Bacterial Genetic Architecture of Ecological Interactions in Co-culture by GWAS-Taking Escherichia coli and Staphylococcus aureus as an Example
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...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2017-11-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | http://journal.frontiersin.org/article/10.3389/fmicb.2017.02332/full |
| _version_ | 1818447777222361088 |
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| author | Xiaoqing He Xiaoqing He Yi Jin Yi Jin Meixia Ye Meixia Ye Nan Chen Jing Zhu Jingqi Wang Libo Jiang Libo Jiang Rongling Wu Rongling Wu Rongling Wu |
| author_facet | Xiaoqing He Xiaoqing He Yi Jin Yi Jin Meixia Ye Meixia Ye Nan Chen Jing Zhu Jingqi Wang Libo Jiang Libo Jiang Rongling Wu Rongling Wu Rongling Wu |
| author_sort | Xiaoqing He |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-14T20:09:00Z |
| format | Article |
| id | doaj.art-21649aa0550e4ac6aa3467440a5efd4f |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-14T20:09:00Z |
| publishDate | 2017-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-21649aa0550e4ac6aa3467440a5efd4f2022-12-21T22:48:58ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2017-11-01810.3389/fmicb.2017.02332288511Bacterial Genetic Architecture of Ecological Interactions in Co-culture by GWAS-Taking Escherichia coli and Staphylococcus aureus as an ExampleXiaoqing He0Xiaoqing He1Yi Jin2Yi Jin3Meixia Ye4Meixia Ye5Nan Chen6Jing Zhu7Jingqi Wang8Libo Jiang9Libo Jiang10Rongling Wu11Rongling Wu12Rongling Wu13Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, ChinaCollege of Biological Sciences and Technology, Beijing Forestry University, Beijing, ChinaCenter for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, ChinaCollege of Biological Sciences and Technology, Beijing Forestry University, Beijing, ChinaCenter for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, ChinaCollege of Biological Sciences and Technology, Beijing Forestry University, Beijing, ChinaCollege of Biological Sciences and Technology, Beijing Forestry University, Beijing, ChinaCollege of Biological Sciences and Technology, Beijing Forestry University, Beijing, ChinaCollege of Biological Sciences and Technology, Beijing Forestry University, Beijing, ChinaCenter for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, ChinaCollege of Biological Sciences and Technology, Beijing Forestry University, Beijing, ChinaCenter for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, ChinaCollege of Biological Sciences and Technology, Beijing Forestry University, Beijing, ChinaCenter for Statistical Genetics, Pennsylvania State University, Hershey, PA, United StatesHow 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.http://journal.frontiersin.org/article/10.3389/fmicb.2017.02332/fullbacterial interactionsbacterial phenotypeswhole-genome sequencinggenome-wide association studiessignificant SNPs |
| spellingShingle | Xiaoqing He Xiaoqing He Yi Jin Yi Jin Meixia Ye Meixia Ye Nan Chen Jing Zhu Jingqi Wang Libo Jiang Libo Jiang Rongling Wu Rongling Wu Rongling Wu Bacterial Genetic Architecture of Ecological Interactions in Co-culture by GWAS-Taking Escherichia coli and Staphylococcus aureus as an Example Frontiers in Microbiology bacterial interactions bacterial phenotypes whole-genome sequencing genome-wide association studies significant SNPs |
| title | Bacterial Genetic Architecture of Ecological Interactions in Co-culture by GWAS-Taking Escherichia coli and Staphylococcus aureus as an Example |
| title_full | Bacterial Genetic Architecture of Ecological Interactions in Co-culture by GWAS-Taking Escherichia coli and Staphylococcus aureus as an Example |
| title_fullStr | Bacterial Genetic Architecture of Ecological Interactions in Co-culture by GWAS-Taking Escherichia coli and Staphylococcus aureus as an Example |
| title_full_unstemmed | Bacterial Genetic Architecture of Ecological Interactions in Co-culture by GWAS-Taking Escherichia coli and Staphylococcus aureus as an Example |
| title_short | Bacterial Genetic Architecture of Ecological Interactions in Co-culture by GWAS-Taking Escherichia coli and Staphylococcus aureus as an Example |
| title_sort | bacterial genetic architecture of ecological interactions in co culture by gwas taking escherichia coli and staphylococcus aureus as an example |
| topic | bacterial interactions bacterial phenotypes whole-genome sequencing genome-wide association studies significant SNPs |
| url | http://journal.frontiersin.org/article/10.3389/fmicb.2017.02332/full |
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