Fine-Grained Analysis of Spontaneous Mutation Spectrum and Frequency in Arabidopsis thaliana.
Mao-Lun Weng,Claude Becker,Julia Hildebrandt,Manuela Neumann,Matthew T. Rutter,Ruth G. Shaw,Detlef Weigel,Charles B. Fenster +7 more
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TLDR
The results suggest that high mutation rate potentially contributes to high polymorphism and low mutation rate to reduced polymorphism in natural populations providing insights of mutational inputs in generating natural genetic diversity.Abstract:
Mutations are the ultimate source of all genetic variation. However, few direct estimates of the contribution of mutation to molecular genetic variation are available. To address this issue, we first analyzed the rate and spectrum of mutations in the Arabidopsis thaliana reference accession after 25 generations of single-seed descent. We then compared the mutation profile in these mutation accumulation (MA) lines against genetic variation observed in the 1001 Genomes Project. The estimated haploid single nucleotide mutation (SNM) rate for A. thaliana is 6.95 × 10−9 (SE ± 2.68 × 10−10) per site per generation, with SNMs having higher frequency in transposable elements (TEs) and centromeric regions. The estimated indel mutation rate is 1.30 × 10−9 (±1.07 × 10−10) per site per generation, with deletions being more frequent and larger than insertions. Among the 1694 unique SNMs identified in the MA lines, the positions of 389 SNMs (23%) coincide with biallelic SNPs from the 1001 Genomes population, and in 289 (17%) cases the changes are identical. Of the 329 unique indels identified in the MA lines, 96 (29%) overlap with indels from the 1001 Genomes dataset, and 16 indels (5% of the total) are identical. These overlap frequencies are significantly higher than expected, suggesting that de novo mutations are not uniformly distributed and arise at polymorphic sites more frequently than assumed. These results suggest that high mutation rate potentially contributes to high polymorphism and low mutation rate to reduced polymorphism in natural populations providing insights of mutational inputs in generating natural genetic diversity.read more
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Integrative Genomics Viewer
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Mutation bias reflects natural selection in Arabidopsis thaliana
J. Grey Monroe,Thanvi Srikant,Pablo Carbonell-Bejerano,Claude Becker,Mariele Lensink,Moises Exposito-Alonso,Marie Klein,Julia Hildebrandt,Manuela Neumann,Daniel J. Kliebenstein,Mao-Lun Weng,Eric Imbert,John Ågren,Matthew T. Rutter,Charles B. Fenster,Detlef Weigel +15 more
TL;DR: In this paper , a large survey of de novo mutations in the plant Arabidopsis thaliana was conducted and it was shown that mutations occur less often in functionally constrained regions of the genome.
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The Plant DNA Damage Response: Signaling Pathways Leading to Growth Inhibition and Putative Role in Response to Stress Conditions.
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Transposition favors the generation of large effect mutations that may facilitate rapid adaption
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TL;DR: It is shown in Arabidopsis that TEs accumulate exponentially once mobilized and that COPIA retrotransposons preferentially integrate in environmental response genes in a H2A.Z-dependent manner, and that epigenetic silencing of new Ty1/copia copies can affect their impact on major fitness-related traits, including flowering time.
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The Genomic Ecosystem of Transposable Elements in Maize
TL;DR: It is concluded that while the impact of transposition is highly family- and context-dependent, a family-level understanding of the ecology of TEs in the genome can refine the ability to predict the role ofTEs in generating genetic and phenotypic diversity.
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