title: Identification of internal transcribed spacer sequence motifs in truffles: a first step toward their DNA bar coding.
abstract: This work presents DNA sequence motifs from the internal transcribed spacer (ITS) of the nuclear rRNA repeat unit which are useful for the identification of five European and Asiatic truffles (Tuber magnatum, T. melanosporum, T. indicum, T. aestivum, and T. mesentericum). Truffles are edible mycorrhizal ascomycetes that show similar morphological characteristics but that have distinct organoleptic and economic values. A total of 36 out of 46 ITS1 or ITS2 sequence motifs have allowed an accurate in silico distinction of the five truffles to be made (i.e., by pattern matching and/or BLAST analysis on downloaded GenBank sequences and directly against GenBank databases). The motifs considered the intraspecific genetic variability of each species, including rare haplotypes, and assigned their respective species from either the ascocarps or ectomycorrhizas. The data indicate that short ITS1 or ITS2 motifs (< or = 50 bp in size) can be considered promising tools for truffle species identification. A dot blot hybridization analysis of T. magnatum and T. melanosporum compared with other close relatives or distant lineages allowed at least one highly specific motif to be identified for each species. These results were confirmed in a blind test which included new field isolates. The current work has provided a reliable new tool for a truffle oligonucleotide bar code and identification in ecological and evolutionary studies.
authors.affiliation: Unité des Rickettsies, CNRS UMR 6020, Faculté de Médecine, Université de la Méditerranée, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France. khalid.elkarkouri@medecine.univ-mrs.fr
authors.forename: Khalid
authors.initials: K
authors.lastname: El Karkouri
authors.forename: Claude
authors.initials: C
authors.lastname: Murat
authors.forename: Elisa
authors.initials: E
authors.lastname: Zampieri
authors.forename: Paola
authors.initials: P
authors.lastname: Bonfante
mesh_terms: D001203:Ascomycota / Q000145:classification / Q000235:genetics*; D001483:Base Sequence; D004271:DNA, Fungal / Q000235:genetics*; D021903:DNA, Ribosomal Spacer / Q000235:genetics*; D030561:Databases, Nucleic Acid; D010802:Phylogeny; D013045:Species Specificity
chemical_list: D004271:DNA, Fungal; D021903:DNA, Ribosomal Spacer