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Citation for Study 16421

Citation title: "Evolutionary history of Methyltransferase 1 genes in hexaploid wheat".

Study name: "Evolutionary history of Methyltransferase 1 genes in hexaploid wheat".

This study is part of submission 16421 (Status: Published).

Citation

Thomas M., Pingault L., Poulet A., Throude M., Duarte J., Faure S., Pichon J., Paux E., Probst A.V., & Tatout C. 2014. Evolutionary history of Methyltransferase 1 genes in hexaploid wheat. BMC Genomics, 15(October): 922.

Authors

• Thomas M.
• Pingault L.
• Poulet A.
• Throude M.
• Duarte J.
• Faure S.
• Pichon J.
• Paux E.
• Probst A.V.
• Tatout C.

Abstract

Background: Plant and animal methyltransferases are key enzymes with DNA methylation maintenance activity at cytosine residues, required for gene expression control and genome stability. Taking advantage of the new sequence surveys of the wheat genome recently released by the International Wheat Genome Sequencing Consortium, we identified and characterized MET1 genes in hexaploid wheat Triticum aestivum (TaMET1). Results: Nine TaMET1 genes were identified and mapped on homoeologous chromosome groups 2A/2B/2D, 5A/5B/5D and 7A/7B/7D. Synteny analysis and evolution rates suggest that the genome organization of TaMET1 genes results from a whole genome duplication shared within the grass family, and a second gene duplication, which occurred specifically in the Triticeae tribe prior to the speciation of diploid wheat. Higher expression levels were observed for TaMET1 homoeologous group 2 genes compared to group 5 and 7 indicating that group 2 homoeologous genes are the predominant genes encoding methyltransferase 1 based on transcript level, while group 5 evolved into pseudogenes. We show the connection between low expression levels, elevated evolution rates and unexpected enrichment in CG-dinucleotides (CG-rich isochores) at putative promoter regions of homoeologous groups 5 and 7 but not of group 2 TaMET1 genes. Bisulfite sequencing reveals that these CG-rich isochores are highly methylated in a CG context, which is the expected target of TaMET1. Conclusions: We retraced the evolutionary history of MET1 genes in wheat highlighting the predominance of group 2 homoeologous genes and suggest CG-DNA methylation as one of the mechanisms involved in wheat genome dynamics.

Keywords

DNA methylation, Evolution, Genome dynamics, CG-rich isochores

External links

• DOI: 10.1186/1471-2164-15-922
• PMID: 25342325
• Other URL: http://www.biomedcentral.com/1471-2164/15/922

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S16421
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref23700,
  	 author = {M?lanie  Thomas and Lise  Pingault and Axel  Poulet and Micka?l  throude and Jorge  Duarte and S?bastien  Faure and jean-Philippe  Pichon and Etienne  Paux and aline valeska Probst and Christophe  Tatout},
  	 title = {Evolutionary history of Methyltransferase 1 genes in hexaploid wheat},
  	 year = {2014},
  	 keywords = {DNA methylation, Evolution, Genome dynamics, CG-rich isochores},
  	 doi = {10.1186/1471-2164-15-922},
  	 url = {http://www.biomedcentral.com/1471-2164/15/922},
  	 pmid = {25342325},
  	 journal = {BMC Genomics},
  	 volume = {15},
  	 number = {October},
  	 pages = {922},
  	 abstract = {Background: Plant and animal methyltransferases are key enzymes with DNA methylation maintenance activity at cytosine residues, required for gene expression control and genome stability. Taking advantage of the new sequence surveys of the wheat genome recently released by the International Wheat Genome Sequencing Consortium, we identified and characterized MET1 genes in hexaploid wheat Triticum aestivum (TaMET1).
  
  Results: Nine TaMET1 genes were identified and mapped on homoeologous chromosome groups 2A/2B/2D, 5A/5B/5D and 7A/7B/7D. Synteny analysis and evolution rates suggest that the genome organization of TaMET1 genes results from a whole genome duplication shared within the grass family, and a second gene duplication, which occurred specifically in the Triticeae tribe prior to the speciation of diploid wheat. Higher expression levels were observed for TaMET1 homoeologous group 2 genes compared to group 5 and 7 indicating that group 2 homoeologous genes are the predominant genes encoding methyltransferase 1 based on transcript level, while group 5 evolved into pseudogenes. We show the connection between low expression levels, elevated evolution rates and unexpected enrichment in CG-dinucleotides (CG-rich isochores) at putative promoter regions of homoeologous groups 5 and 7 but not of group 2 TaMET1 genes. Bisulfite sequencing reveals that these CG-rich isochores are highly methylated in a CG context, which is the expected target of TaMET1.
  
  Conclusions: We retraced the evolutionary history of MET1 genes in wheat highlighting the predominance of group 2 homoeologous genes and suggest CG-DNA methylation as one of the mechanisms involved in wheat genome dynamics.
  }
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 23700
  AU  - Thomas,M?lanie 
  AU  - Pingault,Lise 
  AU  - Poulet,Axel 
  AU  - throude,Micka?l 
  AU  - Duarte,Jorge 
  AU  - Faure,S?bastien 
  AU  - Pichon,jean-Philippe 
  AU  - Paux,Etienne 
  AU  - Probst,aline valeska
  AU  - Tatout,Christophe 
  T1  - Evolutionary history of Methyltransferase 1 genes in hexaploid wheat
  PY  - 2014
  KW  - DNA methylation
  KW  - Evolution
  KW  - Genome dynamics
  KW  - CG-rich isochores
  UR  - http://www.biomedcentral.com/1471-2164/15/922
  N2  - Background: Plant and animal methyltransferases are key enzymes with DNA methylation maintenance activity at cytosine residues, required for gene expression control and genome stability. Taking advantage of the new sequence surveys of the wheat genome recently released by the International Wheat Genome Sequencing Consortium, we identified and characterized MET1 genes in hexaploid wheat Triticum aestivum (TaMET1).
  
  Results: Nine TaMET1 genes were identified and mapped on homoeologous chromosome groups 2A/2B/2D, 5A/5B/5D and 7A/7B/7D. Synteny analysis and evolution rates suggest that the genome organization of TaMET1 genes results from a whole genome duplication shared within the grass family, and a second gene duplication, which occurred specifically in the Triticeae tribe prior to the speciation of diploid wheat. Higher expression levels were observed for TaMET1 homoeologous group 2 genes compared to group 5 and 7 indicating that group 2 homoeologous genes are the predominant genes encoding methyltransferase 1 based on transcript level, while group 5 evolved into pseudogenes. We show the connection between low expression levels, elevated evolution rates and unexpected enrichment in CG-dinucleotides (CG-rich isochores) at putative promoter regions of homoeologous groups 5 and 7 but not of group 2 TaMET1 genes. Bisulfite sequencing reveals that these CG-rich isochores are highly methylated in a CG context, which is the expected target of TaMET1.
  
  Conclusions: We retraced the evolutionary history of MET1 genes in wheat highlighting the predominance of group 2 homoeologous genes and suggest CG-DNA methylation as one of the mechanisms involved in wheat genome dynamics.
  
  L3  - 10.1186/1471-2164-15-922
  JF  - BMC Genomics
  VL  - 15
  IS  - October
  ER  -