全基因组分析揭示玉米基因组中同义突变的选择较弱。

Genome-wide analysis on the maize genome reveals weak selection on synonymous mutations.

机构信息

College of Life Sciences, Beijing Normal University, No. 19 Xinjiekouwai Street, Haidian District, Beijing, China.

出版信息

BMC Genomics. 2020 Apr 29;21(1):333. doi: 10.1186/s12864-020-6745-3.

BACKGROUND

Synonymous mutations are able to change the tAI (tRNA adaptation index) of a codon and consequently affect the local translation rate. Intuitively, one may hypothesize that those synonymous mutations which increase the tAI values are favored by natural selection.

RESULTS

We use the maize (Zea mays) genome to test our assumption. The first supporting evidence is that the tAI-increasing synonymous mutations have higher fixed-to-polymorphic ratios than the tAI-decreasing ones. Next, the DAF (derived allele frequency) or MAF (minor allele frequency) of the former is significantly higher than the latter. Moreover, similar results are obtained when we investigate CAI (codon adaptation index) instead of tAI.

CONCLUSION

The synonymous mutations in the maize genome are not strictly neutral. The tAI-increasing mutations are positively selected while those tAI-decreasing ones undergo purifying selection. This selection force might be weak but should not be automatically ignored.

背景

同义突变能够改变密码子的 tAI（tRNA 适应指数），从而影响局部翻译速率。直观地说，人们可能会假设那些增加 tAI 值的同义突变受到自然选择的青睐。

结果

我们使用玉米（Zea mays）基因组来检验我们的假设。第一个支持性证据是，增加 tAI 的同义突变的固定到多态性比例高于减少 tAI 的同义突变。其次，前者的 DAF（衍生等位基因频率）或 MAF（次要等位基因频率）明显高于后者。此外，当我们研究 CAI（密码子适应指数）而不是 tAI 时，也得到了类似的结果。