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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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Relative percentage of different mutation types. Our mutated genomes had varied percentages of base changes in each chromosome and unmapped regions. A high percentage of G/A and C/T changes was observed in both genomes.
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fig1: Relative percentage of different mutation types. Our mutated genomes had varied percentages of base changes in each chromosome and unmapped regions. A high percentage of G/A and C/T changes was observed in both genomes.

Mentions: Based on the mutation frequency, how each mutation type was located in individual chromosomes can be observed by calculating the percentage of mutation type in relation to the SNP total in each chromosome (Figure 1). Both genomes comprised of C/T or G/A transitions as the most frequent mutation type in their chromosomes or unmapped regions. In the AS genome, G/A transitions were the highest in Chromosomes 1, 2, 5, and 6. Chromosomes 3 and 4 and unmapped regions had C/T transitions as the highest percentage of mutation type. The lowest percentage of mutation type was C/G transversions which were present the least in all individual chromosomes and unmapped regions of the AS mutant. The distribution of transitions and transversions in the AM genome was relatively similar to the AS genome. The greatest percentage of mutation type in each chromosome of the AM genome was C/T transitions except Chromosome 3. Unmapped regions and Chromosome 3 of AM have G/A transitions as the greatest percentage of mutation type. Meanwhile, the lowest percentage of mutation type was detected to be either A/T or C/G transversions in the AM genome.


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)

Relative percentage of different mutation types. Our mutated genomes had varied percentages of base changes in each chromosome and unmapped regions. A high percentage of G/A and C/T changes was observed in both genomes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig1: Relative percentage of different mutation types. Our mutated genomes had varied percentages of base changes in each chromosome and unmapped regions. A high percentage of G/A and C/T changes was observed in both genomes.
Mentions: Based on the mutation frequency, how each mutation type was located in individual chromosomes can be observed by calculating the percentage of mutation type in relation to the SNP total in each chromosome (Figure 1). Both genomes comprised of C/T or G/A transitions as the most frequent mutation type in their chromosomes or unmapped regions. In the AS genome, G/A transitions were the highest in Chromosomes 1, 2, 5, and 6. Chromosomes 3 and 4 and unmapped regions had C/T transitions as the highest percentage of mutation type. The lowest percentage of mutation type was C/G transversions which were present the least in all individual chromosomes and unmapped regions of the AS mutant. The distribution of transitions and transversions in the AM genome was relatively similar to the AS genome. The greatest percentage of mutation type in each chromosome of the AM genome was C/T transitions except Chromosome 3. Unmapped regions and Chromosome 3 of AM have G/A transitions as the greatest percentage of mutation type. Meanwhile, the lowest percentage of mutation type was detected to be either A/T or C/G transversions in the AM genome.

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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