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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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Distribution of mutation across individual chromosomes in both AS (left) and AM (right) genomes. Mutations were plotted in every 1000 kb of genomic sequences. Chromosome (Chr) number is shown above its designated graph. Chromosome position was plotted based on the assembled length of L. japonicus genome.
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fig2: Distribution of mutation across individual chromosomes in both AS (left) and AM (right) genomes. Mutations were plotted in every 1000 kb of genomic sequences. Chromosome (Chr) number is shown above its designated graph. Chromosome position was plotted based on the assembled length of L. japonicus genome.

Mentions: We determined how many SNPs occurred every 1000 kb to show the distribution of mutations across our mutagenized genomes (Figure 2). Regardless of mutation types, the distribution of SNPs is unique between AS and AM when comparing the same chromosome. SNPs were randomly located along the genomes with no specific chromosome position being particularly abundant or lacking in SNPs for both genomes. However, Chromosomes 1 and 2 were highly “corrupted” in their arms. Meanwhile, some chromosomes (Chromosomes 3, 4, and 5 for AS; Chromosome 3 for AM) have a high peak of SNPs toward their center. The density of mutations in every 1000 kb was relatively apparent in Chromosomes 1 and 2 of AS and AM. Meanwhile, Chromosome 6 had less dense mutations for both genomes.


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)

Distribution of mutation across individual chromosomes in both AS (left) and AM (right) genomes. Mutations were plotted in every 1000 kb of genomic sequences. Chromosome (Chr) number is shown above its designated graph. Chromosome position was plotted based on the assembled length of L. japonicus genome.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig2: Distribution of mutation across individual chromosomes in both AS (left) and AM (right) genomes. Mutations were plotted in every 1000 kb of genomic sequences. Chromosome (Chr) number is shown above its designated graph. Chromosome position was plotted based on the assembled length of L. japonicus genome.
Mentions: We determined how many SNPs occurred every 1000 kb to show the distribution of mutations across our mutagenized genomes (Figure 2). Regardless of mutation types, the distribution of SNPs is unique between AS and AM when comparing the same chromosome. SNPs were randomly located along the genomes with no specific chromosome position being particularly abundant or lacking in SNPs for both genomes. However, Chromosomes 1 and 2 were highly “corrupted” in their arms. Meanwhile, some chromosomes (Chromosomes 3, 4, and 5 for AS; Chromosome 3 for AM) have a high peak of SNPs toward their center. The density of mutations in every 1000 kb was relatively apparent in Chromosomes 1 and 2 of AS and AM. Meanwhile, Chromosome 6 had less dense mutations for both genomes.

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