Retrotransposon-like elements in the genome of Verticillium dahliae may be used as DNA markers for fungal species and pathotypes

Using differential hybridization, two DNA fragments, VDf35 and VDf90, specific to Verticillium dahliae, were isolated. These fragments contained truncated open reading frames (ORFs) homologous to the gypsy-type retrotransposon. The ORFs of VDf35 and VDf90 were pol and gag homologs, respectively. In addition, VDf90 had a pol homolog without an ORF sequence. The pol homologs in VDf35 and VDf90 were similar to each other, and these two DNA fragments had completely identical sequences. Genomic Southern analysis revealed that numerous copies of these homologs existed in V. dahliae, suggesting that V. dahliae carries a gypsy-like retroelement. Genomic Southern and polymerase chain reaction (PCR) analysis also indicated that a large number of these homologs exist in V. longisporum as well as in V. dahliae, but only a few were present in V. albo-atrum. No homolog was found in either V. nigrescens or V. tricorpus. The uneven distribution of these homologs of the retroposon-like elements among Verticillium species suggested a close genetic kinship between V. dahliae and V. longisporum. PCR primers designed from VDf35 showed species- or pathotype-specific amplification. Therefore, this sequence may be useful as a DNA marker to identify species and pathotypes of V. dahliae. This is the first report on a retrotransposon-like sequence in the genome of phytopathogenic Verticillium species.