Bacterial Genetic Architecture of Ecological Interactions in Co-culture by GWAS-Taking Escherichia coli and Staphylococcus aureus as an Example.
Bacterial Genetic Architecture of Ecological Interactions in Co-culture by GWAS-Taking Escherichia coli and Staphylococcus aureus as an Example.
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DOI：
10.3389/fmicb.2017.02332
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发表时间：
2017
影响因子：
5.2
通讯作者：
Wu R
中科院分区：
文献类型：
--
作者：
He X;Jin Y;Ye M;Chen N;Zhu J;Wang J;Jiang L;Wu R
物种如何对群落中这样的生物环境做出反应，最终导致其进化，一直是生态进化生物学家感兴趣的话题。直到最近，关于表型改变背后的基因改变的知识还很有限。我们的研究实施了GWAS(基因组范围关联研究)来说明发生在微生物种群中的生态相互作用的遗传结构。通过选择在整个基因组中都进行了基因分型的45对这样的种间大肠杆菌和金黄色葡萄球菌菌株，我们使用Q-Road Trips分析了单个SNPs与分别在单一培养和联合培养中培养的细菌种群在每个时间点测量的微生物丰度之间的关联。我们在基因组中发现了大量的SNPs和Indels(35.69G的大肠杆菌和50.41G的金黄色葡萄球菌的清洁数据)。我们分别报道了与大肠杆菌和金黄色葡萄球菌相互作用相关的66个和111个SNPs。在66个多态变化中有23个导致氨基酸变化。12个重要基因，如Mure、Trea、args和relA，也在先前的进化研究中被发现。在金黄色葡萄球菌中，从编码序列中检测到的111个SNP可分为35个非同义SNPs和76个同义SNPs。我们的研究展示了全基因组关联方法在研究细菌快速进化特征方面的潜力。遗传关联研究方法将有助于识别可能导致感兴趣的表型的遗传因素，并为进一步的实验室研究提供目标。
How a species responds to such a biotic environment in the community, ultimately leading to its evolution, has been a topic of intense interest to ecological evolutionary biologists. Until recently, limited knowledge was available regarding the genotypic changes that underlie phenotypic changes. Our study implemented GWAS (Genome-Wide Association Studies) to illustrate the genetic architecture of ecological interactions that take place in microbial populations. By choosing 45 such interspecific pairs of Escherichia coli and Staphylococcus aureus strains that were all genotyped throughout the entire genome, we employed Q-ROADTRIPS to analyze the association between single SNPs and microbial abundance measured at each time point for bacterial populations reared in monoculture and co-culture, respectively. We identified a large number of SNPs and indels across the genomes (35.69 G clean data of E. coli and 50.41 G of S. aureus). We reported 66 and 111 SNPs that were associated with interaction in E. coli and S. aureus, respectively. 23 out of 66 polymorphic changes resulted in amino acid alterations.12 significant genes, such as murE, treA, argS, and relA, which were also identified in previous evolutionary studies. In S. aureus, 111 SNPs detected in coding sequences could be divided into 35 non-synonymous and 76 synonymous SNPs. Our study illustrated the potential of genome-wide association methods for studying rapidly evolving traits in bacteria. Genetic association study methods will facilitate the identification of genetic elements likely to cause phenotypes of interest and provide targets for further laboratory investigation.