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Citation for Study 20196

Citation title: "Globally distributed root endophyte Phialocephala subalpina links pathogenic and saprophytic lifestyles".

Study name: "Globally distributed root endophyte Phialocephala subalpina links pathogenic and saprophytic lifestyles".

This study is part of submission 20196 (Status: Published).

Citation

Schlegel M., M?nsterk?tter M., G?ldener U., Bruggmann R., Du? A., Hainaut M., Henrissat B., Hoffmeister D., & Gr? C.R. 2016. Globally distributed root endophyte Phialocephala subalpina links pathogenic and saprophytic lifestyles. BMC Genomics , .

Authors

• Schlegel M. (submitter)
• M?nsterk?tter M.
• G?ldener U.
• Bruggmann R.
• Du? A.
• Hainaut M.
• Henrissat B.
• Hoffmeister D.
• Gr? C.R.

Abstract

Background: Whereas an increasing number of pathogenic and mutualistic ascomycetous species were sequenced in the past decade, species showing a seemingly neutral association such as root endophytes received less attention. In the present study, the genome of Phialocephala subalpina, the most frequent species of the Phialocephala fortinii s.l. ? Acephala applanata species complex, was sequenced for insight in the genome structure and gene inventory of these wide-spread root endophytes. Results: The genome of P. subalpina was sequenced using Roche/454 GS FLX technology and a whole genome shotgun strategy. The assembly resulted in 205 scaffolds and a genome size of 69.7 Mb. The expanded genome size in P. subalpina was not due to the proliferation of transposable elements or other repeats, as is the case with other ascomycetous genomes. Instead, P. subalpina revealed an expanded gene inventory that includes 20,173 gene models. Comparative genome analysis of P. subalpina with 13 ascomycetes shows that P. subalpina uses a versatile gene inventory including genes specific for pathogens and saprophytes. Moreover, the gene inventory for carbohydrate active enzymes (CAZymes) was expanded including genes involved in degradation of biopolymers, such as pectin, hemicellulose, cellulose and lignin. Conclusions: The analysis of a globally distributed root endophyte allowed detailed insights in the gene inventory and genome organization of a yet largely neglected group of organisms. We showed that the ubiquitous root endophyte P. subalpina has a broad gene inventory that links pathogenic and saprophytic lifestyles.

Keywords

comparative genomics, lifestyle, root endophyte, species complex, parasitism-mutualism continuum

External links

• Other URL: http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3369-8

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S20196
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref26568,
  	 author = {Markus  Schlegel and Martin  M?nsterk?tter and Ulrich  G?ldener and R?my  Bruggmann and Angelo  Du? and Matthieu  Hainaut and Bernard  Henrissat and Dirk  Hoffmeister and Christoph R. Gr?},
  	 title = {Globally distributed root endophyte Phialocephala subalpina links pathogenic and saprophytic lifestyles},
  	 year = {2016},
  	 keywords = {comparative genomics, lifestyle, root endophyte, species complex, parasitism-mutualism continuum},
  	 doi = {},
  	 url = {http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3369-8},
  	 pmid = {},
  	 journal = {BMC Genomics },
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 abstract = {Background:
  Whereas an increasing number of pathogenic and mutualistic ascomycetous species were sequenced in the past decade, species showing a seemingly neutral association such as root endophytes received less attention. In the present study, the genome of Phialocephala subalpina, the most frequent species of the Phialocephala fortinii s.l. ? Acephala applanata species complex, was sequenced for insight in the genome structure and gene inventory of these wide-spread root endophytes.
  
  Results:
  The genome of P. subalpina was sequenced using Roche/454 GS FLX technology and a whole genome shotgun strategy. The assembly resulted in 205 scaffolds and a genome size of 69.7 Mb. The expanded genome size in P. subalpina was not due to the proliferation of transposable elements or other repeats, as is the case with other ascomycetous genomes. Instead, P. subalpina revealed an expanded gene inventory that includes 20,173 gene models. Comparative genome analysis of P. subalpina with 13 ascomycetes shows that P. subalpina uses a versatile gene inventory including genes specific for pathogens and saprophytes. Moreover, the gene inventory for carbohydrate active enzymes (CAZymes) was expanded including genes involved in degradation of biopolymers, such as pectin, hemicellulose, cellulose and lignin. 
  
  Conclusions:
  The analysis of a globally distributed root endophyte allowed detailed insights in the gene inventory and genome organization of a yet largely neglected group of organisms. We showed that the ubiquitous root endophyte P. subalpina has a broad gene inventory that links pathogenic and saprophytic lifestyles. 
  }
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 26568
  AU  - Schlegel,Markus 
  AU  - M?nsterk?tter,Martin 
  AU  - G?ldener,Ulrich 
  AU  - Bruggmann,R?my 
  AU  - Du?,Angelo 
  AU  - Hainaut,Matthieu 
  AU  - Henrissat,Bernard 
  AU  - Hoffmeister,Dirk 
  AU  - Gr?,Christoph R.
  T1  - Globally distributed root endophyte Phialocephala subalpina links pathogenic and saprophytic lifestyles
  PY  - 2016
  KW  - comparative genomics
  KW  - lifestyle
  KW  - root endophyte
  KW  - species complex
  KW  - parasitism-mutualism continuum
  UR  - http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3369-8
  N2  - Background:
  Whereas an increasing number of pathogenic and mutualistic ascomycetous species were sequenced in the past decade, species showing a seemingly neutral association such as root endophytes received less attention. In the present study, the genome of Phialocephala subalpina, the most frequent species of the Phialocephala fortinii s.l. ? Acephala applanata species complex, was sequenced for insight in the genome structure and gene inventory of these wide-spread root endophytes.
  
  Results:
  The genome of P. subalpina was sequenced using Roche/454 GS FLX technology and a whole genome shotgun strategy. The assembly resulted in 205 scaffolds and a genome size of 69.7 Mb. The expanded genome size in P. subalpina was not due to the proliferation of transposable elements or other repeats, as is the case with other ascomycetous genomes. Instead, P. subalpina revealed an expanded gene inventory that includes 20,173 gene models. Comparative genome analysis of P. subalpina with 13 ascomycetes shows that P. subalpina uses a versatile gene inventory including genes specific for pathogens and saprophytes. Moreover, the gene inventory for carbohydrate active enzymes (CAZymes) was expanded including genes involved in degradation of biopolymers, such as pectin, hemicellulose, cellulose and lignin. 
  
  Conclusions:
  The analysis of a globally distributed root endophyte allowed detailed insights in the gene inventory and genome organization of a yet largely neglected group of organisms. We showed that the ubiquitous root endophyte P. subalpina has a broad gene inventory that links pathogenic and saprophytic lifestyles. 
  
  L3  - 
  JF  - BMC Genomics 
  VL  - 
  IS  - 
  ER  -