International Commission for the Taxonomy of Fungi (ICTF)
International Union of Microbiological Societies (IUMS, Mycology Division)
Login

TrichOKEY: molecular Barcode

TrichOKEY 2 is a program for the quick molecular identification of Hypocrea and Trichoderma on the genus and species levels based on an oligonucleotide DNA BarCode, a diagnostic combination of several oligonucleotides (hallmarks) specifically allocated within the internal transcribed spacer 1 and 2 (ITS1 and 2) sequences of rRNA gene cluster

read more Druzhinina et al., 2005

Special features of the TrichOKEY second version:

  • recognizes multiple sequences submitted in FASTA format
  • linked to the Hypocrea/Trichoderma sequence similarity search
  • displays results in one of three modes each powered by printer-friendly version
  • has advanced control on sequence quality, which allows to differentiate the new allele of ITS1 and 2
  • is linked to the dynamic Hypocrea/Trichoderma biodiversity profile
  • contains HELP and DISCLIMER


Number of Hypocrea/Trichoderma species: 104 / Number of ITS1 and 2 BarCodes: 153 Biodiversity profile
1. Name the query set of sequences Why it is important to give name to the sequence query :
2. Paste ITS1 and 2 sequence(s) in FASTA or text format Formats supported by TrichOKEY :
3. Select mode Display modes of TrichOKEY results : Full Short Fasta
biodiversity | ITS1 and 2 master alignment | disclimer | Help

An oligonucleotide barcode for species identification in Trichoderma and Hypocrea

Druzhinina, I., Kopchinskiy, A. G., Komon, M., Bissett, J., Szakacs, G., Kubicek, C. P., 2005
Fungal Genetics and Biology, 42: 813828
Download PDF

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.


Resease History

Current version: TrichOKEY 2 final release

Special features of the second version of the DNA oligonucleotide BarCode for species identification of Hypocrea/Trichoderma:

  • recognizes multiple sequences submitted in FASTA format
  • linked to the Hypocrea/Trichoderma sequence similarity search
  • displays results in one of three modes each powered by printer-friendly version
  • has advanced control on sequence quality, which allows to differentiate the new allele of ITS1 and 2
  • linked to the dynamic Hypocrea/Trichoderma biodiversity profile
  • contains HELP and DISCLIMER

rectTrichOKEY 2 final release 03 Aug, 2006
Open Open
rectTrichOKEY v. 1.1, koningii release 11 Nov, 2005
Open Open
rectTrichOKEY v. 1.0, original release 10 Nov, 2005

The barcode was developed on the basis of 979 sequences of 88 vouchered species which displayed in total 139 ITS1 and 2 haplotypes

TrichOKEY v. 1.0 identifies 75 single species, 5 species pairs and1 species triplet

Close Close

Copyright: Irina Druzhinina & Alexey Kopchinskiy 2004 - 2008