Repeat induced point mutation (RIP) is a gene silencing mechanism present in fungal genomes. During RIP, duplicated sequences are efficiently and irreversibly mutated by transitions from C:G to T:A. For the first time, we have identified traces of RIP in transposable elements of Aspergillus niger and Penicillium chrysogenum, two biotechnologically relevant fungi. We found that RIP in P. chrysogenum has affected a large set of sequences, which also contain other mutations. On the other hand, RIP in A. niger is limited to only few sequences, but literally all mutations are RIP-like. Surprisingly, RIP occurred only in transposon sequences that have disrupted open reading frames in A. niger, a phenomenon not yet reported for other fungi. In both fungal species, we identified two sequences with strong sequence similarity to Neurospora crassa RID. RID is a putative DNA methyltransferase and the only known enzyme involved in the RIP process. Our findings suggest that both A. niger and P. chrysogenum either had a sexual past or have a sexual potential. These findings have important implications for future strain development of these fungi.

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Transposons are usually present in multiple copies in their hosts' genomes. Recombination between two transposon copies can result in chromosomal rearrangements. Here, we describe a recombination event between two copies of the retrotransposon ANiTa1 within the genome of the fungus Aspergillus niger (strain CBS513.88). The observed chromosomal rearrangement appears to be strain-specific, as the corresponding genomic region in another strain, ATCC1015, shows a different organization. Strain ATCC1015 actually seems to lack full-length ANiTa1 copies and possesses only solo LTR sequences. Presumably strain ATCC1015 was once colonized by ANiTa1, but then the genome subsequently lost the ANiTa1 copies. The striking genomic differences in ANiTa1 copy distribution leading to differences in the chromosomal structure between the two strains, ATTC1015 and CBS513.88, suggest that the activity of transposons may profoundly affect the evolution of different fungal strains.

The filamentous fungus Aspergillus niger is widely used in biotechnological applications. Strain CBS513.88 is known to harbor 21 copies of the nonautonomous transposon Vader. Upon selection of chlorate-resistant A. niger colonies, one Vader copy was found integrated in the nirA gene. This copy was used for vector construction and development of a transposon-tagging method. Vader showed an excision frequency of about 1 in 2.2 ؋ 10 5 conidiospores. A total of 95 of 97 colonies analyzed exhibited an excision event at the DNA level, and Vader footprints were found. By employing thermal asymmetric interlaced (TAIL)-PCR, the reintegration sites of 21 independent excision events were determined. All reintegration events occurred within or very close to genes. Therefore, this method can be used for transposon mutagenesis in A. niger.

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