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Citation for Study 16971

Citation title: "Comparative functional pan-genome analyses to build connections between genomic dynamics and phenotypic evolution in polycyclic aromatic hydrocarbon metabolism in the genus Mycobacterium".

Study name: "Comparative functional pan-genome analyses to build connections between genomic dynamics and phenotypic evolution in polycyclic aromatic hydrocarbon metabolism in the genus Mycobacterium".

This study is part of submission 16971 (Status: Published).

Citation

Kweon O., Kim S., Blom J., Kim S., Kim B., Baek D., Park S., Sutherland J.B., & Cerniglia C.E. 2015. Comparative functional pan-genome analyses to build connections between genomic dynamics and phenotypic evolution in polycyclic aromatic hydrocarbon metabolism in the genus Mycobacterium. BMC Evolutionary Biology, .

Authors

• Kweon O. (submitter) 01-870-543-7942
• Kim S.
• Blom J.
• Kim S.
• Kim B.
• Baek D.
• Park S.
• Sutherland J.B.
• Cerniglia C.E.

Abstract

Background: The genus Mycobacterium is of great interest for the medical and biotechnological fields. Despite a flood of genome sequencing and functional genomics data, there are still significant gaps in knowledge between genome and phenome, which seriously hinder efforts toward the treatment of mycobacterial diseases and practical biotechnological applications. In this study, we propose the use of systematic, comparative functional pan-genomic analysis to build connections between genomic dynamics and phenotypic evolution in polycyclic aromatic hydrocarbon (PAH) metabolism in the genus Mycobacterium. Results: Phylogenetic, phenotypic, and genomic information for 27 completely genome-sequenced mycobacteria was systematically integrated to reconstruct a mycobacterial phenotype network (MPN) with a pan-genomic concept at a network level. In the MPN, mycobacterial phenotypes show typical scale-free relationships. PAH degradation is an isolated phenotype with the lowest connection degree, consistent with phylogenetic and environmental isolation of PAH degraders. A series of functional pan-genomic analyses provide conserved and unique types of genomic evidence for strong epistatic and pleiotropic impacts on evolutionary trajectories of the PAH-degrading phenotype. Under strong natural selection, the detailed gene gain/loss patterns by horizontal gene transfer (HGT)/deletion events hypothesize a plausible evolutionary path, an epistasis-based birth and pleiotropy-dependent death, for bacterial PAH metabolism in the genus Mycobacterium. This study generated a practical mycobacterial compendium of phenotypic and genomic changes, focusing on the PAH-degrading phenotype with a pan-genomic perspective of the evolutionary events and the environmental challenges. Conclusions: Our findings suggest that when selection acts on PAH metabolism, only a small fraction of possible trajectories is likely to be observed, owing mainly to a combination of the ambiguous phenotypic effects of PAHs and the corresponding pleiotropy- and epistasis-dependent evolutionary adaptation. Evolutionary constraints on the selection of trajectories, like those seen in PAH-degrading phenotypes, are likely to apply to the evolution of other phenotypes in the genus Mycobacterium.

Keywords

Mycobacterium; PAH metabolism; Pan-genome; Functional genomics; Functional pan-genome; Phenotype Network; Evolution; epistasis; pleiotropy

External links

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S16971
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref24102,
  	 author = {ohgew  kweon and Seon-Jae  Kim and Jochen  Blom and Sung-Kwan  Kim and Bong-Soo  Kim and Dong-Heon  Baek and Su Inn  Park and John B. Sutherland and Carl E. Cerniglia},
  	 title = {Comparative functional pan-genome analyses to build connections between genomic dynamics and phenotypic evolution in polycyclic aromatic hydrocarbon metabolism in the genus Mycobacterium},
  	 year = {2015},
  	 keywords = {Mycobacterium; PAH metabolism; Pan-genome; Functional genomics; Functional pan-genome; Phenotype Network; Evolution; epistasis; pleiotropy },
  	 doi = {},
  	 url = {http://},
  	 pmid = {},
  	 journal = {BMC Evolutionary Biology},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 abstract = {Background: The genus Mycobacterium is of great interest for the medical and biotechnological fields. Despite a flood of genome sequencing and functional genomics data, there are still significant gaps in knowledge between genome and phenome, which seriously hinder efforts toward the treatment of mycobacterial diseases and practical biotechnological applications. In this study, we propose the use of systematic, comparative functional pan-genomic analysis to build connections between genomic dynamics and phenotypic evolution in polycyclic aromatic hydrocarbon (PAH) metabolism in the genus Mycobacterium. 
  
