The biology and potential for genetic research of transposable elements in filamentous fungi

Chromosome mapping of a Tc1-like transposon in species of the catfish Ancistrus

The Tc1 mariner element is widely distributed among organisms and have been already described in different species of fish. The genus Ancistrus (Kner, 1854) has 68 nominal species and is part of an interesting taxonomic and cytogenetic group, as well as presenting a variation of chromosome number, ranging from 2n=34 to 54 chromosomes, and the existence of simple and multiple sex chromosome system and the occurrence of chromosomal polymorphisms involving chromosomes that carry the nucleolus organizer region. In this study, a repetitive element by restriction enzyme, from Ancistrus sp.1 "Flecha" was isolated, which showed similarity with a transposable element Tc1-mariner. Its chromosomal location is distributed in heterochromatic regions and along the chromosomal arms of all specimens covered in this study, confirming the pattern dispersed of this element found in other studies carried out with other species. Thus, this result reinforces the hypothesis that the sequence AnDraI is really a dispersed element isolated. As this isolated sequence showed the same pattern in all species which have different sex chromosomes systems, including in all sex chromosomes, we could know that it is not involved in sex chromosome differentiation.

Scatter: a novel family of miniature inverted-repeat transposable elements in the fungus Botrytis cinerea

Miniature inverted-repeat transposable elements (MITEs) are short non-autonomous DNA transposons that play an important role in genome structure and function. Here, we described a novel family of MITEs, named Scatter, identified from the genomes of three strains of the fungus Botrytis cinerea (T4, B05.10, and TBC-A). Intact Scatter elements are typically an average of 247 bp, and contain 41 bp terminal inverted repeats (TIRs) and 2-bp "TA" target site duplications (TSDs). Based a search against the transposable elements database and GenBank, Scatter is a novel and potentially species-specific family of MITEs. Moderate heterogeneity in sequence and size of individual Scatter copies suggests that Scatter elements were not recently proliferated. Most integrated sites were conserved across all three strains tested and elements inserted at equivalent sites shared high identity at the nucleotide level. This conservation, in combination with the presence of a similar copy number (22-24), in B. cinerea strains tested suggests that Scatter may be a relic of an ancient transposition developed prior to the strain divergence of B. cinerea. Two unique insertion instances were observed, indicating that some copies of Scatter may have remained active following strain divergence of B. cinerea. Because only a few subtle insertion differences among B. cinerea strains were observed, Scatter may play only a minor role in the genetic diversity in B. cinerea species. Most Scatter elements appear to be inserted in potential regulatory regions of adjacent coding regions, highlighting their role in transcriptional regulation. The origin of Scatter remains to be addressed. Scatter is the first well-characterized family of MITEs in B. cinerea.

Transposable elements in phytopathogenic Verticillium spp.: insights into genome evolution and inter- and intra-specific diversification

Background

Verticillium dahliae (Vd) and Verticillium albo-atrum (Va) are cosmopolitan soil fungi causing very disruptive vascular diseases on a wide range of crop plants. To date, no sexual stage has been identified in either microorganism suggesting that somatic mutation is a major force in generating genetic diversity. Whole genome comparative analysis of the recently sequenced strains VdLs.17 and VaMs.102 revealed that non-random insertions of transposable elements (TEs) have contributed to the generation of four lineage-specific (LS) regions in VdLs.17.

Results

We present here a detailed analysis of Class I retrotransposons and Class II “cut-and-paste” DNA elements detected in the sequenced Verticillium genomes. We report also of their distribution in other Vd and Va isolates from various geographic origins. In VdLs.17, we identified and characterized 56 complete retrotransposons of the Gypsy-, Copia- and LINE-like types, as well as 34 full-length elements of the “cut-and-paste” superfamilies Tc1/mariner, Activator and Mutator. While Copia and Tc1/mariner were present in multiple identical copies, Activator and Mutator sequences were highly divergent. Most elements comprised complete ORFs, had matching ESTs and showed active transcription in response to stress treatment. Noticeably, we found evidences of repeat-induced point mutation (RIP) only in some of the Gypsy retroelements. While Copia-, Gypsy- and Tc1/mariner-like transposons were prominent, a large variation in presence of the other types of mobile elements was detected in the other Verticillium spp. strains surveyed. In particular, neither complete nor defective “cut-and-paste” TEs were found in VaMs.102.

Conclusions

Copia-, Gypsy- and Tc1/mariner-like transposons are the most wide-spread TEs in the phytopathogens V. dahliae and V. albo-atrum. In VdLs.17, we identified several retroelements and “cut-and-paste” transposons still potentially active. Some of these elements have undergone diversification and subsequent selective amplification after introgression into the fungal genome. Others, such as the ripped Copias, have been potentially acquired by horizontal transfer. The observed biased TE insertion in gene-rich regions within an individual genome (VdLs.17) and the “patchy” distribution among different strains point to the mobile elements as major generators of Verticillium intra- and inter-specific genomic variation.

Strain-specific retrotransposon-mediated recombination in commercially used Aspergillus niger strain

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.