Transposable Elements in Fungi: A Genomic Approach

Abstract

Transposable elements (TEs) include a wide range of DNA sequences that can change positions in the genome. The accessibility of whole fungal genome sequences and analysis of TEs demonstrate the important role they play in genome evolution of fungi species. TE activity is a primary mechanism for high fitness, plasticity and adaptability in certain species of pathogenic fungi. Some of the deleterious effects of transposons may be due to ectopic recombination among transposons of the same family. To prevent possible damage caused by the transposons, some fungi possess TE-silencing mechanisms, for instance, RIP (Repeat Induced Pont mutation) and RNA silencing. In addition, TEs are efficient molecular markers due to their structure and transposition strategy. Copies or remnants of both class I (retrotransposons) and class II (DNA transposons) have been identified, and the number of distinct mobile elements continues to grow. Such repeated sequences vary in number as well as in size, and comprise 3 to 20% of the sequenced genome of most fungi. In contrast, the plant pathogenic fungus Blumeria graminis has a genome estimated at 174 Mb, and 85% of the genome includes TEs [3]. More than 215 genus-specific TEs were found in Laccaria bicolor in addition to many remaining degenerate copies. Additionally, 40 different TE families were detected in the genome of L. bicolor, and less than 5% nucleotide mutations had accumulated, which suggest that they are recently acquired elements, and possible activities can be inferred for such elements [4]. In general, the most abundant TEs in sequenced genomes of fungi are Gypsy, Copia and Tc1-Mariner (Figure 1).