09梨树中两个亚基因组经历unbiased 进化

原文链接 https://www.nature.com/articles/s41438-018-0110-6

不知道的观点

• overfractionated subgenome are more likely to be targeted by 24-nt smRNAs and have higher transposon element (TE) coverage in their upstream regions, resulting in reduction of gene expression and driving subgenome expression dominance

图片

• 关于亚基因组表达主导性

  Fig. 3 Comparison of evolutionary rates and expression patterns between pear subgenome 1 and subgenome 2. a–c Comparison of Ka, Ks, and Ka/Ks between genes in each pear subgenome and their orthologous genes in peach. Ka, Ks, and Ka/Ks values were estimated by pairwise comparison of orthologous genes between pear or peach and strawberry. d–e Comparison of overall expression level between the two subgenomes and the expression pattern of homeologous gene pairs in different pear tissues. Mann–Whitney U test was used for statistical analysis. p-value < 0.05. *p-value < 0.01

• 同源基因甲基化的分析

  Fig. 4 Comparison of DNA methylation levels of homeologous genes between pear subgenome 1 and subgenome 2. a The CG methylation levels of homeologous genes in the two subgenomes. b The CHG methylation levels of homeologous genes in the two subgenomes. TSS transcription start site, TTS transcription termination site. p-value < 0.05. *p-value < 0.01, Mann–Whitney U test

方法

• 鉴定亚基因组同源源基因

• 曼-惠特尼U检验

• deepTools 展示甲基化数据