Adaptation and Phenotypic Diversification in Arabidopsis through Loss-of-Function Mutations in Protein-Coding Genes
Adaptation and Phenotypic Diversification in Arabidopsis through Loss-of-Function Mutations in Protein-Coding Genes
复制标题
拟南芥通过蛋白质编码基因功能丧失突变实现适应和表型多样化
DOI：
10.1105/tpc.18.00791
复制
发表时间：
2019
期刊：
影响因子：
11.6
通讯作者：
Guo Ya Long
中科院分区：
文献类型：
--
作者：
Xu Yong Chao;Niu Xiao Min;Li Xin Xin;He Wenrong;Chen Jia Fu;Zou Yu Pan;Wu Qiong;Zhang Yong E;Busch Wolfgang;Guo Ya Long
根据“少即是多”假说，基因丢失是进化变化的动力。功能缺失（LoF）突变导致蛋白质编码基因的自然敲除，不仅提供了基因功能的信息，而且在适应和表型多样化中起着重要作用。尽管“少即是多”的假说早在20年前就提出了，但它仍有待大规模的探索。在本研究中，我们在1071个拟南芥基因组中鉴定了60819个LoF变异，发现在哥伦比亚-0基因组中注释的34%的拟南芥蛋白编码基因没有任何LoF变异。我们发现核苷酸多样性、转座因子密度和基因家族大小与LoF变异的存在密切相关。有趣的是，在等位基因频率大于0.5%的LoF变异中，有0.9%与气候变化有关。此外，在长江流域种群中，有1%的LoF突变基因处于正选择状态，这为LoF突变对适应的贡献提供了重要的认识。特别是，我们的研究结果表明LoF突变塑造了不同的表型性状。总之，我们的研究结果强调了LoF变异对植物适应和表型多样化的重要性。
According to the less-is-more hypothesis, gene loss is an engine for evolutionary change. Loss-of-function (LoF) mutations resulting in the natural knockout of protein-coding genes not only provide information about gene function but also play important roles in adaptation and phenotypic diversification. Although the less-is-more hypothesis was proposed two decades ago, it remains to be explored on a large scale. In this study, we identified 60,819 LoF variants in 1071 Arabidopsis (Arabidopsis thaliana) genomes and found that 34% of Arabidopsis protein-coding genes annotated in the Columbia-0 genome do not have any LoF variants. We found that nucleotide diversity, transposable element density, and gene family size are strongly correlated with the presence of LoF variants. Intriguingly, 0.9% of LoF variants with minor allele frequency larger than 0.5% are associated with climate change. In addition, in the Yangtze River basin population, 1% of genes with LoF mutations were under positive selection, providing important insights into the contribution of LoF mutations to adaptation. In particular, our results demonstrate that LoF mutations shape diverse phenotypic traits. Overall, our results highlight the importance of the LoF variants for the adaptation and phenotypic diversification of plants.