Abundance, distribution and potential impact of transposable elements in the genome of Mycosphaerella fijiensis

Abstract

Background: Mycosphaerella fijiensis is a ascomycete that causes Black Sigatoka in bananas. Recently, the M. fijiensis genome was sequenced. Repetitive sequences are ubiquitous components of fungal genomes. In most genomic analyses, repetitive sequences are associated with transposable elements (TEs). TEs are dispersed repetitive DNA sequences found in a host genome. These elements have the ability to move from one location to another within the genome, and their insertion can cause a wide spectrum of mutations in their hosts. Some of the deleterious effects of TEs may be due to ectopic recombination among TEs of the same family. In addition, some transposons are physically linked to genes and can control their expression. To prevent possible damage caused by the presence of TEs in the genome, some fungi possess TE-silencing mechanisms, such as RIP (Repeat Induced Point mutation). In this study, the abundance, distribution and potential impact of TEs in the genome of M. fijiensis were investigated.

Results: A total of 613 LTR-Gypsy and 27 LTR-Copia complete elements of the class I were detected. Among the class II elements, a total of 28 Mariner, five Mutator and one Harbinger complete elements were identified. The results of this study indicate that transposons were and are important ectopic recombination sites. A distribution analysis of a transposable element from each class of the M. fijiensis isolates revealed variable hybridization profiles, indicating the activity of these elements. Several genes encoding proteins involved in important metabolic pathways and with potential correlation to pathogenicity systems were identified upstream and downstream of transposable elements. A comparison of the sequences from different transposon groups suggested the action of the RIP silencing mechanism in the genome of this microorganism.

Conclusions: The analysis of TEs in M. fijiensis suggests that TEs play an important role in the evolution of this organism because the activity of these elements, as well as the rearrangements caused by ectopic recombination, can result in deletion, duplication, inversion and translocation. Some of these changes can potentially modify gene structure or expression and, thus, facilitate the emergence of new strains of this pathogen.

Figure 1

Basic structure of the major complete transposable elements found in the genome of M. fijiensis. In 1, the class I representatives are depicted as follows: LTR-Gypsy and LTR-Copia with their respective coding regions as described in the literature. The pol region contains the PR (protease), RT (reverse transcriptase), RH (RNase H) and IN (integrase) domains. In 2, the class II representatives are presented as follows: Tc1-Mariner, Mutator and Harbinger. The LTRs (Long Terminal Repeats) are indicated by wide arrows. The TIRs (Terminal Inverted Repeats) are indicated by small arrows. Each element is flanked by the insertion site or Target Site Repeat (TSR).

Figure 2

Hybridization profiles related to class I and II elements. A) Hybridization of isolates using a 643 bp fragment containing the reverse transcriptase gene of the Sagui element as a probe. B) Hybridization of isolates using a conserved 957 bp fragment containing part of the Mariner transposable element as a probe.