Table 6.
Molecular tools applied for identification of species in Aspergillus section Nigri.
| Method used | Target region | Reference | Comments |
|---|---|---|---|
| RFLP | pelA, pelB, pki | Kusters-van Someren et al. 1991 | A. niger and A. tubingensis could be distinguished |
| RFLP | rDNA (SmaI) | Kusters-van Someren et al. 1991, Varga et al. 2000 | A. niger, A. tubingensis, A. brasiliensis, A. ellipticus, A. heteromorphus, A. japonicus and A. carbonarius could be distinguished |
| RFLP | mtDNA (HaeIII/Bg/II) | Varga et al. 1993, 1994, Hamari et al. 1997 | Could be used to distinguish A. niger and A. brasiliensis from A. tubingensis, and A. japonicus from A. aculeatus; several intraspecific mtDNA types identified |
| RFLP | pelA, pki, rDNA | Parenicova et al. 2001, de Vries et al. 2005 | Could distinguish most species including A. aculeatus, A. japonicus and A. vadensis |
| PCR-RFLP | ITS(RsaI) | Accensi et al. 1999, 2001, Medina et al. 2005, Bau et al. 2005 | N and T types distinguished among species of the A. niger aggregate; pattern T is shared by A. tubingensis, A. foetidus, A. vadensis, A. piperis and A. costaricaensis isolates, while all other species exhibit pattern N |
| PCR-RFLP | ITS (RsaI, HhaI, N/aIII) | Martinez-Culebras & Ramon 2007 | Could distinguish between A. niger, A. tubingensis, A. carbonarius and A. aculeatus isolates |
| PCR-RFLP | ITS (RsaI), IGS (HinfI), β-tubulin (RsaI) | Zanzotto et al. 2006 | Could distinguish between potential OTA-producing and non-producing isolates of the A. niger aggregate (ie. between A. niger and A. tubingensis) |
| AFLP | Perrone et al. 2006a, 2006b | All known species could be distinguished | |
| PCR-SSCP | calmodulin | Susca et al. 2007b | 11 species including A. brasiliensis, A. niger, A. tubingensis, A. foetidus, A. aculeatus, A. uvarum, A. japonicus, A. ellipticus, A. heteromorphus, A. carbonarius and A. ibericus could be distinguished |
| OLISA | calmodulin | Bufflier et al. 2007 | A. carbonarius, A. ibericus and A. japonicus/A. aculeatus could be distinguished. |
| Sequence analysis | ITS | Varga et al. 2007 | Several species have identical ITS sequences (eg. A. niger and A. lacticoffeatus; A. tubingensis, A. foetidus, A. vadensis and A. piperis; A. carbonarius and A. sclerotioniger; A. japonicus, A. aculeatus and A. uvarum) |
| Sequence analysis | Mitochondrial cytochrome b | Yokoyama et al. 2001 | A. japonicus/A. aculeatus, A. niger, A. tubingensis, A. carbonarius and A. ellipticus could be distinguished |
| Sequence analysis | β-tubulin | Samson et al. 2004, Varga et al. 2007 | all except one species (A. lacticoffeatus) could be distinguished |
| Sequence analysis | Calmodulin | Varga et al. 2007 | All species could be distinguished |
| Sequence analysis | Cytochrome oxidase I | Klich et al. 2007 | A. niger and A. tubingensis could not be distinguished; not appropriate to be used for species identification in black aspergilli |
| Sequence analysis | IGS | Unpublished data | Too variable for species identification |
| PCR with species-specific primers | ITS | Gonzales-Salgado et al. 2005 | Species-specific detection of A. niger, A. tubingensis, A. heteromorphus, A. ellipticus and A. japonicus |
| PCR with species-specific primers | calmodulin | Susca et al. 2007a | Species-specific detection of A. carbonarius and A. niger |
| PCR with species-specific primers | RAPD fragment | Fungaro et al. 2004 | Species-specific detection of A. carbonarius |
| PCR with species-specific primers | calmodulin | Perrone et al. 2004 | Species-specific detection of A. carbonarius and A. japonicus |
| PCR with species-specific primers | ITS | Haugland and Vesper 2002 | Species-specific detection of A. carbonarius and A. niger |
| PCR with species-specific primers | AFLP marker | Schmidt et al. 2004 | Species-specific detection of A. carbonarius |
| PCR with species-specific primers | PKS | Lebrihi et al. 2003 | Species-specific detection of OTA producing A. carbonarius isolates |
| PCR with species-specific primers | PKS | Dobson & O”Callagfhan 2004 | Species-specific detection of OTA producing A. carbonarius and A. niger isolates |
| Real time PCR | ITS | Haugland et al. 2004 | Species-specific detection of A. carbonarius and A. niger |
| Real time PCR | calmodulin | Mule et al. 2006 | Species-specific detection of A. carbonarius |
| Real time PCR | AT domain of the PKS gene | Atoui et al. 2007 | Species-specific detection of A. carbonarius |