Lineage-specific sequence evolution and exon edge conservation partially explain the relationship of evolutionary rate and expression level in A. thaliana

Rapidly evolving proteins can aid the identification of genes underlying phenotypic adaptation across taxa, but functional and structural elements of genes can also affect evolutionary rates. In plants, the ‘edges’ of exons, flanking intron junctions, are known to contain splice enhancers and to have a higher degree of conservation compared to the remainder of the coding region. However, the extent to which these regions may be masking indicators of positive selection or account for the relationship between dN/dS and other genomic parameters is unclear. We investigate the effects of exon edge conservation on the relationship of dN/dS to various sequence characteristics and gene expression parameters in the model plant Arabidopsis thaliana. We also obtain lineage-specific dN/dS estimates, making use of the recently sequenced genome of Thellungiella parvula, the second closest sequenced relative after the sister species Arabidopsis lyrata. Overall, we find that the effect of exon edge con...

快速进化的蛋白质有助于识别跨类群表型适应背后的基因，但基因的功能与结构元件也会影响进化速率。在植物中，外显子的“边缘区域”（即内含子连接处两侧的部分）已知含有剪接增强子，且与编码区其余部分相比保守性更高。然而，这些区域在多大程度上可能掩盖正选择的指标，或解释dN/dS与其他基因组参数之间的关系，目前尚不清楚。我们以模式植物拟南芥（Arabidopsis thaliana）为研究对象，探究外显子边缘保守性对dN/dS与多种序列特征及基因表达参数之间关系的影响。我们还利用近期测序的小盐芥（Thellungiella parvula）基因组——其是拟南芥姊妹种阿拉伯芥（Arabidopsis lyrata）之后的第二近缘已测序物种——获得了谱系特异性的dN/dS估计值。总体而言，我们发现外显子边缘保守性的影响...