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PNAS:Epigenomic programming contributes to the genomic drift evolution of the F-Box protein superfamily in Arabidopsis  

2013-10-18 21:58:56|  分类: 文献学习 |  标签: |举报 |字号 订阅

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Significance

Gene families significantly influence organismal diversity and adaptation, but how they evolved and are controlled is not fully clear. Using the Arabidopsis F-Box protein superfamily as a model, we show that both genomic and epigenomic forces are consequential with reversible, suppressive chromatin marks potentially helping dampen the adverse effects of altered gene dosage and the emergence of deleterious alleles. Such forces might be relevant to other highly polymorphic gene families impacted by genomic drift evolution.

Abstract

Comparisons within expanding sequence databases have revealed a dynamic interplay among genomic and epigenomic forces in driving plant evolution. Such forces are especially obvious within the F-Box (FBX) superfamily, one of the largest and most polymorphic gene families in land plants, where its frequent lineage-specific expansions and contractions provide an excellent model to assess how genetic variation impacted gene function before and after speciation. Previous phylogenetic comparisons based on orthology, diversity, and expression patterns identified three plant FBX groups—Common, Lineage-Specific, and Pseudo(genized)—whose emergences are consistent with genomic drift evolution. Here, we examined this variance within Arabidopsis thaliana by evaluating SNPs for all 877 FBX loci from 432 naturally occurring accessions and their relationships to variations in natural selection, expression, and DNA/histone methylation. In line with their phenotypic importance, Common FBX loci have low polymorphism but high deleterious mutation rates indicative of stringent functional constraints. In contrast, the Lineage-Specific and Pseudo groups are enriched in genes with basal expression and higher SNP density and more correlated with methylation marks (RNA-directed DNA methylation and histone H3K27 trimethylation) that promote transcriptional silencing. Taken together, we propose that reversible epigenomic modifications helped shape FBX gene evolution by transcriptionally suppressing the adverse effects of gene dosage imbalance and harmful FBX alleles that arise during genomic drift, while simultaneously allowing innovations to emerge through epigenomic reprogramming.


PNAS:Epigenomic programming contributes to the genomic drift evolution of the F-Box protein superfamily in Arabidopsis - 喜欢吃桃子 - wangyufeng的博客
SNP analyses of Common, Specific, and Pseudo FBX genes from 432 Arabidopsis accessions.
(A) Comparisons of sequence polymorphism (segregating sites per nt) (Upper) and diversity (average nt differences per site, π) (Lower). Each box plot shows the median (solid line), the 25th and 75th percentiles (boxes), and the fifth and 95th percentiles (dashed lines). (B) Spearman rank correlation test between sequence polymorphism and natural selection (Ka/Ks). Correlation coefficients (rho), P values, and lines of best-fit linear regression are included. (C) Frequency spectrum of rare alleles with nonsynonymous and synonymous mutations. (D) Distribution of recently deleterious (MAF < 5%), relaxed, and adaptive mutations (McDonald–Krietman test). P values in A and D were calculated by Wilcoxon rank and Fisher’s exact tests, respectively.
 
  • Zhihua Hua,
  • John E. Pool,
  • Robert J. Schmitz,
  • Matthew D. Schultz,
  • Shin-Han Shiu,
  • Joseph R. Ecker,
  • and Richard D. Vierstra
PNAS 2013 110 (42) 16927-16932; published ahead of print September 30, 2013, doi:10.1073/pnas.1316009110
Full text:http://www.pnas.org/content/110/42/16927/F1.expansion.html
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