: 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.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 identification of these single-point mutations will facilitate the identification of phenotypically causative mutations in EMS-mutated germplasm.

View Article: PubMed Central - PubMed

Affiliation: Centre of Integrative Legume Research, School of Agriculture and Food Science, The University of Queensland, St Lucia, Brisbane QLD 4072, Australia Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.

Show MeSH