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PNAS:Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato  

2013-07-11 21:16:29|  分类: 文献学习 |  标签: |举报 |字号 订阅

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Abstract

Although applied over extremely short timescales, artificial selection has dramatically altered the form, physiology, and life history of cultivated plants. We have used RNAseq to define both gene sequence and expression divergence between cultivated tomato and five related wild species. Based on sequence differences, we detect footprints of positive selection in over 50 genes. We also document thousands of shifts in gene-expression level, many of which resulted from changes in selection pressure. These rapidly evolving genes are commonly associated with environmental response and stress tolerance. The importance of environmental inputs during evolution of gene expression is further highlighted by large-scale alteration of the light response coexpression network between wild and cultivated accessions. Human manipulation of the genome has heavily impacted the tomato transcriptome through directed admixture and by indirectly favoring nonsynonymous over synonymous substitutions. Taken together, our results shed light on the pervasive effects artificial and natural selection have had on the transcriptomes of tomato and its wild relatives. 

PNAS:Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato - 喜欢吃桃子 - wangyufeng的博客
Fig. 1.

Diversity in cultivated and wild tomatoes. (A) Bayesian relaxed-clock consensus chronogram, and examples of fruit and leaf divergence among tomato and wild relatives; nodes on the tree correspond to median branch lengths and blue bars represent 95% Bayesian confidence interval. (B) Distribution of mean distance to adjacent gene, larger distances are associated with centromeric sequences. (C) Single rate dS (gray) and single rate dN/dS (orange). (D) Frequency of expressed genes (red) and genes differentially expressed between tomato relatives (black). All plots reflect sliding windows (mean of 100 gene windows).


 
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