Guo Xingyi, Gui Yijie, Wang Yu, Zhu Qian-Hao, Helliwell Chris, Fan Longjiang
Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310029, PR China.
BMC Genomics. 2008 Oct 2;9:454. doi: 10.1186/1471-2164-9-454.
MicroRNAs (miRNAs) posttranscriptionally down-regulate gene expression by binding target mRNAs. Analysis of the evolution of miRNA binding sites is helpful in understanding the co-evolution between miRNAs and their targets. To understand this process in plants a comparative analysis of miRNA-targeted duplicated gene pairs derived from a well-documented whole genome duplication (WGD) event in combination with a population genetics study of six experimentally validated miRNA binding sites in rice (O. sativa) was carried out.
Of the 1,331 pairs of duplicate genes from the WGD, 41 genes (29 pairs) were computationally predicted to be miRNA targets. Sequence substitution analysis indicated that the synonymous substitution rate was significantly lower in the miRNA binding sites than their 5' and 3' flanking regions. Of the 29 duplicated gene pairs, 17 have only one paralog been targeted by a miRNA. This could be due to either gain of a miRNA binding site after the WGD or because one of the duplicated genes has escaped from being a miRNA target after the WGD (loss of miRNA binding site). These possibilities were distinguished by separating miRNAs conserved in both dicots and monocot plants from rice-specific miRNAs and by phylogenetic analysis of miRNA target gene families. The gain/loss rate of miRNA binding sites was estimated to be 3.0 x 10(-9) gain/loss per year. Most (70.6%) of the gains/losses were due to nucleotide mutation. By analysis of cultivated (O. sativa; n = 30) and wild (O. rufipogon; n = 15) rice populations, no segregating site was observed in six miRNA binding sites whereas 0.12-0.20 SNPs per 21-nt or 1.53-1.80 x 10(-3) of the average pairwise nucleotide diversity (pi) were found in their flanking regions.
Both molecular evolution and population genetics support the hypothesis that conservation of miRNA binding sites is maintained by purifying selection through elimination of deleterious alleles. Nucleotide mutations play a major role in the gain/loss of miRNA binding sites during evolution.
微小RNA（miRNA）通过与靶mRNA结合在转录后下调基因表达。分析miRNA结合位点的进化有助于理解miRNA与其靶标之间的共同进化。为了在植物中理解这一过程，我们对源自一个有充分记录的全基因组复制（WGD）事件的miRNA靶向重复基因对进行了比较分析，并结合对水稻（O. sativa）中六个经实验验证的miRNA结合位点的群体遗传学研究。
在来自WGD的1331对重复基因中，有41个基因（29对）通过计算预测为miRNA靶标。序列替换分析表明，miRNA结合位点的同义替换率显著低于其5'和3'侧翼区域。在这29对重复基因对中，17对只有一个旁系同源基因被miRNA靶向。这可能是由于WGD后miRNA结合位点的获得，或者是由于重复基因中的一个在WGD后逃脱了成为miRNA靶标的命运（miRNA结合位点的丢失）。通过将双子叶植物和单子叶植物中都保守的miRNA与水稻特有的miRNA分开，并对miRNA靶标基因家族进行系统发育分析，区分了这些可能性。估计miRNA结合位点的获得/丢失率为每年3.0×10⁻⁹次获得/丢失。大多数（70.6%）的获得/丢失是由于核苷酸突变。通过对栽培水稻（O. sativa；n = 30）和野生水稻（O. rufipogon；n = 15）群体的分析，在六个miRNA结合位点中未观察到分离位点，而在其侧翼区域每21个核苷酸发现0.12 - 0.20个单核苷酸多态性（SNP），或平均成对核苷酸多样性（pi）的1.53 - 1.80×10⁻³。
分子进化和群体遗传学都支持这样的假设，即通过消除有害等位基因的纯化选择来维持miRNA结合位点的保守性。核苷酸突变在进化过程中miRNA结合位点的获得/丢失中起主要作用。
