Abstract
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.
| Original language | English (US) |
|---|---|
| Article number | 2332 |
| Journal | Frontiers in Microbiology |
| Volume | 8 |
| Issue number | NOV |
| DOIs | |
| State | Published - Nov 27 2017 |
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All Science Journal Classification (ASJC) codes
- Microbiology
- Microbiology (medical)
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Bacterial genetic architecture of ecological interactions in co-culture by GWAS-taking Escherichia coli and Staphylococcus aureus as an example. / He, Xiaoqing; Jin, Yi; Ye, Meixia; Chen, Nan; Zhu, Jing; Wang, Jingqi; Jiang, Libo; Wu, Rongling.
In: Frontiers in Microbiology, Vol. 8, No. NOV, 2332, 27.11.2017.Research output: Contribution to journal › Article
TY - JOUR
T1 - Bacterial genetic architecture of ecological interactions in co-culture by GWAS-taking Escherichia coli and Staphylococcus aureus as an example
AU - He, Xiaoqing
AU - Jin, Yi
AU - Ye, Meixia
AU - Chen, Nan
AU - Zhu, Jing
AU - Wang, Jingqi
AU - Jiang, Libo
AU - Wu, Rongling
PY - 2017/11/27
Y1 - 2017/11/27
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85035065855&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85035065855&partnerID=8YFLogxK
U2 - 10.3389/fmicb.2017.02332
DO - 10.3389/fmicb.2017.02332
M3 - Article
C2 - 29230205
AN - SCOPUS:85035065855
VL - 8
JO - Frontiers in Microbiology
JF - Frontiers in Microbiology
SN - 1664-302X
IS - NOV
M1 - 2332
ER -