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). Since their discovery during the late 1940s by Barbara McClintock [5], the importance of TEs in genome structuring and evolution becomes increasingly clear due to the completion of several genome sequencing projects. Some of the effects of transposable elements may be due to ectopic recombination among elements of the same family. Ectopic recombination occurs between homologous DNA sequences on different chromosomes. An analysis of TEs distributed across the Magnaporthe grisea genome has demonstrated extensive past ectopic recombination events. Thus, ectopic recombination events can aid in fitness because many host-specific genes are in transposable element-rich regions. Therefore, recombination events delete or alter the structure of such genes, which consequently alters their expression [6]. In Coprinus cinereus, the elements are in regions with medium and high recombination rates [7]. Certain species-specific genomic islands in Aspergillus fumigatus include a disproportionate number of TEs compared with syntenic areas, which may be involved in origination or modification of such areas. These areas include genes involved in carbohydrate transport and catabolism, secondary metabolite biosynthesis and detoxification. Lineage specific (LS) genes are a key point in many comparative genomics studies because such regions may be responsible for phenotypic differences between species and reflect Transposable Elements in Fungi The availability of fungal genomes has led to the elucidation of the number and distribution of transposable elements (TEs) in several species of fungi. TEs are moderately repetitive DNA sequences dispersed throughout the genome. Such elements can move from one site to another within the genome, and their insertion can produce a broad spectrum of host mutations [1]. Transposable elements are hierarchically classified into class, subclass, order, superfamily, family and subfamily. There are two classes of TEs that differ in the presence (class I) or absence (class II) of an RNA intermediate. Class I TEs transpose via an RNA intermediate that is transcribed from a single copy of the genome and produces a cDNA via reverse transcription, which is encoded by the element itself. Class I have two major subclasses, the LTR (Long Terminal Repeat) retrotransposons and the non-LTR retrotransposons (LINEs, Long Interspersed Nuclear Elements, and SINEs, Short Interspersed Nuclear Elements), which are distinguished mainly by the respective presence or absence of LTRs at their ends. The class II TEs are divided into two subclasses. Subclass1 are TEs that are transposed by integration and excision mechanisms and subclass 2 are TEs that duplicate before insertion. Subclass 1 contains two orders; the most wellknown is the TIR (Terminal Inverted Repeated) order. This order contains nine superfamilies: Tc1-Mariner, Mutator, hAT, Merlin, Transib, P, PIF/Harbinger, CACTA and Crypton. Subclass 2 has two orders: Helitron and Maverick. Furthermore, there are groups of non-autonomous TEs that lack one or more of the genes essential for transposition, including MITEs (Miniature Inverted-repeat Terminal Elements) for class II, SINEs for non-LTR retrotransposons, and TRIM retrotransposons (Terminal-repeat Retrotransposon In Miniature) and LARDs (Large Retrotransposon Derivates) for LTR retrotransposons [2].