Noncoding RNAs (ncRNAs) play important roles in many biological processes and provide materials for evolutionary adaptations beyond protein-coding genes, such as in the arms race between the host and pathogen. However, currently, a comprehensive high-resolution analysis of primate genomes that includes the latest annotated ncRNAs is not available. Here, we developed a computational pipeline to estimate the selections that act on noncoding regions based on comparisons with a large number of reference sequences in introns adjacent to the interested regions. Our method yields result comparable with those of the established codon-based method and phyloP method for coding genes; thus, it provides a holistic framework for estimating the selection on the entire genome. We further showed that fast-evolving protein-coding genes and their corresponding 5′ UTRs have a significantly lower frequency of the CpG dinucleotides than those evolving at an average pace, and these fast-evolving genes are enriched in the process of immunity and host defense. We also identified fast-evolving miRNAs with antiviral functions in cells. Our results provide a resource for high-resolution evolution analysis of the primate genomes.

非编码RNA（ncRNA）在许多生物学过程中都起着重要作用，并且为蛋白质以外的蛋白质进化基因的进化适应提供了材料，例如宿主与病原体之间的军备竞赛。但是，目前尚无包括最新注释的ncRNA在内的灵长类动物基因组的全面高分辨率分析。在这里，我们开发了一条计算流水线，根据与感兴趣区域相邻的内含子中大量参考序列的比较，估计作用于非编码区域的选择。我们的方法产生的结果与已建立的基于密码子的方法和phyloP方法编码基因的结果相当；因此，它为估计整个基因组的选择提供了一个整体框架。我们进一步表明，快速进化的蛋白质编码基因及其相应的5'UTRs的CpG二核苷酸的频率明显低于以平均速度进化的基因，并且这些快速进化的基因在免疫和宿主防御过程中富集了。我们还确定了在细胞中具有抗病毒功能的快速发展的miRNA。我们的结果为灵长类动物基因组的高分辨率进化分析提供了资源。