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Citation for Study 1437

Citation title: "An oligonucleotide barcode for species identification on Trichoderma and Hypocrea".

This study was previously identified under the legacy study ID S1411 (Status: Published).

Citation

Druzhinina I., Kopchinskiy A., Komon M., Bissett J., Szakacs G., & Kubicek C. 2005. An oligonucleotide barcode for species identification on Trichoderma and Hypocrea. Fungal Genetics and Biology, 42: 813-828.

Authors

• Druzhinina I.
• Kopchinskiy A.
• Komon M.
• Bissett J.
• Szakacs G.
• Kubicek C.

Abstract

One of the biggest obstructions to studies on Trichoderma has been the incorrect and confused application of species names to isolates used in industry, biocontrol of plant pathogens and ecological surveys, thereby making the comparison of results questionable. Here we provide a convenient, on-line method for the quick molecular identification of Hypocrea/Trichoderma at the genus and species levels based on an oligonucleotide barcode: a diagnostic combination of several oligonucleotides (hallmarks) specifically allocated within the internal transcribed spacer 1 and 2 (ITS1 and 2) sequences of rDNA repeat. The barcode was developed on the basis of 979 sequences of 88 vouchered species which displayed in total 135 ITS1 and 2 haplotypes. Oligonucleotide sequences which are constant in all known ITS1 and 2 of Hypocrea/Trichoderma but different in closely related fungal genera, were used to define genus specific hallmarks. The library of species-, clade- and genus-specific hallmarks is stored in the MySQL database and integrated in the TrichOKey v. 1.0 - barcode sequence identification program with the web interface located on www.isth.info. TrichOKey v. 1.0 identifies 75 single species, 5 species pairs and 1 species triplet. Verification of the DNA-barcode was done by a blind test on 53 unknown isolates of Trichoderma, collected in Central and South America. The obtained results were in a total agreement with phylogenetic identification based on tef1 (large intron), NCBI BLAST of vouchered records and postum morphological analysis. We conclude that oligonucleotide barcode is a powerful tool for the routine identification of Hypocrea/Trichoderma species and should be useful as a complement to traditional methods

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S1437
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref15318,
  	 author = {Irina S.  Druzhinina and Alexey G  Kopchinskiy and Monika  Komon and John  Bissett and George  Szakacs and Christian P.  Kubicek},
  	 title = {An oligonucleotide barcode for species identification on Trichoderma and Hypocrea},
  	 year = {2005},
  	 keywords = {},
  	 doi = {},
  	 url = {},
  	 pmid = {},
  	 journal = {Fungal Genetics and Biology},
  	 volume = {42},
  	 number = {},
  	 pages = {813--828},
  	 abstract = {One of the biggest obstructions to studies on Trichoderma has been the incorrect and confused application of species names to isolates used in industry, biocontrol of plant pathogens and ecological surveys, thereby making the comparison of results questionable. Here we provide a convenient, on-line method for the quick molecular identification of Hypocrea/Trichoderma at the genus and species levels based on an oligonucleotide barcode: a diagnostic combination of several oligonucleotides (hallmarks) specifically allocated within the internal transcribed spacer 1 and 2 (ITS1 and 2) sequences of rDNA repeat. The barcode was developed on the basis of 979 sequences of 88 vouchered species which displayed in total 135 ITS1 and 2 haplotypes. Oligonucleotide sequences which are constant in all known ITS1 and 2 of Hypocrea/Trichoderma but different in closely related fungal genera, were used to define genus specific hallmarks. The library of species-, clade- and genus-specific hallmarks is stored in the MySQL database and integrated in the TrichOKey v. 1.0 - barcode sequence identification program with the web interface located on www.isth.info. TrichOKey v. 1.0 identifies 75 single species, 5 species pairs and 1 species triplet. Verification of the DNA-barcode was done by a blind test on 53 unknown isolates of Trichoderma, collected in Central and South America. The obtained results were in a total agreement with phylogenetic identification based on tef1 (large intron), NCBI BLAST of vouchered records and postum morphological analysis. We conclude that oligonucleotide barcode is a powerful tool for the routine identification of Hypocrea/Trichoderma species and should be useful as a complement to traditional methods}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 15318
  AU  - Druzhinina,Irina S. 
  AU  - Kopchinskiy,Alexey G 
  AU  - Komon,Monika 
  AU  - Bissett,John 
  AU  - Szakacs,George 
  AU  - Kubicek,Christian P. 
  T1  - An oligonucleotide barcode for species identification on Trichoderma and Hypocrea
  PY  - 2005
  UR  - 
  N2  - One of the biggest obstructions to studies on Trichoderma has been the incorrect and confused application of species names to isolates used in industry, biocontrol of plant pathogens and ecological surveys, thereby making the comparison of results questionable. Here we provide a convenient, on-line method for the quick molecular identification of Hypocrea/Trichoderma at the genus and species levels based on an oligonucleotide barcode: a diagnostic combination of several oligonucleotides (hallmarks) specifically allocated within the internal transcribed spacer 1 and 2 (ITS1 and 2) sequences of rDNA repeat. The barcode was developed on the basis of 979 sequences of 88 vouchered species which displayed in total 135 ITS1 and 2 haplotypes. Oligonucleotide sequences which are constant in all known ITS1 and 2 of Hypocrea/Trichoderma but different in closely related fungal genera, were used to define genus specific hallmarks. The library of species-, clade- and genus-specific hallmarks is stored in the MySQL database and integrated in the TrichOKey v. 1.0 - barcode sequence identification program with the web interface located on www.isth.info. TrichOKey v. 1.0 identifies 75 single species, 5 species pairs and 1 species triplet. Verification of the DNA-barcode was done by a blind test on 53 unknown isolates of Trichoderma, collected in Central and South America. The obtained results were in a total agreement with phylogenetic identification based on tef1 (large intron), NCBI BLAST of vouchered records and postum morphological analysis. We conclude that oligonucleotide barcode is a powerful tool for the routine identification of Hypocrea/Trichoderma species and should be useful as a complement to traditional methods
  L3  - 
  JF  - Fungal Genetics and Biology
  VL  - 42
  IS  - 
  SP  - 813
  EP  - 828
  ER  -