  Results: Phylogenetic, phenotypic, and genomic information for 27 completely genome-sequenced mycobacteria was systematically integrated to reconstruct a mycobacterial phenotype network (MPN) with a pan-genomic concept at a network level. In the MPN, mycobacterial phenotypes show typical scale-free relationships. PAH degradation is an isolated phenotype with the lowest connection degree, consistent with phylogenetic and environmental isolation of PAH degraders. A series of functional pan-genomic analyses provide conserved and unique types of genomic evidence for strong epistatic and pleiotropic impacts on evolutionary trajectories of the PAH-degrading phenotype. Under strong natural selection, the detailed gene gain/loss patterns by horizontal gene transfer (HGT)/deletion events hypothesize a plausible evolutionary path, an epistasis-based birth and pleiotropy-dependent death, for bacterial PAH metabolism in the genus Mycobacterium. This study generated a practical mycobacterial compendium of phenotypic and genomic changes, focusing on the PAH-degrading phenotype with a pan-genomic perspective of the evolutionary events and the environmental challenges.       
  
  Conclusions: Our findings suggest that when selection acts on PAH metabolism, only a small fraction of possible trajectories is likely to be observed, owing mainly to a combination of the ambiguous phenotypic effects of PAHs and the corresponding pleiotropy- and epistasis-dependent evolutionary adaptation. Evolutionary constraints on the selection of trajectories, like those seen in PAH-degrading phenotypes, are likely to apply to the evolution of other phenotypes in the genus Mycobacterium. 
  }
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 24102
  AU  - kweon,ohgew 
  AU  - Kim,Seon-Jae 
  AU  - Blom,Jochen 
  AU  - Kim,Sung-Kwan 
  AU  - Kim,Bong-Soo 
  AU  - Baek,Dong-Heon 
  AU  - Park,Su Inn 
  AU  - Sutherland,John B.
  AU  - Cerniglia,Carl E.
  T1  - Comparative functional pan-genome analyses to build connections between genomic dynamics and phenotypic evolution in polycyclic aromatic hydrocarbon metabolism in the genus Mycobacterium
  PY  - 2015
  KW  - Mycobacterium; PAH metabolism; Pan-genome; Functional genomics; Functional pan-genome; Phenotype Network; Evolution; epistasis; pleiotropy 
  UR  - http://dx.doi.org/
  N2  - Background: The genus Mycobacterium is of great interest for the medical and biotechnological fields. Despite a flood of genome sequencing and functional genomics data, there are still significant gaps in knowledge between genome and phenome, which seriously hinder efforts toward the treatment of mycobacterial diseases and practical biotechnological applications. In this study, we propose the use of systematic, comparative functional pan-genomic analysis to build connections between genomic dynamics and phenotypic evolution in polycyclic aromatic hydrocarbon (PAH) metabolism in the genus Mycobacterium. 
  
  Results: Phylogenetic, phenotypic, and genomic information for 27 completely genome-sequenced mycobacteria was systematically integrated to reconstruct a mycobacterial phenotype network (MPN) with a pan-genomic concept at a network level. In the MPN, mycobacterial phenotypes show typical scale-free relationships. PAH degradation is an isolated phenotype with the lowest connection degree, consistent with phylogenetic and environmental isolation of PAH degraders. A series of functional pan-genomic analyses provide conserved and unique types of genomic evidence for strong epistatic and pleiotropic impacts on evolutionary trajectories of the PAH-degrading phenotype. Under strong natural selection, the detailed gene gain/loss patterns by horizontal gene transfer (HGT)/deletion events hypothesize a plausible evolutionary path, an epistasis-based birth and pleiotropy-dependent death, for bacterial PAH metabolism in the genus Mycobacterium. This study generated a practical mycobacterial compendium of phenotypic and genomic changes, focusing on the PAH-degrading phenotype with a pan-genomic perspective of the evolutionary events and the environmental challenges.       
  
  Conclusions: Our findings suggest that when selection acts on PAH metabolism, only a small fraction of possible trajectories is likely to be observed, owing mainly to a combination of the ambiguous phenotypic effects of PAHs and the corresponding pleiotropy- and epistasis-dependent evolutionary adaptation. Evolutionary constraints on the selection of trajectories, like those seen in PAH-degrading phenotypes, are likely to apply to the evolution of other phenotypes in the genus Mycobacterium. 
  
  L3  - 
  JF  - BMC Evolutionary Biology
  VL  - 
  IS  - 
  ER  -